PaperBLAST
PaperBLAST Hits for Q93ZS6 AT3g05090/T12H1_5 (Arabidopsis thaliana) (753 a.a., MHRVGSAGSN...)
Show query sequence
>Q93ZS6 AT3g05090/T12H1_5 (Arabidopsis thaliana)
MHRVGSAGSNGGSVRTRKEKKLTYVLNDANDTKHCAGINCLDVLKSSVSNDQSYLFTGSR
DGTLKRWAFDEDATFCSATFESHVDWVNDAALAGESTLVSCSSDTTVKTWDGLSDGVCTR
TLRQHSDYVTCLAVAAKNNNVVASGGLGGEVFIWDIEAALSPVTKPNDANEDSSSNGANG
PVTSLRTVGSSNNISVQSSPSHGYTPTIAKGHKESVYALAMNDTGTMLVSGGTEKVLRVW
DPRTGSKSMKLRGHTDNVRVLLLDSTGRFCLSGSSDSMIRLWDLGQQRCLHTYAVHTDSV
WALACNPSFSHVYSGGRDQCLYLTDLATRESVLLCTKEHPIQQLALQDNSIWVATTDSSV
ERWPAEVQSPKTVFQRGGSFLAGNLSFNRARVSLEGLNPAPAYKEPSITVPGTHPIVQHE
ILNNKRQILTKDAAGSVKLWDITRGVVVEDYGKISFEEKKEELFEMVSIPSWFTVDTRLG
CLSVHLETPQCFSAEMYSADLKVSGRPEDDKINLARETLKGLLGHWLAKKKHKPKPQVLA
SGDTLSVKDTKKNLSASKTEESSAASDPVYPPFEFSSVSPPSIITEGSQGGPWRKKITEF
TGTEDEKDFPLWCLDAVLNNRLPPRENTKLSFFLHPCEGSSVQVVTLGKLSAPRILRVHK
VTNYVVEKMVLDNPLDSLAIDAASVSGGQPQPLFSGNGLLQSGLKPWQKLRPSIEILCNS
QVLSPDMSLATVRAYVWKKPEDLILNYRVAIAR
Running BLASTp...
Found 698 similar proteins in the literature:
AT3G05090 transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
Q93ZS6 AT3g05090/T12H1_5 from Arabidopsis thaliana
100% identity, 100% coverage
- Identification of mitogen-activated protein kinases substrates in <i>Arabidopsis</i> using kinase client assay
Bahk, Plant signaling & behavior 2024 - “...AAEEEFS*TPPSSPVFHDAK 50 S(7): 88.4; T(8): 11.2 10 At3g19330 VASTSRNDASISSPTFNLS*R 48 T(15): 0.4; S(19): 95.3 11 At3g05090 KTVFQRGGS*FLAGNLS*F 38 S(9): 99.8; S(16): 100.0 12 At4g30480 IES*SES*EDEILIKNEPK 32 S(3): 79.4; S(6): 93.4 13 At4g39680 EAQITNSATPT*T*T*PRSTGL 28 T(11): 52.1; T(12): 63.5; T(13): 59.0 14 At1g73980 LS*LDDDTVSSPKEALSRASV 25 S(2): 87.4;...”
- “...9 At3g04470 Ankyrin repeat family protein + Plasma membrane 10 At3g19330 DUF677 + Nucleus 11 At3g05090 Lateral root stimulator + Nucleus 12 At4g30480 AtTPR1 + Cytosol 13 At4g39680 SAP domain-containing protein ++ Nucleus Hoehenwarter et al. 2013 18 14 At1g73980 Phosphoribulokinase ++ Cytosol 15 At2g21150 XAP5...”
- Genome-Wide Identification of WD40 Proteins in Cucurbita maxima Reveals Its Potential Functions in Fruit Development
Chen, Genes 2023 - “...defects in both embryo and seedling development [ 57 ]. The mutants of LRS1 ( AT3G05090 ) show defects in lateral root development and affect the auxin accumulation during lateral root primordium development and meristem emergence [ 58 ]. Interestingly, these genes were grouped in the...”
- Selective autophagy: adding precision in plant immunity
Leong, Essays in biochemistry 2022 - “...(PUX7) PUX7 468 AT1G14570 UIM/UBA/UBX + Q93ZS6 Q93ZS6_ARATH AT3g05090/T12H1_5 (Transducin/WD40 repeat-like superfamily protein) (Uncharacterized protein At3g05090) LRS1 753 AT3G05090 WD40 Q8W4Q5 RIN3_ARATH E3 ubiquitin protein ligase RIN3 (EC 2.3.2.27) (RING-type E3 ubiquitin transferase RIN3) (RPM1-interacting protein 3) RIN3 577 AT5G51450 CUE Q8W4F0 DAR1_ARATH Protein DA1-related 1...”
- Unraveling Reticulate Evolution in Opuntia (Cactaceae) From Southern Mexico
Granados-Aguilar, Frontiers in plant science 2020 - “...Caryophyllales genes that matched with at least two Cactaceae genomes. Five candidate genes were recovered, AT3G05090 , AT4G24040 , AT3G48380 , AT1G18270 , and AT1G36980 (names based on the A. thaliana annotation). Additional Cactaceae species coding sequences from these five genes were mined from oneKP 2...”
- “...intron-flanking exons from selected genes. Gene Primer ID Forward sequence 53 Reverse sequence 53 Tested AT3G05090 a TGACGGGACATTGAAGAGG GTGGCTCCAGTTTCTAAGTC Yes b TAGCTACTTGCTCCGCTAC GTCTAGGTGGGGAGGTTTT No c GGGCTTCTCTTGAAGGATCTAC GTGGTGATTCAAGATTATGGCG No AT4G24040 a AGAAATCTCTTCCTGCTCTAC GACAACATTGGCTACTACATC Yes b AATGGTGCCAGAGCTTATTAC AGAAATCTCTTCCTGCTCTAC No c GACAACATTGGCTACTACATC GTTTGTGCTGCTGGGATTGC No AT3G48380 a GTCTTACACCCRGTATCARTT TATTGCATCTCTGGTTCAAGG Yes...”
- Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
Lee, Nature biotechnology 2010 - “...development genes. By interrogating network neighborhoods, we identify At1g80710 (now Drought sensitive 1; Drs1) and At3g05090 (now Lateral root stimulator 1; Lrs1) as novel regulators of drought sensitivity and lateral root development, respectively. AraNet ( http://www.functionalnet.org/aranet/ ) provides a global resource for plant gene function identification...”
- “...biological roles for 4,479 previously uncharacterized genes. We selected three uncharacterized genes (At1g80710, At2g17900, and At3g05090) based on several criteria: 1) no known biological process assigned; 2) predicted by AraNet to be involved in developmental regulatory processes; and 3) exist as single copy genes. These represent...”
- Selective autophagy: adding precision in plant immunity
Leong, Essays in biochemistry 2022 - “...proven + Q94JZ8 PUX7_ARATH Plant UBX domain-containing protein 7 (PUX7) PUX7 468 AT1G14570 UIM/UBA/UBX + Q93ZS6 Q93ZS6_ARATH AT3g05090/T12H1_5 (Transducin/WD40 repeat-like superfamily protein) (Uncharacterized protein At3g05090) LRS1 753 AT3G05090 WD40 Q8W4Q5 RIN3_ARATH E3 ubiquitin protein ligase RIN3 (EC 2.3.2.27) (RING-type E3 ubiquitin transferase RIN3) (RPM1-interacting protein 3)...”
F6HTW0 Uncharacterized protein from Vitis vinifera
74% identity, 93% coverage
- Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid
Rattanakan, Horticulture research 2016 - “...pyruvate dehydrogenase complex (D7TZW9), a Nck-associated protein 1 (D7T9L3) involved in actin remodeling, a component (F6HTW0) of the Cul4-RING E3 ubiquitin ligase complex, a DNA/RNA helicase (F6GT26), a protein involved in stability of Photosystem II (F6HVA4), a eukaryotic translation initiation factor (F6I2I6) and a ribosomal protein...”
- “...P value Peptide sequence Variable modification VIT_14s0066g01120 F6HUY8 Tudor/PWWP/MBTsuperfamilyprotein 1.59 1.12E04 GNEAESHVVNSNLAsPR S526 Phospho VIT_14s0030g01350 F6HTW0 Transducin/WD40 repeat-like superfamily protein 1.66 6.69E04 VGSAGNTSNsTRPR S18 Phospho VGSAGNTSNsTRPR S20 Phospho VIT_17s0000g06950 F6GT26 RNA helicase family protein 1.24 6.51E03 TSQDEDDDsELEEESLRDR S173 Phospho VITISV_031115 A5AI30 Ribosomal protein S21 family protein...”
NP_001026135 WD repeat-containing protein 48 from Gallus gallus
36% identity, 99% coverage
NP_080512 WD repeat-containing protein 48 isoform 1 from Mus musculus
35% identity, 99% coverage
WDR48_HUMAN / Q8TAF3 WD repeat-containing protein 48; USP1-associated factor 1; WD repeat endosomal protein; p80 from Homo sapiens (Human) (see 18 papers)
NP_065890 WD repeat-containing protein 48 isoform 1 from Homo sapiens
35% identity, 99% coverage
- function: Regulator of deubiquitinating complexes, which acts as a strong activator of USP1, USP12 and USP46 (PubMed:18082604, PubMed:19075014, PubMed:26388029, PubMed:31253762). Enhances the USP1- mediated deubiquitination of FANCD2; USP1 being almost inactive by itself (PubMed:18082604, PubMed:31253762). Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate (PubMed:19075014, PubMed:27373336). Also activates deubiquitinating activity of complexes containing USP12 (PubMed:19075014, PubMed:27373336, PubMed:27650958). In complex with USP12, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). Docks at the distal end of the USP12 fingers domain and induces a cascade of structural changes leading to the activation of the enzyme (PubMed:27373336, PubMed:27650958). Together with RAD51AP1, promotes DNA repair by stimulating RAD51-mediated homologous recombination (PubMed:27239033, PubMed:27463890, PubMed:32350107). Binds single- stranded DNA (ssDNA) and double-stranded DNA (dsDNA) (PubMed:27239033, PubMed:31253762, PubMed:32350107). DNA-binding is required both for USP1-mediated deubiquitination of FANCD2 and stimulation of RAD51- mediated homologous recombination: both WDR48/UAF1 and RAD51AP1 have coordinated role in DNA-binding during these processes (PubMed:31253762, PubMed:32350107). Together with ATAD5 and by regulating USP1 activity, has a role in PCNA-mediated translesion synthesis (TLS) by deubiquitinating monoubiquitinated PCNA (PubMed:20147293). Together with ATAD5, has a role in recruiting RAD51 to stalled forks during replication stress (PubMed:31844045).
function: (Microbial infection) In case of infection by Herpesvirus saimiri, may play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes. Induces lysosomal vesicle formation via interaction with Herpesvirus saimiri tyrosine kinase- interacting protein (TIP). Subsequently, TIP recruits tyrosine-protein kinase LCK, resulting in down-regulation of T-cell antigen receptor TCR. May play a role in generation of enlarged endosomal vesicles via interaction with TIP (PubMed:12196293). In case of infection by papillomavirus HPV11, promotes the maintenance of the viral genome via its interaction with HPV11 helicase E1 (PubMed:18032488).
subunit: Interacts with USP46 (PubMed:19075014, PubMed:26388029). Interacts with USP1 (PubMed:18082604, PubMed:26388029). Interacts with USP12 (PubMed:19075014, PubMed:27373336, PubMed:27650958). Component of the USP12-WDR20-WDR48 deubiquitinating complex (PubMed:27373336). Component of the USP12-DMWD-WDR48 deubiquitinating complex (PubMed:33844468). Interacts with PHLPP1 (PubMed:24145035). Interacts with RAD51AP1; the interaction is direct and promotes formation of a trimeric complex with RAD51 via RAD51AP1 (PubMed:27239033, PubMed:27463890). Interacts with ATAD5; the interaction regulates USP1- mediated PCNA deubiquitination (PubMed:20147293). Interacts with RAD51; the interaction is enhanced under replication stress (PubMed:31844045). Interacts with ITCH; the interaction is more efficient when both USP12 and WDR48/UAF1 are involved and may facilitate recruitment of the USP12 deubiquitinating complex to Notch (PubMed:22778262).
subunit: (Microbial infection) Interacts with papillomavirus HPV11 E1 protein.
subunit: (Microbial infection) Interacts with Saimiriine herpesvirus TIP protein.
subunit: (Microbial infection) Interacts with human cytomegalovirus protein UL138.
subunit: (Microbial infection) Interacts with Epstein-Barr virus protein EBNA3. - The UAF1-USP1 Deubiquitinase Complex Stabilizes cGAS and Facilitates Antiviral Responses.
Yu, Journal of immunology (Baltimore, Md. : 1950) 2024 (PubMed)- GeneRIF: The UAF1-USP1 Deubiquitinase Complex Stabilizes cGAS and Facilitates Antiviral Responses.
- USP1-WDR48 deubiquitinase complex enhances TGF-β induced epithelial-mesenchymal transition of TNBC cells via stabilizing TAK1.
Han, Cell cycle (Georgetown, Tex.) 2021 - GeneRIF: USP1-WDR48 deubiquitinase complex enhances TGF-beta induced epithelial-mesenchymal transition of TNBC cells via stabilizing TAK1.
- Structural basis of FANCD2 deubiquitination by USP1-UAF1.
Rennie, Nature structural & molecular biology 2021 (PubMed)- GeneRIF: Structural basis of FANCD2 deubiquitination by USP1-UAF1.
- The DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair.
Liang, The Journal of biological chemistry 2020 - GeneRIF: The DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair.
- ATAD5 suppresses centrosome over-duplication by regulating UAF1 and ID1.
Kim, Cell cycle (Georgetown, Tex.) 2020 - GeneRIF: ATAD5 suppresses centrosome over-duplication by regulating UAF1 and ID1.
- Interaction of the Human Papillomavirus E1 Helicase with UAF1-USP1 Promotes Unidirectional Theta Replication of Viral Genomes.
Orav, mBio 2019 - GeneRIF: In this report, the authors provide evidence that the previously described interaction between the viral E1 helicase and the cellular UAF1-USP1 deubiquitinating enzyme complex is required for the completion of the bidirectional theta replication of the human papilloma virus type 11 genome and the subsequent initiation of the unidirectional replication.
- The Role of the Complex USP1/WDR48 in Differentiation and Proliferation Processes in Cancer Stem Cells.
Goncalves, Current stem cell research & therapy 2017 (PubMed)- GeneRIF: There is evidence that USP1/WDR48 complex promotes cancer stem cell conservation and regulation of DNA damage repair. [REVIEW]
- USP1-UAF1 deubiquitinase complex stabilizes TBK1 and enhances antiviral responses.
Yu, The Journal of experimental medicine 2017 - GeneRIF: These results outline a novel mechanism for the control of TBK1 activity and suggest USP1-UAF1 complex as a potential target for the prevention of viral diseases.
- More
- Screening and identification of endometrial proteins as novel potential biomarkers for repeated implantation failure.
Wang, PeerJ 2021 - “...E3A 0.58 P43403 ZAP70 Tyrosine-protein kinase ZAP-70 0.59 P46781 RS9 40S ribosomal protein S9 0.59 Q8TAF3 WDR48 WD repeat-containing protein 48 0.60 Q8N4H5 TOM5 Mitochondrial import receptor subunit TOM5 homolog 0.60 P08729 K2C7 Keratin, type II cytoskeletal 7 0.61 Q07020 RL18 60S ribosomal protein L18 0.62...”
- Lysosomal perturbations in human dopaminergic neurons derived from induced pluripotent stem cells with PARK2 mutation.
Okarmus, Scientific reports 2020 - “...4A 0.83 0.036 8 P86790 CCZ1B Vacuolar fusion protein CCZ1 homolog B 0.82 0.020 3 Q8TAF3 WDR48 WD repeat-containing protein 48 0.81 0.042 8 O14964 HGS Hepatocyte growth factor-regulated tyrosine kinase substrate 0.79 0.015 5 P61073 CXCR4 C-X-C chemokine receptor type 4 0.79 0.016 3 O43237...”
- PTMs in conversation: activity and function of deubiquitinating enzymes regulated via post-translational modifications.
Kessler, Cell biochemistry and biophysics 2011 - “...86 , 92 , 93 ] Lys408 [ 114 ] Lys870 (Ub) [ 110 ] Q8TAF3 WDR48_HUMAN WD repeat-containing protein 48 (WD repeat endosomal protein) (USP1-associated factor 1) (p80) 677 Lys121, Lys214, Lys578 [ 114 ] Q9UGI0 ZRAN1_HUMAN Ubiquitin thioesterase ZRANB1 (zinc finger Ran-binding domain-containing protein...”
D3Z8C7 WD repeat-containing protein 48 from Rattus norvegicus
34% identity, 97% coverage
5l8eA / Q8TAF3 Structure of uaf1 (see paper)
40% identity, 64% coverage
WDR48_CAEEL / Q20059 WD repeat-containing protein 48 homolog from Caenorhabditis elegans (see paper)
29% identity, 97% coverage
- function: Together with wdr-20, binds to and stimulates the activity of the deubiquitinating enzyme usp-46, leading to deubiquitination and stabilization of the glr-1 glutamate receptor.
subunit: Interacts with usp-46; the interaction increases the catalytic activity of usp-46 in the presence of wdr-20.
disruption phenotype: Changed locomotion behavior with mutants displaying decreased reversal frequencies consistent with decreased glutamergic signaling.
NP_497931 WD repeat-containing protein 48 homolog from Caenorhabditis elegans
29% identity, 97% coverage
Q7PXD9 WD repeat-containing protein 48 homolog from Anopheles gambiae
30% identity, 98% coverage
WDR48_DROME / Q1LZ08 WD repeat-containing protein 48 homolog; USP1-associated factor 1 from Drosophila melanogaster (Fruit fly) (see paper)
29% identity, 98% coverage
- function: Regulatory component of the Usp12-46 deubiquitylase complex (PubMed:37798281). activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate (By similarity). The complex deubiquitylates the wg/wingless-signaling receptor arr/arrow, which stabilizes the receptor and increases its concentration at the cell surface; this enhances the sensitivity of cells to wg/wingless-signal stimulation (PubMed:37798281). This increases the amplitude and spatial range of the signaling response to the wg/wingless morphogen gradient, facilitating the precise concentration-dependent regulation of its target genes (PubMed:37798281). Together with Wdr20 and Usp12-46 required for wg/wingless-mediated signaling in the wing imaginal disc and for wg/wingless-dependent regulation of intestinal stem cell proliferation (PubMed:37798281).
subunit: Catalytic component of the Usp12-46 deubiquitylase complex consisting of Usp12-46, Wdr20 and Uaf1; regulatory subunit that, together wtih Wdr20, stabilizes Usp12-46 (PubMed:37798281). The Usp12- 46 deubiquitylase complex associates with arr/arrow; the interaction leads to deubiquitination and stabilization of arr/arrow (PubMed:37798281).
disruption phenotype: Viable but sterile with reduced lifespan.
BU107_SCHPO / Q09731 UBP9-binding protein bun107; Binding ubp9 protein of 107 kDa from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPAC31A2.14 WD repeat protein, human WRDR48 family from Schizosaccharomyces pombe
29% identity, 54% coverage
- function: Required for the ubp9 recruitment to septa and cell tips but also for its enzymatic activity at these specific locations.
subunit: Interacts with ubp9 and bun62. - A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity
Kouranti, PLoS biology 2010 - “...105 kDa. Third, Ubp9 co-purifies two nonessential WD repeatcontaining proteins encoded by the chromosomal loci SPAC31A2.14 (8 WD repeats, 107 kDa) and SPAC12B10.03 (6 WD repeats, 62 kDa). We named these two proteins Bun107 and Bun62 for binding Ubp9 of 107 and 62 kDa, respectively. Lastly,...”
- “...http://old.genedb.org/genedb/pombe/ ) accession numbers for the previously unnamed proteins discussed in this paper are Bun107, SPAC31A2.14; Bun62, SPAC12B10.03, Ecm29, SPAC1782.01; Ftp105, SPAC17A5.16; Rpn1301, SPBC342.04; Rpn1302, SPCC16A11.16c; and Sfp47, SPAC7D4.02c. All the DUB UniProt accession numbers are provided in Table 1 , and all DUB and interactor...”
Afu7g08290 vegetative incompatibility WD repeat protein, putative from Aspergillus fumigatus Af293
28% identity, 45% coverage
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...0.36 [1.28, 2.02] Afu3g07200 1.96 [1.83, 0.67] Afu2g16320 0.36 [0.82, 1.5] Afu4g06050 2.59 [2.09, 0.65] Afu7g08290 0.31 [0.35, 0.89] Afu7g07030 1.28 [0.87, 0.02] Afu5g09950 0.30 [1.01, 1.66] Afu1g10900 0.87 [1.83, 1.59] Afu7g05650 0.30 [1.32, 1.99] Afu7g04870 1.06 [1.85, 1.46] Afu8g00680 0.26 [1.02, 1.64] Afu3g03620 2.51 [2.16,...”
- Coding tandem repeats generate diversity in Aspergillus fumigatus genes
Levdansky, Eukaryotic cell 2007 - “...and GPI anchor consensus sequence Afu7g07100 Afu7g08290 Afu7g08310 Afu6g09340 Afu4g10350 Afu7g08240 Afu8g06150 Afu6g09360 Afu5g15090 Afu7g07060 NACHT domain...”
- “...ORFs with variable-size repeat regions (Afu7g08290, Afu7g08310, Afu6g09340, Afu8g06150, Afu6g09360, Afu5g15090, Downloaded from http://ec.asm.org/ on February...”
Q00808 Vegetative incompatibility protein HET-E-1 from Podospora anserina
32% identity, 21% coverage
alr7129 WD-repeat protein from Nostoc sp. PCC 7120
29% identity, 24% coverage
AFUA_7G07030, Afu7g07030 vegetative incompatibility WD repeat protein, putative from Aspergillus fumigatus Af293
30% identity, 37% coverage
- Regulation of sulphur assimilation is essential for virulence and affects iron homeostasis of the human-pathogenic mould Aspergillus fumigatus
Amich, PLoS pathogens 2013 - “...MFS siderophore iron transporter (SM) 13.99 3,4E-12 AFUA_3G03445 * short-chain alcohol dehydrogenase, putative 13.65 1,2E-11 AFUA_7G07030 vegetative incompatibility WD repeat protein, putative 13.42 0,01565 AFUA_1G17190 * long-chain-fatty-acid-CoA ligase SidI (SM) 12.70 0,01015 AFUA_8G06100 * integral membrane protein 12.19 0,00010 AFUA_8G06090 amino acid permease, putative 12.17 0,00015...”
- Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Yang, Evolutionary bioinformatics online 2012 - “...1.96 [1.83, 0.67] Afu2g16320 0.36 [0.82, 1.5] Afu4g06050 2.59 [2.09, 0.65] Afu7g08290 0.31 [0.35, 0.89] Afu7g07030 1.28 [0.87, 0.02] Afu5g09950 0.30 [1.01, 1.66] Afu1g10900 0.87 [1.83, 1.59] Afu7g05650 0.30 [1.32, 1.99] Afu7g04870 1.06 [1.85, 1.46] Afu8g00680 0.26 [1.02, 1.64] Afu3g03620 2.51 [2.16, 0.81] Afu6g09300 0.24 [0.26,...”
Ava_2183 Peptidase C14, caspase catalytic subunit p20 from Anabaena variabilis ATCC 29413
27% identity, 18% coverage
6y7pA The complex between the eight-bladed symmetrical designer protein tako8 and 1:2 zirconium(iv) wells-dawson (zrwd)
30% identity, 39% coverage
- Ligand: w-zr-cluster (6y7pA)
6y7oC The complex between the eight-bladed symmetrical designer protein tako8 and the silicotungstic acid keggin (sta)
30% identity, 42% coverage
- Ligand: keggin (sta) (6y7oC)
Ava_2629 Possible Transcriptional Regulator, Fis family from Anabaena variabilis ATCC 29413
27% identity, 24% coverage
- Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes
Xu, BMC genomics 2009 - “...Ava_1172 Ava_0874 Ava_4457 Ava_0873 Ava_0613 Ava_4753 Ava_1559 Ava_3542 Ava_1149 Ava_3207 Ava_3867 Ava_4503 Ava_3009 Ava_3703 Ava_1629 Ava_2629 Ava_1558 Ava_1021 A-prime CYA_0295 CYA_2315 B-prime CYB_2824 CYB_0465 CYB_2795 PCC7120 asr0847 alr0317 alr0318 alr0523 alr0524 alr0525 alr0169 alr0874 all3335 all3334 all3333 all3332 alr2210 alr2211 alr2212 alr2213 alr2118 alr2119 asr2220 all3335...”
NLE1_HUMAN / Q9NVX2 Notchless protein homolog 1 from Homo sapiens (Human) (see 2 papers)
NP_060566 notchless protein homolog 1 isoform a from Homo sapiens
28% identity, 36% coverage
- function: Plays a role in regulating Notch activity. Plays a role in regulating the expression of CDKN1A and several members of the Wnt pathway, probably via its effects on Notch activity. Required during embryogenesis for inner mass cell survival (By similarity).
subunit: Associates with the pre-60S ribosomal particle. Interacts (via WD repeats) with uL18 (By similarity). Interacts (via UBL domain) with MDN1 (via VWFA/MIDAS domain) (PubMed:26601951). - SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis.
Loevenich, Cancer research 2022 - GeneRIF: SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis.
- The murine ortholog of notchless, a direct regulator of the notch pathway in Drosophila melanogaster, is essential for survival of inner cell mass cells
Cormier, Molecular and cellular biology 2006 - “...sequences are as follows: Homo sapiens, NP_060566; Mus musculus, NP_663406; D. melanogaster, NP_477294.1; C. elegans, NP_493745; Arabidopsis thaliana,...”
alr4877 WD-repeat protein from Nostoc sp. PCC 7120
29% identity, 39% coverage
- The composition of the global and feature specific cyanobacterial core-genomes
Simm, Frontiers in microbiology 2015 - “...7,5 Nod1 0/11 None alr4812 PatN Heterocyst differentiation related protein 1,3 1,4 Fis1 0/0 None alr4877 WD40-repeat protein 2,5 2,7 Nod1 0/0 None alr4898 Transcriptional regulator 2,1 1,6 Fis1 3/90 None alr4984 Peptidoglycan binding domain 1 containing protein 25,4 5,7 0/1 d None asr5289 Similar to...”
Q58D20 Notchless protein homolog 1 from Bos taurus
27% identity, 39% coverage
NLE1_MOUSE / Q8VEJ4 Notchless protein homolog 1 from Mus musculus (Mouse) (see 2 papers)
NP_663406 notchless protein homolog 1 from Mus musculus
27% identity, 36% coverage
- function: Plays a role in regulating Notch activity (Probable). Plays a role in regulating the expression of CDKN1A and several members of the Wnt pathway, probably via its effects on Notch activity. Required during embryogenesis for inner mass cell survival.
disruption phenotype: Embryonic lethality prior to 6.5 dpc with death of inner mass cells. Embryos implant but die shortly after. - ITRAQ-based quantitative proteomic analysis of processed Euphorbia lathyris L. for reducing the intestinal toxicity.
Zhang, Proteome science 2018 - “...0.915 1.331 P42225 Signal transducer and activator of transcription 1 Stat1 1 1.2437 1.533 0.9722 Q8VEJ4 Notchless protein homolog 1 Nle1 1 1.2432 1.251 1.3997 F6S522 Claspin Clspn 1 1.2415 1.134 7.6765 Q8BHN5 RNA-binding protein 45 Rbm45 Drb1 Drbp1 1 1.2387 1.232 1.4235 P31725 Protein S100-A9...”
- Knockdown of NLE1 inhibits development of malignant melanoma in vitro and in vivo NLE1 promotes development of malignant melanoma.
Ren, Experimental cell research 2021 (PubMed)- GeneRIF: Knockdown of NLE1 inhibits development of malignant melanoma in vitro and in vivo NLE1 promotes development of malignant melanoma.
- Notchless defines a stage-specific requirement for ribosome biogenesis during lineage progression in adult skeletal myogenesis.
Gayraud-Morel, Development (Cambridge, England) 2018 (PubMed)- GeneRIF: activated skeletal muscle satellite cells in conditional Nle mutant mice are arrested in proliferation; however, deletion of Nle in myofibres does not impair myogenesis.
- Notchless is required for axial skeleton formation in mice.
Beck-Cormier, PloS one 2014 - GeneRIF: These data demonstrate an essential role for Nle1 during organogenesis and in particular during axial development.
- Notchless-dependent ribosome synthesis is required for the maintenance of adult hematopoietic stem cells.
Le, The Journal of experimental medicine 2013 - GeneRIF: These indings establish an essential role for Nle in hematopoietic stem cells.
- The murine ortholog of notchless, a direct regulator of the notch pathway in Drosophila melanogaster, is essential for survival of inner cell mass cells
Cormier, Molecular and cellular biology 2006 - GeneRIF: mNle is mainly required in inner cell mass cells, being instrumental for their survival, and raise the possibility that the death of mNle-deficient embryos might result from abnormal Notch signaling during the first steps of development.
- “...as follows: Homo sapiens, NP_060566; Mus musculus, NP_663406; D. melanogaster, NP_477294.1; C. elegans, NP_493745; Arabidopsis thaliana, NP_200094.1; and S....”
- The murine ortholog of notchless, a direct regulator of the notch pathway in Drosophila melanogaster, is essential for survival of inner cell mass cells.
Cormier, Molecular and cellular biology 2006 - GeneRIF: mNle is mainly required in inner cell mass cells, being instrumental for their survival, and raise the possibility that the death of mNle-deficient embryos might result from abnormal Notch signaling during the first steps of development.
- “...as follows: Homo sapiens, NP_060566; Mus musculus, NP_663406; D. melanogaster, NP_477294.1; C. elegans, NP_493745; Arabidopsis thaliana, NP_200094.1; and S....”
Q3TC83 Notchless protein homolog 1 from Mus musculus
27% identity, 36% coverage
P49695 Probable serine/threonine-protein kinase PkwA from Thermomonospora curvata
28% identity, 41% coverage
8q1nA / P61964 Cyclic peptide binder of the wbm-site of wdr5 (see paper)
25% identity, 43% coverage
8inkW / Q9NVX2 8inkW (see paper)
28% identity, 36% coverage
Glo7428_1095 caspase family protein from Gloeocapsa sp. PCC 7428
27% identity, 36% coverage
- The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria
Bhattacharjee, Journal of experimental botany 2020 - “...portion. This presumed topology prevailed in six true OCAs: Ava_0039, Ava_3079, Cri9333_3253, GEI7407_1667, GEI7407_1667, and Glo7428_1095. Among these, the presence of NACHT in the predicted cytoplasmic portion of GEI7407_1667 implies its activity during PCD. Moreover, Ava_0039, Ava_3079, and GEI7407_1667 have an AAA_16 domain placed N-terminally to...”
NP_001086974 WD repeat domain 5 L homeolog from Xenopus laevis
26% identity, 39% coverage
LOC105664430 protein will die slowly from Ceratitis capitata
26% identity, 39% coverage
NP_001011411 WD repeat-containing protein 5 from Xenopus tropicalis
26% identity, 39% coverage
NLE1_XENLA / Q7ZXK9 Notchless protein homolog 1 from Xenopus laevis (African clawed frog) (see paper)
28% identity, 36% coverage
- function: Plays a role in regulating the expression of CDKN1A and several members of the Wnt pathway, probably via its effects on Notch activity. Required for normal embryogenesis (By similarity). Plays a role in regulating Notch activity.
subunit: Associates with the pre-60S ribosomal particle. Interacts (via WD repeats) with uL18 (By similarity). Interacts (via UBL domain) with MDN1 (via VWFA/MIDAS domain) (By similarity).
LOC105559784 coatomer subunit alpha from Vollenhovia emeryi
25% identity, 24% coverage
- QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees
Miyakawa, PLoS genetics 2015 - “...production factor 1 LOC105559780 THUMP domain-containing protein 3-like LOC105559782 cysteine-rich with EGF-like domain protein 2 LOC105559784 coatomer subunit alpha LOC105559783 uncharacterized LOC105559785 host cell factor LOC105559786 probable myosin heavy chain ECU04_1000 LOC105559787 GTP-binding protein Rit2 LOC105559788 ero1-like protein LOC105559790 protein dispatched-like LOC105559789 protein dispatched-like LOC105559791 Bardet-Biedl...”
NP_001006198 WD repeat-containing protein 5 from Gallus gallus
26% identity, 39% coverage
LOTGIDRAFT_218145 hypothetical protein from Lottia gigantea
25% identity, 26% coverage
- Proteomics Studies on the three Larval Stages of Development and Metamorphosis of Babylonia areolata
Shen, Scientific reports 2018 - “...c268643_g1 deleted in malignant brain tumors 1 protein-like isoform X2 1802.72 976 c268439_g1 hypothetical protein LOTGIDRAFT_218145 1899.02 968 c267364_g1 translational activator GCN1 1925.98 946 c268713_g4 dynein beta chain, ciliary-like 1924.83 937 c268768_g2 dynein beta chain, ciliary-like 1825.83 937 c263230_g7 dynein heavy chain 7, axonemal-like 1858.57 919...”
- “...deleted in malignant brain tumors 1 protein-like isoform X2 scavenger receptor activi c268439_g1 hypothetical protein LOTGIDRAFT_218145 calcium ion binding c267364_g1 translational activator GCN1 kinase regulator activity c268713_g4 dynein beta chain, ciliary-like ATP binding c268768_g2 dynein beta chain, ciliary-like ATP binding c263230_g7 dynein heavy chain 7, axonemal-like...”
WDR5_HUMAN / P61964 WD repeat-containing protein 5; BMP2-induced 3-kb gene protein from Homo sapiens (Human) (see 26 papers)
WDR5_MOUSE / P61965 WD repeat-containing protein 5; BMP2-induced 3-kb gene protein; WD repeat-containing protein BIG-3 from Mus musculus (Mouse) (see 5 papers)
WDR5_RAT / Q498M4 WD repeat-containing protein 5 from Rattus norvegicus (Rat) (see paper)
NP_543124 WD repeat-containing protein 5 from Mus musculus
26% identity, 39% coverage
- function: Contributes to histone modification (PubMed:16600877, PubMed:16829960, PubMed:19103755, PubMed:19131338, PubMed:19556245, PubMed:20018852). May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4' (PubMed:16829960). As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3 (PubMed:19556245). H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation (PubMed:18840606). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (PubMed:19103755, PubMed:20018852). May regulate osteoblasts differentiation (By similarity). In association with RBBP5 and ASH2L, stimulates the histone methyltransferase activities of KMT2A, KMT2B, KMT2C, KMT2D, SETD1A and SETD1B (PubMed:21220120, PubMed:22266653).
subunit: Interacts with PAXBP1; the interaction is direct and links a WDR5-containing histone methyltransferase complex to PAX7 and PAX3 (By similarity). Interacts with HCFC1 (PubMed:12670868). Component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4 (PubMed:19103755). Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30 (PubMed:16253997, PubMed:17355966, PubMed:17998332, PubMed:18838538). Core component of several methyltransferase-containing complexes including MLL1/MLL, MLL2/3 (also named ASCOM complex) and MLL4/WBP7 (PubMed:15199122, PubMed:15960975, PubMed:17021013, PubMed:17500065). Each complex is at least composed of ASH2L, RBBP5, WDR5, DPY30, one or more specific histone methyltransferases (KMT2A/MLL1, KMT2D/MLL2, KMT2C/MLL3 and KMT2B/MLL4), and the facultative components PAGR1, BAP18, CHD8, E2F6, HCFC1, HCFC2, HSP70, INO80C, KDM6A, KANSL1, LAS1L, MAX, MCRS1, MEN1, MGA, MYST1/MOF, NCOA6, PAXIP1/PTIP, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9, TEX10 and alpha- and beta-tubulin (PubMed:14992727, PubMed:18378692). Component of the NSL complex at least composed of MOF/KAT8, KANSL1, KANSL2, KANSL3, MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1 (PubMed:20018852). Interacts with KMT2A/MLL1 (via WIN motif) and RBBP5; the interaction is direct (PubMed:18829459, PubMed:18840606, PubMed:19556245, PubMed:21220120, PubMed:22266653, PubMed:22665483). Component of the ADA2A-containing complex (ATAC), composed of KAT14, KAT2A, TADA2L, TADA3L, ZZ3, MBIP, WDR5, YEATS2, CCDC101 and DR1 (PubMed:19103755). In the complex, it probably interacts directly with KAT2A, MBIP and KAT14 (PubMed:19103755). Interacts with histone H3 (PubMed:16600877, PubMed:16829959, PubMed:16829960, PubMed:16946699). Interacts with SETD1A (via WIN motif) (PubMed:17998332, PubMed:22266653, PubMed:22665483). Component of a histone methylation complex composed of at least ZNF335, RBBP5, ASH2L and WDR5; the complex may have histone H3-specific methyltransferase activity, however does not have specificity for 'Lys-4' of histone H3 (PubMed:19131338). Interacts with ZNF335 (PubMed:19131338, PubMed:23178126). Components of this complex may associate with components of the ZNF335-CCAR2-EMSY nuclear receptor-mediated transcription complex to form a complex at least composed of ZNF335, HCFC1, CCAR2, EMSY, MKI67, RBBP5, ASH2L and WDR5 (PubMed:19131338). Interacts with PER1 (By similarity). Interacts with KMT2B (via WIN motif), KMT2C (via WIN motif), KMT2D (via WIN motif) and SETD1B (via WIN motif) (PubMed:18840606, PubMed:22266653, PubMed:22665483).
subunit: (Microbial infection) Interacts with herpes virus 8/HHV-8 protein LANA1; this interaction regulates the MLL1 histone methyltransferase activity on viral DNA. - function: Contributes to histone modification (By similarity). May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4' (By similarity). As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3 (By similarity). H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation (By similarity). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (By similarity). May regulate osteoblasts differentiation (PubMed:11551928). In association with RBBP5 and ASH2L, stimulates the histone methyltransferase activities of KMT2A, KMT2B, KMT2C, KMT2D, SETD1A and SETD1B (By similarity).
subunit: Interacts with PAXBP1; the interaction is direct and links a WDR5-containing histone methyltransferase complex to PAX7 and PAX3 (PubMed:22862948). Interacts with HCFC1 (By similarity). Component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4 (By similarity). Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30 (By similarity). Core component of several methyltransferase-containing complexes including MLL1/MLL, MLL2/3 (also named ASCOM complex) and MLL4/WBP7 (PubMed:21335234). Each complex is at least composed of ASH2L, RBBP5, WDR5, DPY30, one or more specific histone methyltransferases (KMT2A/MLL1, KMT2D/MLL2, KMT2C/MLL3 and KMT2B/MLL4), and the facultative components PAGR1, BAP18, CHD8, E2F6, HCFC1, HCFC2, HSP70, INO80C, KDM6A, KANSL1, LAS1L, MAX, MCRS1, MEN1, MGA, MYST1/MOF, NCOA6, PAXIP1/PTIP, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9, TEX10 and alpha- and beta-tubulin (PubMed:21335234). Component of the NSL complex at least composed of MOF/KAT8, KANSL1, KANSL2, KANSL3, MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1 (By similarity). Interacts with KMT2A/MLL1 (via WIN motif) and RBBP5; the interaction is direct (By similarity). Component ofthe ADA2A-containing complex (ATAC), composed of KAT14, KAT2A, TADA2L, TADA3L, ZZ3, MBIP, WDR5, YEATS2, CCDC101 and DR1 (By similarity). In the complex, it probably interacts directly with KAT2A, MBIP and KAT14 (By similarity). Interacts with histone H3 (By similarity). Interacts with SETD1A (via WIN motif) (By similarity). Component of a histone methylation complex composed of at least ZNF335, RBBP5, ASH2L and WDR5; the complex may have histone H3-specific methyltransferase activity, however does not have specificity for 'Lys-4' of histone H3 (By similarity). Interacts with ZNF335 (PubMed:23178126). Components of this complex may associate with components of the ZNF335-CCAR2-EMSY nuclear receptor-mediated transcription complex to form a complex at least composed of ZNF335, HCFC1, CCAR2, EMSY, MKI67, RBBP5, ASH2L and WDR5 (By similarity). Interacts with PER1 (By similarity). Interacts with KMT2D (via WIN motif) (PubMed:21335234). Interacts with KMT2B (via WIN motif), KMT2C (via WIN motif) and SETD1B (via WIN motif) (By similarity). - function: Contributes to histone modification (By similarity). May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4' (By similarity). As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3 (By similarity). H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation (By similarity). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (By similarity). May regulate osteoblasts differentiation (By similarity). In association with RBBP5 and ASH2L, stimulates the histone methyltransferase activities of KMT2A, KMT2B, KMT2C, KMT2D, SETD1A and SETD1B (By similarity).
subunit: Interacts with PAXBP1; the interaction is direct and links a WDR5-containing histone methyltransferase complex to PAX7 and PAX3 (By similarity). Interacts with HCFC1 (By similarity). Component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4 (By similarity). Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30 (By similarity). Core component of several methyltransferase-containing complexes including MLL1/MLL, MLL2/3 (also named ASCOM complex) and MLL4/WBP7 (By similarity). Each complex is at least composed of ASH2L, RBBP5, WDR5, DPY30, one or more specific histone methyltransferases (KMT2A/MLL1, KMT2D/MLL2, KMT2C/MLL3 and KMT2B/MLL4), and the facultative components PAGR1, BAP18, CHD8, E2F6, HCFC1, HCFC2, HSP70, INO80C, KDM6A, KANSL1, LAS1L, MAX, MCRS1, MEN1, MGA, MYST1/MOF, NCOA6, PAXIP1/PTIP, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9, TEX10 and alpha- and beta-tubulin (By similarity). Component of the NSL complex at least composed of MOF/KAT8, KANSL1, KANSL2, KANSL3, MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1 (By similarity). Interacts with KMT2A/MLL1 (via WIN motif) and RBBP5; the interaction is direct (By similarity). Component ofthe ADA2A-containing complex (ATAC), composed of KAT14, KAT2A, TADA2L, TADA3L, ZZ3, MBIP, WDR5, YEATS2, CCDC101 and DR1 (By similarity). In the complex, it probably interacts directly with KAT2A, MBIP and KAT14 (By similarity). Interacts with histone H3 (By similarity). Interacts with SETD1A (via WIN motif) (By similarity). Component of a histone methylation complex composed of at least ZNF335, RBBP5, ASH2L and WDR5; the complex may have histone H3-specific methyltransferase activity, however does not have specificity for 'Lys-4' of histone H3 (By similarity). Interacts with ZNF335 (By similarity). Components of this complex may associate with components of the ZNF335-CCAR2-EMSY nuclear receptor-mediated transcription complex to form a complex at least composed of ZNF335, HCFC1, CCAR2, EMSY, MKI67, RBBP5, ASH2L and WDR5 (By similarity). Interacts with PER1 (PubMed:15860628). Interacts with KMT2B (via WIN motif), KMT2C (via WIN motif), KMT2D (via WIN motif) and SETD1B (via WIN motif) (By similarity). - The Urine Proteome as a Biomarker of Radiation Injury: Submitted to Proteomics- Clinical Applications Special Issue: "Renal and Urinary Proteomics (Thongboonkerd)".
Sharma, Proteomics. Clinical applications 2008 - Loss of Wdr5 attenuates MLL-rearranged leukemogenesis by suppressing Myc targets.
Liu, Biochimica et biophysica acta. Molecular basis of disease 2023 (PubMed)- GeneRIF: Loss of Wdr5 attenuates MLL-rearranged leukemogenesis by suppressing Myc targets.
- p53 inactivation unmasks histone methylation-independent WDR5 functions that drive self-renewal and differentiation of pluripotent stem cells.
Li, Stem cell reports 2021 - GeneRIF: p53 inactivation unmasks histone methylation-independent WDR5 functions that drive self-renewal and differentiation of pluripotent stem cells.
- Mll-COMPASS complexes mediate H3K4me3 enrichment and transcription of the osteoblast master gene Runx2/p57 in osteoblasts.
Rojas, Journal of cellular physiology 2019 - GeneRIF: Our results show that an enrichment of activating histone marks at the Runx2/p57 P1 promoter is accompanied by the simultaneous interaction of Wdr5 and Utx proteins in differentiating MC3T3 mouse osteoblasts
- Cbx8 Acts Non-canonically with Wdr5 to Promote Mammary Tumorigenesis.
Chung, Cell reports 2016 - GeneRIF: Cbx8 associates with non-PRC1 complexes containing the H3K4 methyltransferase complex component WDR5, which together regulate Notch gene expression.
- Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC.
Thomas, Molecular cell 2015 - GeneRIF: Data show that broad association of myc proto-oncogene protein MYC with chromatin depends on interaction with the WD40-repeat protein WDR5.
- The TrxG Complex Mediates Cytokine Induced De Novo Enhancer Formation in Islets.
Tennant, PloS one 2015 - GeneRIF: Wdr5 suppression also reduced IFNgamma, Il-1beta, and TNFalpha induced chemokine gene expression in b-cells without affecting islet-cell survival or b-cell function after 48hrs, but did begin to increase islet-cell apoptosis
- Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency.
Yang, eLife 2014 - GeneRIF: results suggest that specific RNAs are integral inputs into the WDR5-MLL complex for maintenance of the active chromatin state and embryonic stem cell fates
- BIG3 inhibits insulin granule biogenesis and insulin secretion.
Li, EMBO reports 2014 - GeneRIF: BIG3 inhibits insulin granule biogenesis and insulin secretion.
- More
- Complement C3 is downregulated following ranibizumab intervention in experimental central retinal vein occlusion
Cehofski, Molecular vision 2024 - “...0.8 P52294 Importin subunit alpha-5 KPNA1 0.014 0.79 O15240 Neurosecretory protein VGF VGF 0.035 0.78 P61964 WD repeat-containing protein 5 WDR5 0.02 0.78 P12026 Acyl-CoA-binding protein DBI 0.029 0.76 P52209-2 6-phosphogluconate dehydrogenase. decarboxylating PGD 0.039 0.75 O60502 Protein O-GlcNAcase MGEA5 0.025 0.74 P15145 Aminopeptidase N ANPEP...”
- Combined High-Throughput Proteomics and Random Forest Machine-Learning Approach Differentiates and Classifies Metabolic, Immune, Signaling and ECM Intra-Tumor Heterogeneity of Colorectal Cancer
Contini, Cells 2024 - “...( S100A9 ) S100-A9 0.0000 S>H 8.1 0.0001 0.08 qPCR, WB, IHC [ 42 ] P61964 ( WDR5) WDR5 ND in H 0.0003 S>H >100 0.0008 0.01 qPCR, WB [ 43 ] Proteins changing in the comparison DH with D P15121 ( AKR1B1 ) Aldo-keto reductase...”
- AAMP and MTSS1 Are Novel Negative Regulators of Endothelial Barrier Function Identified in a Proteomics Screen.
Podieh, Cells 2024 - “...GCLM Glutamate-cysteine ligase regulatory subunit P48507 glutathione biosynthesis 0.044 3.48 WDR5 WD repeat-containing protein 5 P61964 histone modification 0.045 6.25 MTSS1 Metastasis suppressor protein 1 O43312 actin cytoskeleton 0.045 6.22 CDKAL1 Threonylcarbamoyladenosine tRNA methylthiotransferase Q5VV42 tRNA processing 0.045 6.10 CPNE2 Copine-2 Q96FN4 calcium-mediated signaling 0.045 6.09...”
- Histone H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.
Fox, The Journal of biological chemistry 2024 - “...recombinant expression construct containing the MLL1 SET domain (Uniprot Q03164 ; residues 37453969), WDR5 (Uniprot P61964 ; residues 2334), RbBP5 (Uniprot Q15291 ; residues 1538), and ASH2L (Uniprot Q9UBL3-3; residues 1534) in pST44 vector (a kind gift from Dr Song Tan) was swapped with the SET...”
- Discovery of Potent and Selective WDR5 Proteolysis Targeting Chimeras as Potential Therapeutics for Pancreatic Cancer.
Yu, Journal of medicinal chemistry 2023 - Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS.
Zafarullah, International journal of molecular sciences 2023 - “...103 Q9BQE9 BCL7B 2.06 13.52 0.00078504 0.0165087 B-cell CLL/lymphoma 7 protein family member B 104 P61964 WDR5 1.58 13.48 0.00080743 0.01675991 WD repeat-containing protein 5 105 Q9Y3B7 MRPL11 0.83 13.36 0.00081246 0.01675991 39S ribosomal protein L11, mitochondrial 106 Q8IX12 CCAR1 0.87 13.45 0.00084694 0.01730627 Cell division...”
- Phase separation promotes a highly active oligomeric scaffold of the MLL1 core complex for regulation of histone H3K4 methylation.
Namitz, The Journal of biological chemistry 2023 - “...MWRA polycistronic expression MLL1 SET domain (Uniprot #: Q03164 ) (a.a. 37453969), WDR5 (Uniprot #: P61964 ) (aa. 2334 with a 6xHis-tobacco etch virus (TEV) recognition site), RbBP5 (Uniprot #: Q15291 ) (aa. 1538), and Ash2L (Uniprot#: Q9UBL3-3) (aa. 1534) ( 63 ) combined in the...”
- An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability.
Jain, eLife 2023 - “...polycistronic recombinant expression construct containing the MLL1 SET domain (Uniprot Q03164; residues 37453969), WDR5 (Uniprot P61964; residues 2334), RbBP5 (Uniprot Q15291; residues 1538), and Ash2L (Uniprot Q9UBL3-3; residues 1534) in pST44 vector ( aka . MWRA construct) was a kind gift from Dr. Song Tan (...”
- More
Q2KIG2 WD repeat-containing protein 5 from Bos taurus
26% identity, 39% coverage
XP_003353752 WD repeat-containing protein 5 from Sus scrofa
26% identity, 39% coverage
WDR51_CAEEL / Q17963 WD repeat-containing protein wdr-5.1 from Caenorhabditis elegans (see 11 papers)
NP_497749 WD repeat-containing protein wdr-5.1 from Caenorhabditis elegans
26% identity, 40% coverage
- function: Contributes to histone modification (PubMed:16710447, PubMed:17967446, PubMed:20188723, PubMed:20555324, PubMed:21455483, PubMed:22012258). May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4' (PubMed:21455483). Required for di- and trimethylation, particularly for the trimethylation at 'Lys-4' of histone H3 (PubMed:20555324, PubMed:21455483, PubMed:21527717, PubMed:24682813). Not required for demethylation of histone H3 'Lys-27' (PubMed:21455483). H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation, germline establishment, maintenance and function (PubMed:21455483). Implicated in the epigenetic inheritance of lifespan over several generations (PubMed:22012258). Acts in the germline to limit the longevity of the soma, probably by regulating a lipid metabolism pathway that signals from the germline to the intestine, thereby preventing accumulation of mono-unsaturated fatty acids (PubMed:17967446, PubMed:20555324, PubMed:28379943). Required for RNA interference with probable antagonistic role against hpl-2 function (PubMed:17967446). Plays a role in vulval cell fate specification by acting in the synthetic multivulva pathway independent of set-2 (PubMed:17967446). Sex determining protein required in the germline to promote the spermatogenesis to oogenesis switch during the late larval stages of development (PubMed:24682813). Acts with the sex determining factor tra-1, and redundantly with wdr-5.2, to regulate fog-3 expression, which in turn determines germ cell fate (PubMed:24682813). Cooperates with jmjd-3.1, egl-27 and unc-3 to ensure robust transdifferentiation of the Y rectal cell to the PDA motor neuron during larval development (PubMed:25124442).
subunit: Component of the SET2 complex (also known as the SET1/COMPASS complex), which contains at least set-2, swd-2.1, cfp-1, rbbp-5, wdr- 5.1, dpy-30 and ash-2 (PubMed:31602465). Within the complex, interacts with cfp-1, ash-2, dpy-30 and hda-1 (PubMed:31602465). Interacts with histone H3 both unmethylated and methylated at 'Lys-4' (PubMed:21455483). Interacts with jmjd-3.1, ceh-6, sox-2, sem-4 and egl-27 (PubMed:25124442). Interacts with set-2 (PubMed:21527717).
disruption phenotype: Increase in life span (PubMed:17967446). Longer time span to reach adulthood and reduced brood size resulting in sterility between generations F3 and F4 (PubMed:17967446). Associated embryonic lethality and additional somatic defects at elevated temperatures (PubMed:17967446). Defects in germ cells including defective sperm development and endomitotic oocytes (PubMed:17967446, PubMed:24682813). Significantly reduced H3 'Lys-4' trimethylation in both embryonic and adult germ cells in a sex-independent manner (PubMed:17967446). Increased fog-3 expression at 20 degrees Celsius (PubMed:24682813). At 20 and 25 degrees Celsius, double knockdown mutants with wdr-5.2 have increased fog-3 expression (PubMed:24682813). At 25 degrees Celsius, these mutants have increased wdr-5.2 and fog-1 expression, reduced brood size accompanied by 42% embryonic lethality with 100% of the surviving progeny being sterile (PubMed:24682813). Surviving progeny display enhanced defects in the spermatogenesis to oogenesis transition compared to the single wdr-5.1 knockout with 88% of the gonads only containing sperm (PubMed:24682813). The remaining germ cells in the gonads switch to oogenesis, but the oocytes display either an endoreplication or endomitotic phenotype (PubMed:24682813). Germ cells also have increased expression of the sex determining factor tra-1 in the cytoplasm and as a result there is reduced binding of tra- 1 to the fog-3 promoter (PubMed:24682813). RNAi-mediated knockdown leads to an enrichment of mono-unsaturated fatty acids (PubMed:28379943). - Repressive H3K9me2 protects lifespan against the transgenerational burden of COMPASS activity in C. elegans.
Lee, eLife 2019 - GeneRIF: Data show that the transgenerational aspects of wdr-5 mutant longevity require the H3K9me2 methyltransferase MET-2 (MET-2).
- A role for WDR5 in TRA-1/Gli mediated transcriptional control of the sperm/oocyte switch in C. elegans.
Li, Nucleic acids research 2014 - GeneRIF: WDR-5.1 associates with the fog-3 promoter and is required for TRA-1 to bind to fog-3 promoter.
WDR53_CAEEL / Q23256 WD repeat-containing protein wdr-5.3 from Caenorhabditis elegans (see 2 papers)
28% identity, 35% coverage
- function: Not required for methylation of histone H3 'Lys-4'.
disruption phenotype: RNAi-mediated knockdown does not result in detectable defects in histone H3 'Lys-4' di- or tri-methylation in embryos or adults germ cells at 20 or 25 degrees Celsius.
WDR52_CAEEL / Q93847 WD repeat-containing protein wdr-5.2 from Caenorhabditis elegans (see paper)
26% identity, 39% coverage
- function: Sex determining protein required in the germline to promote the spermatogenesis to oogenesis switch during the late larval stages of development. Acts with the sex determining factor tra-1, and redundantly with wdr-5.1, to regulate fog-3 expression, which in turn determines germ cell fate. Not required for methylation of histone H3 'Lys-4'.
disruption phenotype: No obvious phenotype at 20 degrees Celsius or 25 degrees Celsius. At 20 and 25 degrees Celsius, double knockdown mutants with wdr-5.1 have increased fog-3 expression. At 25 degrees Celsius, these mutants have increased fog-1 expression, reduced brood size accompanied by 42% embryonic lethality with 100% of the surviving progeny being sterile. Surviving progeny display defective spermatogenesis to oogenesis transition with 88% of the gonads only containing sperm. The remaining germ cells in the gonads switch to oogenesis, but the oocytes display either an endoreplication or endomitotic phenotype. Germ cells also have increased expression of the sex determining factor tra-1 in the cytoplasm and as a result there is reduced binding of tra-1 to the fog-3 promoter. No detectable defects in histone H3 'Lys-4' di- or tri-methylation in embryos or adults germ cells at 20 or 25 degrees Celsius.
XP_002127700 WD repeat-containing protein 5 from Ciona intestinalis
25% identity, 42% coverage
NP_491069 Coatomer subunit alpha from Caenorhabditis elegans
25% identity, 28% coverage
LOC5577214, XP_001663309 coatomer subunit alpha from Aedes aegypti
24% identity, 26% coverage
NP_001083934 lissencephaly-1 homolog from Xenopus laevis
26% identity, 36% coverage
LACBIDRAFT_395470 uncharacterized protein from Laccaria bicolor S238N-H82
26% identity, 26% coverage
V5HP83 Putative copi vesicle coat from Ixodes ricinus
24% identity, 44% coverage
WDR5B_MOUSE / Q9D7H2 WD repeat-containing protein 5B from Mus musculus (Mouse) (see paper)
26% identity, 37% coverage
- function: May function as a substrate receptor for CUL4-DDB1 ubiquitin E3 ligase complex.
subunit: Probable part of a cullin-RING E3 protein ligase complex containing CUL4B-DDB1 and a substrate-recruiting component (DCAF). Interacts with CUL4B and DDB1.
DAW1_CHLRE / Q3Y8L7 Dynein assembly factor with WD repeat domains 1; Outer row dynein assembly protein 16 from Chlamydomonas reinhardtii (Chlamydomonas smithii) (see paper)
28% identity, 37% coverage
- function: Functions as a cargo-specific adapter between intraflagellar transport (IFT) particles and outer row dynein. Required for efficient dynein-mediated transport into the flagellar compartment.
subunit: Interacts with IFT46 and FLA10.
Q86VZ2 WD repeat-containing protein 5B from Homo sapiens
NP_061942 WD repeat-containing protein 5B from Homo sapiens
25% identity, 40% coverage
Ava_4855 Serine/Threonine protein kinase with WD40 repeats from Anabaena variabilis ATCC 29413
28% identity, 37% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...HiskA Ava_2109 cbSTKII CHASE2 Ava_4716 cbSTKIII GAF, HiskA Ava_2519 cbSTKI-other Ava_4764 cbSTKII CHASE2 Ava_2528 cbSTKI Ava_4855 cbSTKII WD40 (7) Ava_2684 cbSTKI-other Ava_4862 cbSTKI-other Ava_2791 cbSTKII ANF Ava_4863 cbSTKI-other Ava_2803 cbSTKIII GAF, HiskA Ava_4923 cbSTKII Pentapeptide (2) Ava_2809 cbSTKI-other Ava_5054 cbSTKII DUF323 Ava_2845 cbSTKIII GAF, PAC, HiskA...”
Q9W0B8 Coatomer subunit alpha from Drosophila melanogaster
25% identity, 24% coverage
Tery_0184 serine/threonine protein kinase with WD40 repeats from Trichodesmium erythraeum IMS101
27% identity, 42% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...erythraeum IMS101 Tery_0059 cbSTKII WD40 (7) Tery_2348 cbSTKI-other Tery_0088 cbSTKII FHA Tery_2556 cbSTKIII GAF, HiskA Tery_0184 cbSTKII WD40 (7) Tery_2609 cbSTKII RDD Tery_0247 cbSTKII DUF323 Tery_2829 cbSTKII DUF323 Tery_0460 cbSTKII DUF323 Tery_2831 cbSTKII DUF323 Tery_0461 cbSTKII DUF323 Tery_2857 cbSTKII GAF, CYCc Tery_0462 cbSTKII DUF323 Tery_3150 cbSTKI...”
CG10931 uncharacterized protein from Drosophila melanogaster
27% identity, 42% coverage
- Epistatic selection on a selfish Segregation Distorter supergene - drive, recombination, and genetic load
Navarro-Dominguez, eLife 2022 - “...the 3 UTR of the sns gene ( 2R :8,798,4898,856,091) and the CDS of the CG10931 gene ( 2R :17,748,93517,750,136). Figure 1figure supplement 4. Crossing scheme to generate recombinants along SD-Mal . ( A ) We crossed 810 b c px/b c px virgin females to...”
- “...these four breakpoints span genes ( Figure 1figure supplement 3 ): sns ( 2R :8,798,4898,856,091), CG10931 ( 2R :17,748,93517,750,136), and Mctp ( 2R :18,761,75818,774,824). The CDSs of both sns and Mctp remain intact in the In(2R)Mal arrangement, with the inversion disrupting their 3 UTRs. Neither of...”
- CRL4Mahj E3 ubiquitin ligase promotes neural stem cell reactivation
Ly, PLoS biology 2019 - “...CG14941 110785KK 19 esc CG14941 5692GD 20 Rae1 CG9862 101338KK 21 CG1523 CG1523 110437KK 22 CG10931 CG10931 51704GD 23 CG9945 CG9945 105944KK 24 CG12134 CG12134 31654GD 25 Lethal (2) 09851 CG12792 110333KK 26 Wdr24 CG7609 108562KK 27 WDA CG4448 34847GD 28 CG4705 CG4705 108007KK 29 WDR82...”
- subito encodes a kinesin-like protein required for meiotic spindle pole formation in Drosophila melanogaster
Giunta, Genetics 2002 - “...therefore might reduce the expression of the sub neighbor CG10931. Furthermore, due to the close juxtaposition of sub and CG14487, we do not know if sub22...”
- “...Because these mutations should not influence the expression of CG10931 and CG14487, they represent the null phenotype of sub. Despite the caveats of whether the...”
- Using the P[wHy] hybrid transposable element to disrupt genes in region 54D-55B in Drosophila melanogaster
Mohr, Genetics 2002 - “...suggests that the following genes are similarly dispensable: CG10931 and CG5002, which are completely removed in class B/class II animals, and CG6385, which is...”
LIS1_DICDI / Q8I0F4 Lissencephaly-1 homolog; DdLIS1 from Dictyostelium discoideum (Social amoeba) (see paper)
lis1 / CAD55133.1 LIS1 protein from Dictyostelium discoideum (see paper)
30% identity, 37% coverage
- function: Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the coupling of the nucleus and centrosome and dynein/dynactin-mediated interactions of microtubule tips with the cell cortex.
subunit: Interacts with dynein and mtaA/CP224 in the cortical attachment of microtubules. Interacts with rac1A
An16g02460 uncharacterized protein from Aspergillus niger
23% identity, 33% coverage
- A Library of Aspergillus niger Chassis Strains for Morphology Engineering Connects Strain Fitness and Filamentous Growth With Submerged Macromorphology
Cairns, Frontiers in bioengineering and biotechnology 2021 - “...Sphingolipid C9-methyltransferase important for cell membrane biosynthesis and signalling Oura and Kajiwara, (2010) SEC27 An02g05870 An16g02460 TC8.5 Golgi/vesicle 0.85 Component of the COPI coatomer; involved in ER-to-Golgi and Golgi-to-ER transport Gabriely et al. (2007) SEC26 An08g03270 None TC10.1 Golgi/vesicle 0.75 Component of the COPI coatomer; involved...”
- Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture
Cairns, Fungal biology and biotechnology 2019 - “...the TCA cycle GO Name ORF code Predicted function Golgi associated vesicle membrane (GO:0030660) copA An16g02460 COPI complex, alpha subunit sec26 An08g03270 COPI complex, beta subunit sec21 An07g06030 COPI complex, gamma subunit sec27 An02g05870 COPI complex, beta subunit sec23 An01g04730 COPII complex subunit ret2 An01g14250 COPI...”
- “...coefficients above 0.5 were retrieved for query genes citA (An09g06680), idh2 (An08g05580), fumR (An12g07850), copA (An16g02460), sec13 (An04g00360) and sec26 (An08g03270). Next, genes common to all 6 sub-networks were identified, giving 259 candidates. GO-enriched biological processes in this list were identified relative to the A. niger...”
- Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway
Jørgensen, BMC genomics 2009 - “...-2 An18g02490 GEA2 (YEL022w) guanine nucleotide exchange factor on ARF 1.3 6.810 -4 1.310 -2 An16g02460 COP1 (YDL145c) COPI complex, SU 1.4 3.510 -5 1.710 -3 An07g06030 SEC21 (YNL287w) COPI complex, SU 1.4 2.910 -5 1.510 -3 An08g06330 SEC28 (YIL076w) COPI complex, SU 1.5 3.210 -5...”
alr4559 WD-40 repeat-protein from Nostoc sp. PCC 7120
26% identity, 33% coverage
Q94A40 Coatomer subunit alpha-1 from Arabidopsis thaliana
AT1G62020 coatomer protein complex, subunit alpha, putative from Arabidopsis thaliana
25% identity, 22% coverage
- Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns
Ojosnegros, International journal of molecular sciences 2023 - “...82340-277_1_ORF2 Q39196 PIP1.4 PROBABLE AQUAPORIN PIP1-4 33 6 2 3 3.75 10 170 Sorting 272341-85_2_ORF2 Q94A40 AT1G62020 COATOMER SUBUNIT ALPHA-1 137 1 0 1 0 Sorting 29489-466_3_ORF1 Q0WW26 AT4G34450 COATOMER SUBUNIT GAMMA 103 2 1 1 0 Sorting 43675-385_1_ORF2 Q67YI9 EPSIN2 CLATHRIN INTERACTOR EPSIN 2 85.2...”
- iTRAQ-based quantitative proteomic analysis reveals the lateral meristem developmental mechanism for branched spike development in tetraploid wheat (Triticum turgidum L.)
Chen, BMC genomics 2018 - “...tauschii Traes_7AL_D93FC054C W5HB91 0.551 0.319 P25858 glyceraldehyde-3-phosphate dehydrogenase 1,cytosolic Aegilops tauschii Traes_4DL_852DF544C W5EJA0 0.568 0.529 Q94A40 coatomer subunit alpha-3-like Aegilops tauschii Traes_7BS_3FE10DB62 W5HTI2 0.573 0.640 Q9FJH6 ABC transporter F family member 1-like Aegilops tauschii Traes_5BL_5A9F5F455 W5FBW2 0.574 0.567 A0A178VSW7 long chain acyl-CoA synthetase 8 Aegilops tauschii...”
- Proteome and Interactome Linked to Metabolism, Genetic Information Processing, and Abiotic Stress in Gametophytes of Two Woodferns
Ojosnegros, International journal of molecular sciences 2023 - “...molecules through the cell membrane: PROBABLE AQUAPORIN PIP1-4 (PIP1.4) [ 71 ]. COATOMER SUBUNIT ALPHA-1 (AT1G62020) and COATOMER SUBUNIT GAMMA (AT4G34450) are associated with clathrin-uncoated vesicles that are transported from the endoplasmic reticulum to the Golgi apparatus and vice versa. In contrast, the proteins CLATHRIN INTERACTOR...”
- “...Q39196 PIP1.4 PROBABLE AQUAPORIN PIP1-4 33 6 2 3 3.75 10 170 Sorting 272341-85_2_ORF2 Q94A40 AT1G62020 COATOMER SUBUNIT ALPHA-1 137 1 0 1 0 Sorting 29489-466_3_ORF1 Q0WW26 AT4G34450 COATOMER SUBUNIT GAMMA 103 2 1 1 0 Sorting 43675-385_1_ORF2 Q67YI9 EPSIN2 CLATHRIN INTERACTOR EPSIN 2 85.2 1...”
- Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation
Félix, International journal of molecular sciences 2023 - “...mitochondrial cytochrome c1-1 heme protein (AT5G40810), the ribonuclease TUDOR 1 (AT5G07350), the coatomer subunit alpha-1 (AT1G62020), the ERBB-3 binding protein 1 (AT3G51800), the adenylate kinase 4 (AT5G50370), and the hypothetical protein COCNU_10G003830 (AT3G20050), which were down-accumulated along the maturation event ( Table S1 ). In contrast,...”
- Light Quality Modulates Plant Cold Response and Freezing Tolerance
Kameniarová, Frontiers in plant science 2022 - “...in B20 plants indicated a putative stimulatory effect on protein trafficking, including the coatomer subunit (AT1G62020) that mediates protein transport from the endoplasmic reticulum, protein AT5G16880 ESCRT (endosomal sorting complex required for transport), a subunit of clathrin-associated adapter protein complex HAP13 (AT1G60780), dynamin-related protein 13 (AT3G60190),...”
- Unbiased proteomic and forward genetic screens reveal that mechanosensitive ion channel MSL10 functions at ER-plasma membrane contact sites in Arabidopsis thaliana
Codjoe, eLife 2022 - “...RAB GTPase homolog 1C (RAB1c, At4G17530), METHIONINE OVERACCUMULATOR 3 (MTO3, At3G17390), COATOMER ALPHA-1 SUBUNIT (COP1, At1G62020), unnamed protein with a carbohydrate-binding like fold ( At3G62360), unnamed protein-M28 Zn-peptidase nicastrin ( At3G44330), RAS-RELATED NUCLEAR PROTEIN 1 (RAN1, At5G20010), CATALASE 2 (CAT2, At4G35090), LOW EXPRESSION OF OSMOTICALLY RESPONSIVE...”
- Membrane Profiling by Free Flow Electrophoresis and SWATH-MS to Characterize Subcellular Compartment Proteomes in Mesembryanthemum crystallinum
Guo, International journal of molecular sciences 2021 - “...shock 70 kDa protein BIP2 (BIP2) ER ADP-ribosylation factor 1 (ARF1) ER-GA coatomer subunit alpha-1 (At1g62020) ER-GA coatomer subunit beta-1 (At4g31480) ER-GA coatomer subunit beta-2 (At1g52360) ER-GA coatomer subunit gamma (At4g34450) ER-GA transport protein Sec23/24-like (At3g07100) ER-GA apyrase 2 (APY2) GA polygalacturonate 4-alpha-galacturonosyltransferase (GAUT1) GA galacturonosyltransferase...”
- Maize annexin genes ZmANN33 and ZmANN35 encode proteins that function in cell membrane recovery during seed germination
He, Journal of experimental botany 2019 - “...CHC1 (clathrin heavy chain 1), AAP19-1 (AP-1 complex subunit sigma-1), VTI11 (vesicle transport v-SNARE 11), AT1G62020 (coatomer subunit alpha-1), AT1G79990 (coatomer subunit beta-1), and SYP81 (syntaxin-81). Control treatment was at 1 C for 3 h. The relative mRNA levels were normalized to reference gene ( UBQ10...”
- Combined Proteomic and Metabolomic Profiling of the Arabidopsis thaliana vps29 Mutant Reveals Pleiotropic Functions of the Retromer in Seed Development
Durand, International journal of molecular sciences 2019 - “...ENTH/ANTH/VHS superfamily protein (At4g32285, 7.7), plant VAP homolog 12 (At2g45140, 6.0), coatomer -subunit (At2g21390, 7.5; At1g62020, 7.5), and the SNARE VTI11 (At5g39510, 2.3), or to endocytosis, such as dynamin-like proteins (DRP2B At1g59610, 3.6; DRP1E At3g60190, 3.1; and DL1C At1g14830, specific to vps29 seeds). The up-accumulation of...”
- Dissecting the subcellular membrane proteome reveals enrichment of H+ (co-)transporters and vesicle trafficking proteins in acidic zones of Chara internodal cells
Pertl-Obermeyer, PloS one 2018 - “...clathrin, heavy chain 473 280 193 at3g08530 PM, C coatomer, alpha subunit 155 96 59 at1g62020 C, Golgi coatomer, beta subunit 165 116 49 at1g52360, at4g31480, at3g15980 C, Golgi coatomer, epsilon subunit 20 14 6 at1g30630 Golgi coatomer, gamma-2 subunit 75 53 22 at4g34450 C emp24/gp25L/p24...”
- More
H9L3L2 Coatomer subunit alpha from Gallus gallus
23% identity, 26% coverage
- An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.
Dey, Communications biology 2022 - “...coronavirus strain Purdue, P07946; bovine coronavirus strain Mebus, P15777), COPI (bat, XP_032949522.1; camel, XP_031291824.1; chicken, H9L3L2; civet, XP_036778629.1; human, P53621; yeast, NP_595279.1), and COPI (yeast, Q96WV5). The phylogenetic analysis of these sequences was performed in PhyML 3.0 64 . A list of COPI sequences and their...”
NP_001100950 striatin-4 isoform 1 from Rattus norvegicus
F1M6V8 Striatin 4 from Rattus norvegicus
25% identity, 36% coverage
copA coatomer alpha subunit from Emericella nidulans (see 2 papers)
23% identity, 33% coverage
- CharProtDB Description: alpha-COP coatamer-related protein involved in the establishment and maintenance of polarized growth; temperature sensitive mutants defective in nuclear division at the restrictive temperature; Source:AspGD
all3169 WD repeat protein with Ser/Thr protein protein kinase motif from Nostoc sp. PCC 7120
24% identity, 38% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...cbSTKII TPR (10) Anabaena PCC7120 all0192 cbSTKI-other alr3119 cbSTKII WD40 (7) all0323 cbSTKIII GAF, HisKA all3169 cbSTKII WD40 (7) alr0344 cbSTKII ANF all3206 cbSTKI-other alr0354 cbSTKIII GAF, HisKA all3207 cbSTKI-other all0438 cbSTKII WD40 (7) alr3268 cbSTKII Pentapeptide (2) alr0548 cbSTKII FHA all3557 cbSTKIII GAF, HisKA alr0709...”
XP_001928732 coatomer subunit alpha isoform X1 from Sus scrofa
24% identity, 23% coverage
L8I566 Coatomer subunit alpha (Fragment) from Bos mutus
24% identity, 24% coverage
XP_005203500 coatomer subunit alpha isoform X1 from Bos taurus
24% identity, 23% coverage
Q96WV5 Putative coatomer subunit alpha from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
25% identity, 22% coverage
- An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking
Dey, Communications biology 2022 - “...(bat, XP_032949522.1; camel, XP_031291824.1; chicken, H9L3L2; civet, XP_036778629.1; human, P53621; yeast, NP_595279.1), and COPI (yeast, Q96WV5). The phylogenetic analysis of these sequences was performed in PhyML 3.0 64 . A list of COPI sequences and their multiple sequence alignment from the CONSURF server 45 is given...”
- An Extended Motif in the SARS-CoV-2 Spike Modulates Binding and Release of Host Coatomer in Retrograde Trafficking
Dey, 2021
NCU05939 cell division control protein 4 from Neurospora crassa OR74A
29% identity, 25% coverage
- Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa
Horta, Frontiers in microbiology 2019 - “...fbx-19 (NCU08642, FGSC#15478, Fbx19, AN4510), fbx-20 (NCU06250, FGSC#15629, Fbx20, AN4535) and fbx-22 ( cdc4 , NCU05939, FGSC#13190, Fbx22, AN5517). The corresponding deletion strain for cr-1 (NCU08377) is FGSC#11514. Neurospora crassa cultures were grown on Vogels minimal medium (VMM) ( Vogel, 1956 ). Unless noted, 2% (w/v)...”
- “...NCU03658 SPP-1/Fbx-9 1 NCU01154 SUB-1 4 NCU03881 hp 3 NCU01731 VE-1 9 NCU04540 FWD-1 4 NCU05939 CDC4/Fbx-22 7 MAP kinase pathways NCU00587 PBS2/OS-5 7 NCU06250 pc/Fbx-20 1 NCU07024 HOG1/OS-2 5 NCU06483 pc 1 NCU06182 NRC-1 10 NCU06688 pc 13 NCU04612 MEK-2 11 NCU07425 pc 7 NCU02393...”
Q27954 Coatomer subunit alpha from Bos taurus
24% identity, 24% coverage
F8WHL2 Coatomer subunit alpha from Mus musculus
24% identity, 23% coverage
Ava_2184 Peptidase C14, caspase catalytic subunit p20 from Anabaena variabilis ATCC 29413
27% identity, 24% coverage
- The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria
Bhattacharjee, Journal of experimental botany 2020 - “...target proteins may be carried out via this domain. The presence of NACHT in Tery_1841, Ava_2184, and GEI7407_1529 indicated their putative roles in PCD or related pathways. Interestingly, the co-occurrence of NACHT and WD40 domains in the wild-type OCAs, i.e. Ava_2184 and GEI 7407_1529, except Tery_1841,...”
- “...probably indicating energy-dependent activity of OCAs. Nevertheless, three putative cytoplasmic OCAs consisting Tery_2471, AMI_G0162, and Ava_2184 also have an AAA_16 domain providing NTPase and chaperone activities. The prevalence of abhydrolase, a domain having serine protease-like activity due to the catalytic triad of Ser, Glu/Asp, and His...”
B5DFK1 Coatomer subunit alpha from Rattus norvegicus
24% identity, 24% coverage
NP_001099115 coatomer subunit alpha from Bos taurus
24% identity, 24% coverage
DAW1_HUMAN / Q8N136 Dynein assembly factor with WD repeat domains 1; Outer row dynein assembly protein 16 homolog; WD repeat-containing protein 69 from Homo sapiens (Human) (see 3 papers)
27% identity, 35% coverage
COPA_MOUSE / Q8CIE6 Coatomer subunit alpha; Alpha-coat protein; Alpha-COP from Mus musculus (Mouse) (see paper)
NP_034068 coatomer subunit alpha from Mus musculus
24% identity, 24% coverage
- function: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin- coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity).
function: Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor (By similarity).
subunit: Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. Interacts with SCYL1. Interacts with JAGN1 (By similarity). Interacts with TMEM41B (By similarity). Interacts with SVEP1 (PubMed:36792666). Probably interacts with PEX11A. - Periostin Protects Against Alcohol-related Liver Disease by Activating Autophagy by Interacting With Protein Disulfide Isomerase.
Zhang, Cellular and molecular gastroenterology and hepatology 2023 - “...Dnah3 Dynein heavy chain 3 axonemal 0 1 1 Q8C166 Cpne1 Copine-1 3 1 1 Q8CIE6 Copa Coatomer subunit alpha 1 1 1 Q8K1K6 Seripinb10 Serpin B10 3 1 1 Q8R0W0 Eppk1 Epiplakin 1 5 3 Q8R180 Ero1a ERO1-like protein alpha 3 1 1 Q8R2Q0 Trim29...”
- The secreted inhibitor of invasive cell growth CREG1 is negatively regulated by cathepsin proteases.
Gomez-Auli, Cellular and molecular life sciences : CMLS 2021 - “...0.0348 Q8BG07 Phospholipase D4 0.50 0.04 0.97 0.0385 P06797 Cathepsin L1 0.54 0.17 0.91 0.0097 Q8CIE6 Coatomer subunit alpha 0.55 0.01 1.10 0.0479 O08553 Dihydropyrimidinase-related protein 2 0.57 0.20 0.94 7.91E03 Q9ET22 Dipeptidyl peptidase 2 0.57 0.08 1.05 0.0276 O89017 Legumain 0.58 0.22 0.93 0.0063 Q8K2I4...”
- Alport syndrome: Proteomic analysis identifies early molecular pathway alterations in Col4a3 knock out mice.
Nicolaou, Nephrology (Carlton, Vic.) 2020 - “...1.61E03 0.5 NN MM ATPdependent RNA helicase A O88322 NID2 4.49E03 0.5 NN MM Nidogen2 Q8CIE6 COPA 2.24E02 0.5 NN MM Coatomer subunit alpha O70456 1433S 4.88E02 0.5 NN MM 1433 protein sigma P28666 MUG2 4.21E02 0.5 NN MM Murinoglobulin2 P52480 KPYM 6.26E03 0.5 NN MM...”
- Environmental Enrichment Upregulates Striatal Synaptic Vesicle-Associated Proteins and Improves Motor Function
Song, Frontiers in neurology 2018 - “...P40142 Transketolase TKT 1.59 Q8BX70-2 Isoform 2 of Vacuolar protein sorting-associated protein 13C VPS13C 1.58 Q8CIE6 Coatomer subunit alpha COPA 1.56 Q8BMF3 NADP-dependent malic enzyme, mitochondrial ME3 1.56 Q6PB66 Leucine-rich PPR motif-containing protein, mitochondrial LRPPRC 1.55 D3Z7P3 Glutaminase kidney isoform, mitochondrial GLS 1.53 Q9QYX7-2 Isoform 2...”
- Proteomic Analysis of Secretomes of Oncolytic Herpes Simplex Virus-Infected Squamous Cell Carcinoma Cells.
Tada, Cancers 2018 - “...ligase, cytoplasmic 107 15.7 10.3 1.51 0.21 Q61553 Fascin 55 15 10.3 1.45 0.049 * Q8CIE6 Coatomer subunit alpha 138 14.7 10 1.47 0.025 * P21550 Beta-enolase 47 38 25.3 1.5 0.002 * Q922F4 Tubulin beta-6 chain 50 27.7 17.7 1.57 0.011 * cancers-10-00028-t002_Table 2 Table...”
- Proteomic Expression Changes in Large Cerebral Arteries After Experimental Subarachnoid Hemorrhage in Rat Are Regulated by the MEK-ERK1/2 Pathway.
Müller, Journal of molecular neuroscience : MN 2017 - “...SEC22b 2.69 Q5U2T8 Corepressor interacting with RBPJ 1 2.64 Q9WVA3 Mitotic checkpoint protein BUB3 2.61 Q8CIE6 Coatomer subunit alpha 2.59 G3V9C7 Histone H2B type 1-K 2.57 Q9Z340 Partitioning defective 3 homolog 2.55 P97633 Casein kinase I isoform alpha 2.47 P41499 Tyrosine-protein phosphatase non-receptor type 11 2.46...”
- RhoGDIβ Inhibits Bone Morphogenetic Protein 4 (BMP4)-induced Adipocyte Lineage Commitment and Favors Smooth Muscle-like Cell Differentiation.
Huang, The Journal of biological chemistry 2015 - Comparative analyses of differentially induced T-cell receptor-mediated phosphorylation pathways in T lymphoma cells.
Ortiz, Experimental biology and medicine (Maywood, N.J.) 2010 - “...transduction 5.75E-05 TOX2 NP_01092269 TOX high mobility group box family member 2 transcription/translation 5.75E-05 COPA Q8CIE6 coatomer protein complex, subunit alpha vesicle/trafficking 1.00E-04 ANP32A O35381 acidic (leucine-rich) nuclear phosphoprotein 32 family, member A transcription/translation, signal 1.11E-04 PHB2 O35129 prohibitin 2 transcription/translation transduction 1.17E-04 ZAP70 P43404 zeta-chain...”
- More
- Individual and combined effects of GIP and xenin on differentiation, glucose uptake and lipolysis in 3T3-L1 adipocytes.
English, Biological chemistry 2020 (PubMed)- GeneRIF: Individual and combined effects of GIP and xenin on differentiation, glucose uptake and lipolysis in 3T3-L1 adipocytes.
- Interaction between alpha-COP and SMN ameliorates disease phenotype in a mouse model of spinal muscular atrophy.
Custer, Biochemical and biophysical research communications 2019 - GeneRIF: Interaction between alpha-COP and SMN ameliorates disease phenotype in a mouse model of spinal muscular atrophy.
- Relevance of the COPI complex for Alzheimer's disease progression in vivo.
Bettayeb, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: Remarkably, an improvement of the memory impairments was also observed. Importantly, human genetic association studies of different AD cohorts led to the identification of 12 SNPs and 24 mutations located in COPI genes linked to an increased AD risk.
- COPI transport complexes bind to specific RNAs in neuronal cells.
Todd, Human molecular genetics 2013 - GeneRIF: The novel function of Copa in inter-compartmental trafficking of RNA.
- The COPI vesicle complex binds and moves with survival motor neuron within axons.
Peter, Human molecular genetics 2011 - GeneRIF: SMN directly binds to COPI and moves with survival motor neuron within axons.
- Knockdown of COPA, identified by loss-of-function screen, induces apoptosis and suppresses tumor growth in mesothelioma mouse model.
Sudo, Genomics 2010 (PubMed)- GeneRIF: In a a large-scale functional screening of mesothelioma cells, the COPA protein was highly expressed in some mesothelioma cell lines but not in a pleural mesothelial cell line.
COPA_HUMAN / P53621 Coatomer subunit alpha; Alpha-coat protein; Alpha-COP; HEP-COP; HEPCOP from Homo sapiens (Human) (see 4 papers)
NP_004362 coatomer subunit alpha isoform 2 from Homo sapiens
23% identity, 26% coverage
- function: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin- coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity).
function: Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor
subunit: Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits (By similarity). Interacts with SCYL1 (By similarity). Interacts with JAGN1 (PubMed:25129144). Interacts with TMEM41B (PubMed:30352685). Interacts with SVEP1 (By similarity). Probably interacts with PEX11A. - β'-COP mediated loading of PPARγ into trophoblast-derived extracellular vesicles
Luo, Cellular and molecular life sciences : CMLS 2024 - “...subunit betaOS=Homo sapiens GN=COPB2 PE=1 SV=2 59.72 39.29 1 12 26 37 906 102.4 5.27 P53621 Coatomer subunit alpha OS=Homo sapiens GN=COPA PE=1 SV=2 8.00 8.33 1 1 8 9 1224 138.3 7.66 P48444 Coatomer subunit delta OS=Homo sapiens GN=ARCN1 PE=1 SV=1 5.38 12.72 1 1...”
- A systematic review and meta-analysis of proteomic and metabolomic alterations in anaphylaxis reactions
Gallizzi, Frontiers in immunology 2024 - “...CDC42 Cell division control protein 42 homolog NA A0A087WVQ6 CLTC CLTC Clathrin heavy chain NA P53621 COPA COPA Coatomer subunit alpha NA P53618 COPB COPB1 Coatomer subunit beta NA P35606 COPB2 COPB2 Coatomer subunit beta NA Q8N684 CPSF7 CPSF7 Cleavage and polyadenylation specificity factor subunit 7...”
- A genetic screen to uncover mechanisms underlying lipid transfer protein function at membrane contact sites.
Mishra, Life science alliance 2024 - “...40.56 Alpha-thalassaemia/mental retardation syndrome 300032 CG7961 Q9W0B8 35305/GD ++ 35306/GD + Coat protein (coatomer) COP-A P53621 71.64 Autoimmune interstitial lung, joint, and kidney disease 601924 CG7843 Q9V9K7 106344/KK + 22574/GD + Arsenic resistance protein 2 SRRT (Isoform 5) Q9BXP5 46.58 614469 CG42665 Q9VVC6 105885/KK + 101144/KK...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - O-GlcNAc Dynamics: The Sweet Side of Protein Trafficking Regulation in Mammalian Cells.
Ben, Cells 2023 - “...based on PhosphoSitePlus . UniProt Accession UniProt Name Short Name Name O -GlcNAcylated Residues COPI P53621 COPA_HUMAN COPA Coatomer subunit alpha S489, T821 P35606 COPB2_HUMAN COPB2 Coatomer subunit beta S423, S432 P48444 COPD_HUMAN COPD Coatomer subunit delta S192, T203, T207, S223, S383, S385 Q9Y678 COPG1_HUMAN COPG1...”
- The SARS-CoV-2 spike S1 protein induces global proteomic changes in ATII-like rat L2 cells that are attenuated by hyaluronan.
Mobley, American journal of physiology. Lung cellular and molecular physiology 2023 - Dichlorvos-induced formation of isopeptide crosslinks between proteins in SH-SY5Y cells
Schopfer, Analytical biochemistry 2022 - “...50.2 D 794 GLSNASSRR Phosphatidylinositol 4-kinase alpha P42356 IHNELSPLK 432 LR 35 Coatomer subunit alpha P53621 606.9457 33.54 5 41.3 + 6.1 61.1 VTTVTEIGK 1211 DVIGLR Teneurin-4 Q6N022 NLLSLDFD 1844 RVTR 36 Microfibrillar-associated protein 1 P55081 835.1493 29.59 3 27.6 + 3.4 61.6 VKVK 37 RYVSGK...”
- Ellagic Acid Triggers the Necrosis of Differentiated Human Enterocytes Exposed to 3-Nitro-Tyrosine: An MS-Based Proteomic Study
Díaz-Velasco, Antioxidants (Basel, Switzerland) 2022 - “...reticulum membrane Q9P2E9 Coatomer subunit alpha COPA 0.026 0.79 Formation of blebs in Golgi apparatus P53621 Dynactin subunit 1 DCTN1 0.046 0.82 Cofactor involved in microtubule motor cytoplasmic dynein Q14203 Eukaryotic translation initiation factor 2 subunit 3 EIF2S3 0.045 0.86 Early steps of protein synthesis P41091...”
- More
- Heterozygous mutations in the C-terminal domain of COPA underlie a complex autoinflammatory syndrome.
Delafontaine, The Journal of clinical investigation 2024 - GeneRIF: Heterozygous mutations in the C-terminal domain of COPA underlie a complex autoin fl ammatory syndrome.
- A Zebra at the Rodeo: Dyspnea, Hematuria, and a Family History of Arthritis.
Cabrera-Pérez, Arthritis care & research 2022 (PubMed)- GeneRIF: A Zebra at the Rodeo: Dyspnea, Hematuria, and a Family History of Arthritis.
- An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.
Dey, Communications biology 2022 - GeneRIF: An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.
- Hazara Nairovirus Requires COPI Components in both Arf1-Dependent and Arf1-Independent Stages of Its Replication Cycle.
Fuller, Journal of virology 2020 - GeneRIF: Hazara Nairovirus Requires COPI Components in both Arf1-Dependent and Arf1-Independent Stages of Its Replication Cycle.
- Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling.
Lepelley, The Journal of experimental medicine 2020 - GeneRIF: Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling.
- GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation.
Witkos, Nature communications 2019 - GeneRIF: Loss of RAB6-interacting golgin (GORAB) causes impairment of coat protein complex I (COPI)-mediated retrieval of trans-Golgi enzymes, resulting in a deficit in glycosylation of secretory cargo proteins.
- The relationship between elevated serum xenin and insulin resistance in women with polycystic ovary syndrome: a case-control study.
Guclu, Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology 2019 (PubMed)- GeneRIF: median serum levels elevated in polycystic ovary syndrome
- Decreased A-to-I RNA editing as a source of keratinocytes' dsRNA in psoriasis.
Shallev, RNA (New York, N.Y.) 2018 - GeneRIF: Reduced RNA editing of COPA gene is associated with psoriasis.
- More
alr3119 WD repeat protein with Ser/Thr protein kinase motif from Nostoc sp. PCC 7120
27% identity, 37% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...(3) Tery_4781 cbSTKII TPR (11) Tery_2107 cbSTKI-other Tery_4782 cbSTKII TPR (10) Anabaena PCC7120 all0192 cbSTKI-other alr3119 cbSTKII WD40 (7) all0323 cbSTKIII GAF, HisKA all3169 cbSTKII WD40 (7) alr0344 cbSTKII ANF all3206 cbSTKI-other alr0354 cbSTKIII GAF, HisKA all3207 cbSTKI-other all0438 cbSTKII WD40 (7) alr3268 cbSTKII Pentapeptide (2)...”
CNC05910 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
25% identity, 31% coverage
NLE1_YEAST / P25382 Ribosome assembly protein 4; Notchless protein homolog 1; Ribosome biogenesis factor RSA4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
NP_009997, YCR072C Rsa4p from Saccharomyces cerevisiae
NP_009997 Rsa4p from Saccharomyces cerevisiae S288C
26% identity, 36% coverage
- function: Involved in ribosome biogenesis. Required for processing and efficient intra-nuclear transport of pre-60S ribosomal subunits. Interacts with the AAA-ATPase Midasin (MDN1/REA1), which is essential for the ATP-dependent dissociation of a group of nonribosomal factors from the pre-60S particle.
subunit: Associates with the pre-60S ribosomal particle (PubMed:16702403, PubMed:18658244, PubMed:19737519). Interacts (via WD repeats) with uL18 (RPL5) (PubMed:25404745). Interacts (via UBL domain) with MDN1 (via VWFA/MIDAS domain) (PubMed:19737519, PubMed:20542003). Interacts (via WD repeats) with NSA2 (PubMed:25404745). - Arabidopsis NOTCHLESS plays an important role in root and embryo development.
Li, Plant signaling & behavior 2023 - “...used in the phylogenetic analysis with the following accessions numbers: NP_477294.2 ( D. melanogaster ), NP_009997.2 ( S. cerevisiae ), NP_060566.2 ( H. sapiens ), NP_001278731.1 ( Z. mays ), XP_015615305.1( O. sativa ), XP_013680604.1 ( B. napus ), XP_018449712.1 ( R. sativus ), XP_019091290.1 (...”
- Predicting protein complexes using a supervised learning method combined with local structural information
Dong, PloS one 2018 - “...YNL308C YDL208W YHR072W-A YGL078C YCL059C YDL213C 0.0 4.22E-09 rRNA processing 2 YNL182C YDR101C YHR197W YER006W YCR072C YPR016C YGR245C YLR074C YER126C YPL093W YNR053C 0.0 3.11E-14 ribosome biogenesis 3 YDR235W YDL087C YPR057W YDR240C YLR298C YKL012W YBR119W YIL061C YLR275W YML046W YHR086W YGR013W 0.050 3.19E-25 small nuclear ribonucleoprotein complex 4...”
- Dissecting the cis and trans elements that regulate adjacent-gene coregulation in Saccharomyces cerevisiae
Arnone, Eukaryotic cell 2014 - “...functions Standard name YAL036C YBL028C YBL054W YBR247C YCR072C YDL063C YDR101C YDR365C YER049W YGL099W YGR103W YGR145W YGR283C YHL039W YHR196W YIL096C YIL127C...”
- Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription
Yadon, Molecular and cellular biology 2010 - “...YFL039C (loading control); (B) YLL015W; (C) YCL030C; (D) YCR072C. 5120 YADON ET AL. MOL. CELL. BIOL. regulatory mechanisms of cryptic RNA transcription and the...”
- Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum
Bréhélin, BMC genomics 2010 - “...falciparum gene has absolutely no GO data. See, for example, the pairs ( PF11_0471 ; YCR072C ), ( PF07_0121 ; YHR170W ), or ( PF10_0200 ; YNL132W ) in the cluster pair #0 of the LR-GA analysis. The comparative analysis therefore allows correction of incomplete annotations...”
- Fuzzy c-means clustering with prior biological knowledge
Tari, Journal of biomedical informatics 2009 - “...genes. The genes ALB1 / YJL122W [38] and RSA4 / YCR072C [39] are assigned to the cluster that corresponds to ribosome biogenesis using datasets A and B, in...”
- Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data
Bryan, BMC genomics 2008 - “...external experimental and sequence information. One case which stands out in particular is that of YCR072C. This ORF was unclassified by MIPS when we labelled the data. However this ORF has subsequently been labelled by MIPS as being involved in transcription of ribosomal RNA (rRNA) and...”
- “...Human BAP31 homolog. YGR149W Energy: Respiration (02.13) Putative protein, unknown function Predicted integral membrane protein. YCR072C (RSA4) Transcription: rRNA (11.04.01) Recently verified by MIPS ribosomal biogenesis. YDL167C (NRP1) Transcription: rRNA (11.04.01) Role in ribosome biogenesis and assembly (RCA). YMR259C Transcription: rRNA (11.04.01)/ Transport Routes (20.09) Putative...”
- Rapid evolution of yeast centromeres in the absence of drive
Bensasson, Genetics 2008 - “...ATG22, ILV6, CIT2, PGK1, MAK32, FEN2, PER1, CTR86, HCM1, YCR072C, and KIN82. To ensure a high degree of confidence in the polymorphism data, only bases with a...”
- More
- The essential WD-repeat protein Rsa4p is required for rRNA processing and intra-nuclear transport of 60S ribosomal subunits.
de, Nucleic acids research 2005 - GeneRIF: Rsa4p provides a platform of interaction for correct processing of rRNA precursors and nucleolar release of 60S ribosomal subunits.
- The splicing ATPase prp43p is a component of multiple preribosomal particles
Lebaron, Molecular and cellular biology 2005 - “...P40078 P38779 P40010 P38805 P35178 P36080 P25582 Q12153 P22147 P25382 40S Pfa1p Rio1p P53866 Q12196 H/ACA snoRNP Cbf5p Gar1p Nhp2p P33322 P28007 P32495 a b...”
K4BVH7 Coatomer subunit alpha from Solanum lycopersicum
25% identity, 22% coverage
7uoox / P25382 7uoox (see paper)
26% identity, 36% coverage
8xi2T / A0A2K3DAW8 Cryo-em structure of the chlamydomonas c Complex (see paper)
26% identity, 44% coverage
SPSK_02314 glucose repression regulatory protein TUP1 from Sporothrix schenckii 1099-18
29% identity, 35% coverage
- Current Progress in Sporothrix brasiliensis Basic Aspects
Gómez-Gaviria, Journal of fungi (Basel, Switzerland) 2023 - “...SPSK_07311 SPBR_02347 0 100 Hgc1 SPSK_05321 SPBR_07336 0 99 Nrg1 SPSK_00519 SPBR_07150 0 96 Tup1 SPSK_02314 SPBR_00318 0 93 C. neoformans Mob2 SPSK_01925 SPBR_03835 2e 169 100 Cbk1 SPSK_06025 SPBR_04750 0 99 Tao3 SPSK_02910 SPBR_00004 0 99 Sog2 SPSK_03988 SPBR_05624 0 99 Thermotolerance C. albicans Hsp60...”
UABAM_01722 DUF4062 domain-containing protein from Candidatus Uabimicrobium amorphum
23% identity, 23% coverage
- Phagocytosis-like cell engulfment by a planctomycete bacterium
Shiratori, Nature communications 2019 - “...in assembly, stabilisation and cross-link of actin filament 37 ) and found two candidate proteins (UABAM_01722 and UABAM_04996) that are similar to Aip1 and Crn1, respectively (Supplementary Table 11 ). We used F-actin-binding phalloidin and an antibody specific for eukaryotic actin but failed to observe a...”
8ro0E / Q19211 8ro0E (see paper)
25% identity, 42% coverage
SPBR_00318 glucose repression regulatory protein TUP1 from Sporothrix brasiliensis 5110
29% identity, 35% coverage
- Current Progress in Sporothrix brasiliensis Basic Aspects
Gómez-Gaviria, Journal of fungi (Basel, Switzerland) 2023 - “...SPBR_02347 0 100 Hgc1 SPSK_05321 SPBR_07336 0 99 Nrg1 SPSK_00519 SPBR_07150 0 96 Tup1 SPSK_02314 SPBR_00318 0 93 C. neoformans Mob2 SPSK_01925 SPBR_03835 2e 169 100 Cbk1 SPSK_06025 SPBR_04750 0 99 Tao3 SPSK_02910 SPBR_00004 0 99 Sog2 SPSK_03988 SPBR_05624 0 99 Thermotolerance C. albicans Hsp60 SPSK_01586...”
Tsp_00685 lissencephaly-1 from Trichinella spiralis
27% identity, 19% coverage
- Operons are a conserved feature of nematode genomes
Pettitt, Genetics 2014 - “...gene Upstream gene Downstream gene Upstream gene Downstream gene Operon no. Upstream gene Downstream gene Tsp_00685 a Nonoperonic mrps-17 C05D11.9 3372 Bm1_13520 Bm1_13525 Tsp_03140 Tsp_03139 t32947 t32944 T26E3.4 par-6 1672 Bm1_48785 Bm1_48780 Tsp_05540 Tsp_05541 Nonoperonic K11B4.1 K11B4.2 1764 Bm1_55805 Bm1_55810 Tsp_06077 Tsp_06076 Nonoperonic Y62E10A.2 Y62E10A.6 4540...”
Tery_4467 serine/threonine protein kinase with WD40 repeats from Trichodesmium erythraeum IMS101
24% identity, 34% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...Tery_1723 cbSTKII GUN4 Tery_4351 cbSTKII DUF323 (2) Tery_2033 cbSTKII WD40 (7) Tery_4411 cbSTKI-TM Tery_2051 cbSTKI-other Tery_4467 cbSTKII WD40 (7) Tery_2064 cbSTKII Pentapeptide (3) Tery_4781 cbSTKII TPR (11) Tery_2107 cbSTKI-other Tery_4782 cbSTKII TPR (10) Anabaena PCC7120 all0192 cbSTKI-other alr3119 cbSTKII WD40 (7) all0323 cbSTKIII GAF, HisKA all3169...”
slr8038 WD-repeat protein from Synechocystis sp. PCC 6803
26% identity, 21% coverage
AT2G21390 coatomer protein complex, subunit alpha, putative from Arabidopsis thaliana
25% identity, 22% coverage
- Defects in autophagy lead to selective in vivo changes in turnover of cytosolic and organelle proteins in Arabidopsis
Li, The Plant cell 2022 - “...chain1 (At3g11130) associated with plasma membrane and Golgi, and the coatomer alpha, delta, and gamma-subunits (At2g21390, At5g05010, and At4g34450) of the COP1 coat, which is required for intra-Golgi transport, retrograde transport from Golgi to ER, and Golgi maintenance. ER-resident proteins, such as AtBAG7(At5g62390), CNX1 (At5g61790), and...”
- The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes
Singh, Frontiers in plant science 2020 - “...Nucleus/Cytoplasm Component of 26S proteasome/Plant immunity Brukhin et al., 2005 ; Yao et al., 2012 At2g21390 -subunit of coatomer (COP) adaptor complex Golgi apparatus Vesicle Trafficking Brandizzi and Barlowe, 2013 At3g07110 Ribosomal protein L19-type (AtRPL13aA) Cytoplasm Protein synthesis Millar and Heazlewood, 2003 At3g10860 Ubiquinone-binding component of...”
- Combined Proteomic and Metabolomic Profiling of the Arabidopsis thaliana vps29 Mutant Reveals Pleiotropic Functions of the Retromer in Seed Development
Durand, International journal of molecular sciences 2019 - “...(At3g60600, 12), ENTH/ANTH/VHS superfamily protein (At4g32285, 7.7), plant VAP homolog 12 (At2g45140, 6.0), coatomer -subunit (At2g21390, 7.5; At1g62020, 7.5), and the SNARE VTI11 (At5g39510, 2.3), or to endocytosis, such as dynamin-like proteins (DRP2B At1g59610, 3.6; DRP1E At3g60190, 3.1; and DL1C At1g14830, specific to vps29 seeds). The...”
- α2-COP is involved in early secretory traffic in Arabidopsis and is required for plant growth
Gimeno-Ferrer, Journal of experimental botany 2017 - “...loss-of-function approach to characterize the Arabidopsis 2-COP isoform. Two -COP isoforms, 1-COP (At1g62020) and 2-COP (At2g21390), have been identified in Arabidopsis and both isoforms contain an N-terminal WD40 domain that may allow them to recognize C-terminal dilysine-based motifs of COPI cargo proteins ( Eugster et al....”
- “...stop codon was synthesized commercially de novo (Geneart AG) based on the sequence of 2-COP (At2g21390). The coding sequence of 2-COP-HA was cloned into the pCHF3 vector carrying the CaMV 35S promoter ( Ortiz-Masia et al. , 2007 ) through SmaI/SalI. To complement growth defects, 2-cop-3...”
- Cellular reprogramming through mitogen-activated protein kinases
Lee, Frontiers in plant science 2015 - “...the vesicle-fusing ATPase NSF1 (AT4G04910) and multiple proteins of the coatomer/clathrin-mediated vesicle transport [e.g., - (AT2G21390), - (AT4G31480, AT1G79990), 2- (AT1G52360, AT3G15980) or - (AT1G30630) subunits of coatomer protein; - (AT5G22780, AT1G62020), - (AT4G11380, AT4G11380), or - (AT5G46630, AT2G20790) adaptins; auxilin-like proteins (AT4G12770, AT4G12780); clathrin heavy...”
- Parallel action of AtDRB2 and RdDM in the control of transposable element expression
Clavel, BMC plant biology 2015 - “...172.6 4.1 4 4 0.13 >250 ACC1 At1g36160 1959.2 23 43 43 0.7 WD40 containing At2g21390 568.5 10.3 11 11 0.28 AGO4 At2g27040 167.1 4.7 4 4 0.13 CAND1 At2g02560 117.8 3.1 3 3 0.07 TPL At1g15750 113.2 4.7 5 5 0.13 Table summarizing the multiple...”
- “...the IP contains other WD40 containing proteins not classified as DCAFs (TPL, At5g24710, At1g04510, At3g63460, at2g21390). Accordingly, the IP also contains AKIN10, a Snf1-related protein kinase, which is ubiquitylated by the CUL4-DDB1 PRL1 complex to promote its degradation [ 72 ], and CAND1 (CULLIN ASSOCIATED AND...”
- Identification of Regulatory and Cargo Proteins of Endosomal and Secretory Pathways in Arabidopsis thaliana by Proteomic Dissection
Heard, Molecular & cellular proteomics : MCP 2015 - “...AT4G34660 AT1G52360 AT4G31480 AT4G31490 AT1G62020 AT2G21390 AT5G05010 AT3G63460 AT5G16300 AT4G24840 AT1G67930 AT5G51430 AT5G11980 AT2G27600 AT5G03540 AT5G59730...”
- Molecular mechanisms of Sar/Arf GTPases in vesicular trafficking in yeast and plants
Yorimitsu, Frontiers in plant science 2014 - “...At1g02440 Small GTPase AtARFD1b ARF1D At1g02430 Small GTPase Coatomer At1g62020 Coat protein for COPI vesicle At2g21390 Coatomer At4g31480 Coat protein for COPI vesicle At4g31490 Coatomer At1g52360 Coat protein for COPI vesicle At3g15980 At1g79990 Coatomer At4g34450 Coat protein for COPI vesicle Coatomer At5g05010 Coat protein for COPI...”
- More
B0XYA9 Coatomer subunit alpha from Aspergillus fumigatus (strain CBS 144.89 / FGSC A1163 / CEA10)
23% identity, 33% coverage
- Unveiling fungal strategies: Mycoremediation in multi-metal pesticide environment using proteomics
Dey, Scientific reports 2024 - “...and metabolism Beta-glucosidase Cytoplasm 9.34438E05 B0XYC7 3.3 Signal transduction mechanisms Class II aldolase Cytoplasm 0.001906189 B0XYA9 3.2 Energy production and conversion Glucooligosaccharide oxidase Mitochondria 0.027750948 Q0CFN1 3.1 Energy production and conversion Serine protease Mitochondria 0.049773045 Q0CZ22 3.1 Cell cycle control, cell division, chromosome partitioning Coronin Mitochondria...”
Q70I39 Coatomer subunit alpha from Lotus japonicus
24% identity, 22% coverage
LIS1B_DANRE / Q803D2 Lissencephaly-1 homolog B; Platelet-activating factor acetylhydrolase IB subunit alpha b from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
24% identity, 41% coverage
- function: Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in the PAF inactivation. Regulates the PAF-AH (I) activity in a catalytic dimer composition-dependent manner (By similarity). Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule- dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. May be required for proliferation of neuronal precursors and neuronal migration (By similarity). Involved in the positioning of nuclei in photoreceptor cells.
subunit: Can self-associate. Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity (By similarity). Interacts with dynein, dynactin, nde1 and ndel1.
Ava_3867 Serine/Threonine protein kinase with WD40 repeats from Anabaena variabilis ATCC 29413
25% identity, 38% coverage
- Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes
Xu, BMC genomics 2009 - “...Ava_0640 Ava_1491 Ava_4669 Ava_0687 Ava_4995 Ava_1172 Ava_0874 Ava_4457 Ava_0873 Ava_0613 Ava_4753 Ava_1559 Ava_3542 Ava_1149 Ava_3207 Ava_3867 Ava_4503 Ava_3009 Ava_3703 Ava_1629 Ava_2629 Ava_1558 Ava_1021 A-prime CYA_0295 CYA_2315 B-prime CYB_2824 CYB_0465 CYB_2795 PCC7120 asr0847 alr0317 alr0318 alr0523 alr0524 alr0525 alr0169 alr0874 all3335 all3334 all3333 all3332 alr2210 alr2211 alr2212...”
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...HiskA Ava_0762 cbSTKI Ava_3584 cbSTKI-TM Ava_1153 cbSTKI Ava_3596 cbSTKIII GAFGAF, HiskA Ava_1552 cbSTKII TPR (10) Ava_3867 cbSTKII WD40 (7) Ava_1592 cbSTKI-other Ava_3995 cbSTKIII GAF, HiskA Ava_1700 cbSTKI-other Ava_4106 cbSTKI-other Ava_1816 cbSTKI-other Ava_4391 cbSTKI-other Ava_1980 cbSTKIII GAF, HiskA Ava_4489 cbSTKIII GAF, HiskA Ava_1995 cbSTKI-other Ava_4503 cbSTKIII GAF,...”
- “...(including four STKs in marine unicellular Prochlorococcus and Synechococcus , 6803_slr1443, CwatDRAFT_0901, Tery_0088, Tery_4781 and Ava_3867) exhibit some deviations from the canonical motifs (Fig. 2 ) that were deemed tolerable. In all 286 putative STK sequences were considered in this study (Table 1 ). Figure 2...”
UABAM_04996 caspase family protein from Candidatus Uabimicrobium amorphum
25% identity, 16% coverage
- Phagocytosis-like cell engulfment by a planctomycete bacterium
Shiratori, Nature communications 2019 - “...stabilisation and cross-link of actin filament 37 ) and found two candidate proteins (UABAM_01722 and UABAM_04996) that are similar to Aip1 and Crn1, respectively (Supplementary Table 11 ). We used F-actin-binding phalloidin and an antibody specific for eukaryotic actin but failed to observe a signal on...”
L7IXA5 Coatomer subunit alpha from Pyricularia oryzae (strain P131)
24% identity, 26% coverage
PRL1_ARATH / Q42384 Protein pleiotropic regulatory locus 1; Protein PRL1; MOS4-associated complex protein 2; MAC protein 2 from Arabidopsis thaliana (Mouse-ear cress) (see 10 papers)
NP_193325 pleiotropic regulatory locus 1 from Arabidopsis thaliana
AT4G15900 PRL1 (PLEIOTROPIC REGULATORY LOCUS 1); basal transcription repressor/ nucleotide binding / protein binding from Arabidopsis thaliana
25% identity, 45% coverage
- function: Pleiotropic regulator of glucose, stress and hormone responses. Also regulates cytochrome P450 CYP90A1/CPD. Coordinates the expression of hormone- and stress-related genes and genes related to cell wall modification and growth, leading to altered sugar-dependent growth and developmental responses. Component of the MAC complex that probably regulates defense responses through transcriptional control and thereby is essential for plant innate immunity. By suppressing the expression of several (1)O(2)-responsive genes, PRL1 seems to play a major role in modulating responses of plants to environmental changes by interconnecting (1)O(2)-mediated retrograde signaling with other signaling pathways. Acts as a negative regulator of SNF1-related protein kinases AKIN10 and AKIN11 via the inhibition of their interaction with SKP1/ASK1. Component of the CUL4-RBX1-DDB1-PRL1 E3 ubiquitin-protein ligase complex, PRL1 may function as the substrate recognition module within this complex, leading to the AKIN10 degradation.
subunit: Component of the multiprotein assembly MOS4-associated complex (MAC) at least composed of MOS4, CDC5, PRL1 and PRP19 (PubMed:17575050, PubMed:19629177). Interacts with CDC5 (PubMed:17575050). Component of the CUL4-RBX1-DDB1-PRL1 E3 ubiquitin-protein ligase complex. Interacts with DDB1A through its DWD motif (PubMed:18223036). Interacts with AKIN10, AKIN11 and PIPC (PubMed:10220464). Interacts with KAP2 (PubMed:9765207).
disruption phenotype: Hypersensitivity to glucose and sucrose. Enhanced sensitivity of plants to stress and to growth hormones including cytokinin, ethylene, abscisic acid, and auxin. Accumulation of sugars and starch in leaves, and root elongation. Cell elongation defects. Enhanced susceptibility to virulent and avirulent pathogens. - PLEIOTROPIC REGULATORY LOCUS1 maintains actin microfilament integrity to regulate pavement cell morphogenesis.
Gao, Plant physiology 2024 (PubMed)- GeneRIF: PLEIOTROPIC REGULATORY LOCUS1 maintains actin microfilament integrity to regulate pavement cell morphogenesis.
- PRL1 interacts with and stabilizes RPA2A to regulate carbon deprivation-induced senescence in Arabidopsis.
Meng, The New phytologist 2024 (PubMed)- GeneRIF: PRL1 interacts with and stabilizes RPA2A to regulate carbon deprivation-induced senescence in Arabidopsis.
- Protein kinase ATR inhibits E3 ubiquitin ligase CRL4PRL1 to stabilize ribonucleotide reductase in response to replication stress.
Bao, Cell reports 2023 (PubMed)- GeneRIF: Protein kinase ATR inhibits E3 ubiquitin ligase CRL4[PRL1] to stabilize ribonucleotide reductase in response to replication stress.
- The ATR-WEE1 kinase module inhibits the MAC complex to regulate replication stress response.
Wang, Nucleic acids research 2021 - GeneRIF: The ATR-WEE1 kinase module inhibits the MAC complex to regulate replication stress response.
- PRL1, an RNA-binding protein, positively regulates the accumulation of miRNAs and siRNAs in Arabidopsis.
Zhang, PLoS genetics 2014 - GeneRIF: PRL1 is required for the accumulation of microRNAs (miRNAs) and small interfering RNAs (siRNAs). PRL1 positively influences the processing of miRNA primary transcripts (pri-miRNAs) and double-stranded RNAs (dsRNAs).
- Pleiotropic regulatory locus 2 exhibits unequal genetic redundancy with its homolog PRL1.
Weihmann, Plant & cell physiology 2012 (PubMed)- GeneRIF: Identification and characterization of a dominant suppressor of prl1 revealed a regulatory, gain-of-function mutation in PLEIOTROPIC REGULATORY LOCUS 2 (PRL2), a close homolog of PRL1.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_177513 NP_014082 DDB0233739 fSAP35 THOC6 NP_077315 NP_648557 NP_190535 No hit DDB0233741 MGC4238 WDR83 NP_115708 NP_609782 NP_193325 No hit Cap binding proteins DDB0233457 CBP80 NCBP1 NP_002477 NP_726938 NP_565356 NP_013844 DDB0233456 CBP20 NCBP2 NP_031388 NP_524396 NP_199233 NP_015147 Polyadenylation machinery DDB0233359 PAB1 PABPC1 NP_002559 NP_476667 NP_177322 NP_011092 DDB0233678 PAB2...”
- Pleiotropic regulatory locus 1 (PRL1) integrates the regulation of sugar responses with isoprenoid metabolism in Arabidopsis.
Flores-Pérez, Molecular plant 2010 (PubMed)- GeneRIF: PRL1 appears to coordinate isoprenoid metabolism with sugar, hormone, and stress responses.
- More
- Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci
McDaniel, Applications in plant sciences 2013 - “...SW:SUI1_MAIZE P56330 PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG 537 0.072549 JY263171, JY263330 AW098304 similar to SW:PRL1_ARATH Q42384 PP1/PP2A PHOSPHATASES PLEIOTROPIC REGULATOR PRL1 385 0.019139 JY262893, JY263041, JY263238, JY262730 AW098306 similar to SW:RL7_ARATH Q42208 60S RIBOSOMAL PROTEIN L7 203* 0 JY263174, JY263333 AW098317 Moss EST library CPU Ceratodon...”
- Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing
McDonald, Molecular and cellular biology 1999 - “...described function in other species A. thaliana PRL1 (Q42384); Homo sapiens (AF044333) D. melanogaster crn (AL009171) H. sapiens (2463577) H. sapiens SM D...”
- Proteolytic control of the RNA silencing machinery
Genschik, The Plant cell 2024 - “...AT3G03300 HEN1 Gramene: AT4G20910 HEN1 Araport: AT4G20910 PAG1 Gramene: AT2G27020 PAG1 Araport: AT2G27020 PRL1 Gramene: AT4G15900 PRL1 Araport: AT4G15900 NRPD1a Gramene: A09p015000.1_BraROA NRPD1a Araport: A09p015000.1_BraROA AGO1 Gramene: AT1G48410 AGO1 Araport: AT1G48410 FREE1 Gramene: At1G20110 FREE1 Araport: At1G20110 References Achkar NP , Cho SK , Poulsen C...”
- The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism
Yang, Molecular & cellular proteomics : MCP 2024 - “...proteins involved in cold tolerance (ATRZ-1C) Y Y negative regulation of biosynthetic process; RNA binding AT4G15900 Pleiotropic regulatory locus 1 (PRL1) Y RNA splicing; catalytic step 2 spliceosome; negative regulation of biosynthetic process; intracellular protein-containing complex; embryo development; nuclear protein-containing complex AT2G16860 GCIP-interacting family protein (ATSYF2)...”
- Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study
Saroha, Frontiers in plant science 2023 - “...U-box protein 1) (RING-type E3 ubiquitin transferase E4) ath:AT5G15400 Protein ubiquitylation Lus10037500 PRL1_ARATH PRL1 MAC2 At4g15900 dl3990w FCAALL.40 Protein pleiotropic regulatory locus 1 (Protein PRL1) (MOS4-associated complex protein 2) (MAC protein 2) ath:AT4G15900 Pleiotropic regulator of glucose, stress and hormone responses. Lus10017640 ARFF_ARATH ARF6 At1g30330 T4K22.6...”
- Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds
Hermawaty, Tree physiology 2023 - “...and degradation of oxidase protein during oxidation stress. Xiong et al. (2005 , 2007) VIT_05s0077g02310 AT4G15900 Post-embryonic developmental, sugar mediated signaling pathway. PP1/PP2A phosphatases pleiotropic regulator PRL1 A nuclear WD-protein functions as a pleiotropic regulator of glucose and hormone responses during development in Arabidopsis. Nmeth et...”
- Identification of the Karyopherin Superfamily in Maize and Its Functional Cues in Plant Development
Jin, International journal of molecular sciences 2022 - “...AT3G20630 ZmIMP1/2/3/4 (P), ZmIMB1c/d (P) Zm00001d045109 P-0.299, P-0.303 PKL AT2G25170 ZmIMP4 (S) Zm00001d033309 S-0.421 PRL1 AT4G15900 ZmIMB3, ZmIMB4 (S), ZmIPO8 (S), ZmXPOT (S) Zm00001d020810 S-0.716, S-0.640, S-0.505 TRM4B AT2G22400 ZmIMP1/2/3/4 (P), ZmXPO1/5 (S) Zm00001d050139 P-0.270, S-0.805 HDA6 AT5G63110 ZmIMB3, ZmIMB4 (S) Zm00001d013330 S-0.639 PCN AT4G07410 Zm00001d033912...”
- Biogenesis, conservation, and function of miRNA in liverworts
Pietrykowska, Journal of experimental botany 2022 - “...848 49.6 Mp3g09910 TIP_NG-patchGCFC 850 48.8 PPX1 AT4G26720 Metallophos 305 Mp2g13820 Metallophos 304 85.6 PRL1 AT4G15900 WD40WD40WD40WD40 WD40 486 Mp6g09620 WD40WD40WD40WD40 487 64.9 RACK1A AT1G18080 WD40WD40WD40WD40WD40WD40WD40 327 RACK1B AT1G48630 WD40WD40WD40WD40WD40WD40WD40 326 RACK1C AT1G18080 WD40WD40WD40WD40WD40WD40WD40 326 Mp3g15630 WD40WD40WD40WD40WD40WD40WD40 316 71.2 RBM7 AT4G10110 RRM_1 173 Mp1g13100 RRM_1 220...”
- The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes
Singh, Frontiers in plant science 2020 - “...2015 At4g02840 Nuclear Ribonucleoprotein SmD1b Nucleus Splicing and RNA quality control Elvira-Matelot et al., 2016 At4g15900 Core component of spliceosome-associated MAC complex (AtPRL1/AtMAC2) Nucleus Regulation of plant immunity Palma et al., 2007 At4g31570 Kinesin-related protein Cytoplasm Hormone homeostasis Molesini et al., 2012 At4g36020 CSD-type RNA chaperone...”
- Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression
Fonseca, Frontiers in plant science 2019 - “...al., 2008 ; Pritchard et al., 1999 ; Okamura et al., 2015 . miRNA BIOGENESIS AT4G15900 PRL1 (PLEIOTROPIC REGULATORY LOCUS 1) yes yes miRNA biogenesis; CRL4 E3 ubiquitin ligase activity; energy homeostasis; plant innate immunity MAC complex (MOS4-Associated Complex); Targets AKIN10 kinase Lee et al., 2008...”
- More
all0664 WD-40 repeat protein from Nostoc sp. PCC 7120
23% identity, 34% coverage
Ava_2851 Serine/Threonine protein kinase with WD40 repeats from Anabaena variabilis ATCC 29413
28% identity, 31% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...HisKA all5278 cbSTKI all2760 cbSTKI alr7232 cbSTKII TPR (3) Anabaena variabilis ATCC 29413 Ava_0012 cbSTKI Ava_2851 cbSTKII WD40 (6) Ava_0083 cbSTKIII GAF, HiskA Ava_2989 cbSTKI Ava_0084 cbSTKI-other Ava_2990 cbSTKI-TM Ava_0153 cbSTKI-TM Ava_3036 cbSTKI Ava_0219 cbSTKI-other Ava_3308 cbSTKI-other Ava_0220 cbSTKI-other Ava_3310 cbSTKI-other Ava_0353 cbSTKII FHA Ava_3384 cbSTKI-other...”
all0438 serine/threonine kinase with WD-40 repeat from Nostoc sp. PCC 7120
28% identity, 31% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...all3169 cbSTKII WD40 (7) alr0344 cbSTKII ANF all3206 cbSTKI-other alr0354 cbSTKIII GAF, HisKA all3207 cbSTKI-other all0438 cbSTKII WD40 (7) alr3268 cbSTKII Pentapeptide (2) alr0548 cbSTKII FHA all3557 cbSTKIII GAF, HisKA alr0709 cbSTKIII GAF, HisKA all3691 cbSTKIII GAFGAF, HisKA alr0710 cbSTKIII GAF, HisKA alr3706 cbSTKI-TM all0886 cbSTKIII...”
CNAG_03554 coatomer protein complex, subunit alpha (xenin) from Cryptococcus neoformans var. grubii H99
24% identity, 23% coverage
- Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals
Trevijano-Contador, PLoS pathogens 2018 - “...6.4E-03 CNAG_06659 hexosaminidase 0.7 6.2 2.4E-06 Intracellular protein transport (p-value: 1.2E-05) COPI and COPII vesicles CNAG_03554 coatomer, subunit ( COP1 , SEC33 , RET1) 0.9 2.2E-02 2.1 6.0E-03 CNAG_03299 coatomer beta subunit ( SEC26 ) 1.2 1.1E-03 2.4 7.8E-03 CNAG_04074 coatomer beta' subunit ( SEC27 )...”
- “...the COPI-coated vesicles, also known as coatomer (, , ', , and , encoded by CNAG_03554, CNAG_03299, CNAG_04074, CNAG_01274, and CNAG_01211, respectively). COPI-coated vesicles are found associated with Golgi membranes, are involved in Golgi to endoplasmic reticulum (retrograde) vesicle transport, and also likely in intra-Golgi transport....”
FBXW7_RAT / D3Z902 F-box/WD repeat-containing protein 7 from Rattus norvegicus (Rat) (see paper)
NP_001406457 F-box/WD repeat-containing protein 7 from Rattus norvegicus
24% identity, 47% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity). Recognizes and binds phosphorylated sites/phosphodegrons within target proteins and thereafter brings them to the SCF complex for ubiquitination (By similarity). Identified substrates include cyclin-E (CCNE1 or CCNE2), JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NOTCH2, MCL1, MLST8, RICTOR and probably PSEN1 (By similarity). Acts as a negative regulator of JNK signaling by binding to phosphorylated JUN and promoting its ubiquitination and subsequent degradation (By similarity). SCF(FBXW7) complex mediates the ubiquitination and subsequent degradation of NFE2L1 (By similarity). Involved in bone homeostasis and negative regulation of osteoclast differentiation (By similarity). Regulates the amplitude of the cyclic expression of hepatic core clock genes and genes involved in lipid and glucose metabolism via ubiquitination and proteasomal degradation of their transcriptional repressor NR1D1; CDK1- dependent phosphorylation of NR1D1 is necessary for SCF(FBXW7)-mediated ubiquitination (By similarity). Also able to promote 'Lys-63'-linked ubiquitination in response to DNA damage (By similarity). The SCF(FBXW7) complex facilitates double-strand break repair following phosphorylation by ATM: phosphorylation promotes localization to sites of double-strand breaks and 'Lys-63'-linked ubiquitination of phosphorylated XRCC4, enhancing DNA non-homologous end joining (By similarity).
subunit: Homodimer; homodimerization plays a role in substrate binding and/or ubiquitination and degradation (By similarity). Component of the SCF(FBXW7) complex consisting of CUL1, RBX1, SKP1 and FBXW7 (By similarity). Interacts (via F-box domain) with SKP1. Interacts (via F- box domain) with pseudophosphatase STYX; the interaction is direct and prevents FBXW7 interaction with SKP1 (By similarity). Interacts with cyclin-E (CCNE1 or CCNE2) (By similarity). Interacts with PSEN1 (By similarity). Forms a trimeric complex with NOTCH1 and SGK1 (By similarity). Interacts with NOTCH1 intracellular domain/NICD and NOTCH4 intracellular domain/NICD (By similarity). Interacts with NOTCH2 intracellular domain (N2ICD) (By similarity). Interacts with MYC (when phosphorylated) (By similarity). Interacts with USP28, counteracting ubiquitination of MYC (By similarity). Interacts (when phosphorylated at Thr-211) with PIN1, disrupting FBXW7 dimerization and promoting FBXW7 autoubiquitination and degradation (By similarity). Interacts with UBE2QL1 (By similarity). Interacts with FAM83D; promotes FBXW7 degradation (By similarity). Interacts with MYCN; FBXW7 competes with AURKA for binding to unphosphorylated MYCN but not for binding to phosphorylated MYCN (By similarity). Interacts with JUN (By similarity). Found in a complex with JUN and PRR7 (PubMed:27458189). Interacts with JUN and PRR7; the interaction inhibits ubiquitination- mediated JUN degradation, promoting its phosphorylation and transcriptional activity (By similarity). Interacts with NFE2L1 (By similarity). Interacts with NR1D1 (By similarity). Interacts with RICTOR; mediates RICTOR ubiquitination and degradation (By similarity). - lncRNA DLX6-AS1 Promotes Myocardial Ischemia-Reperfusion Injury through Mediating the miR-204-5p/FBXW7 Axis.
Wang, Mediators of inflammation 2023 - GeneRIF: lncRNA DLX6-AS1 Promotes Myocardial Ischemia-Reperfusion Injury through Mediating the miR-204-5p/FBXW7 Axis.
- FBXW7 alleviates hyperglycemia-induced endothelial oxidative stress injury via ROS and PARP inhibition.
Li, Redox biology 2022 - GeneRIF: FBXW7 alleviates hyperglycemia-induced endothelial oxidative stress injury via ROS and PARP inhibition.
- Calpain-mediated cleavage of Fbxw7 during excitotoxicity.
Ko, Neuroscience letters 2020 (PubMed)- GeneRIF: Calpain-mediated cleavage of Fbxw7 during excitotoxicity.
- E3 ligase Fbw7 participates in oxidative stress‑induced myocardial cell injury via interacting with Mcl‑1.
Li, Molecular medicine reports 2019 - GeneRIF: Fbw7 participates in oxidative stress-induced myocardial cell injury via interacting with Mcl1.
FBXW7_MOUSE / Q8VBV4 F-box/WD repeat-containing protein 7; F-box and WD-40 domain-containing protein 7; F-box protein FBW7; F-box protein Fbxw6; F-box-WD40 repeat protein 6; SEL-10 from Mus musculus (Mouse) (see 7 papers)
XP_006501719 F-box/WD repeat-containing protein 7 isoform X1 from Mus musculus
24% identity, 47% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:21953459, PubMed:22748924). Recognizes and binds phosphorylated sites/phosphodegrons within target proteins and thereafter brings them to the SCF complex for ubiquitination (PubMed:22748924). Mediates ubiquitination and subsequent degradation of CCNE1 and MYC (PubMed:22748924). Identified substrates include cyclin-E (CCNE1 or CCNE2), DISC1, JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NOTCH2, MCL1, MLST8, RICTOR and probably PSEN1 (By similarity). Acts as a negative regulator of JNK signaling by binding to phosphorylated JUN and promoting its ubiquitination and subsequent degradation (By similarity). SCF(FBXW7) complex mediates the ubiquitination and subsequent degradation of NFE2L1 (PubMed:21953459). Involved in bone homeostasis and negative regulation of osteoclast differentiation (PubMed:29149593). Regulates the amplitude of the cyclic expression of hepatic core clock genes and genes involved in lipid and glucose metabolism via ubiquitination and proteasomal degradation of their transcriptional repressor NR1D1; CDK1-dependent phosphorylation of NR1D1 is necessary for SCF(FBXW7)-mediated ubiquitination (PubMed:27238018). Also able to promote 'Lys-63'-linked ubiquitination in response to DNA damage (By similarity). The SCF(FBXW7) complex facilitates double-strand break repair following phosphorylation by ATM: phosphorylation promotes localization to sites of double-strand breaks and 'Lys-63'-linked ubiquitination of phosphorylated XRCC4, enhancing DNA non-homologous end joining (By similarity).
subunit: Homodimer; homodimerization plays a role in substrate binding and/or ubiquitination and degradation (By similarity). Component of the SCF(FBXW7) complex consisting of CUL1, RBX1, SKP1 and FBXW7 (PubMed:11735228). Interacts (via F-box domain) with SKP1 (PubMed:11735228). Interacts (via F-box domain) with pseudophosphatase STYX; the interaction is direct and prevents FBXW7 interaction with SKP1 (By similarity). Interacts with cyclin-E (CCNE1 or CCNE2) (By similarity). Interacts with PSEN1 (By similarity). Forms a trimeric complex with NOTCH1 and SGK1 (By similarity). Interacts with NOTCH1 intracellular domain/NICD and NOTCH4 intracellular domain/NICD (PubMed:11425854, PubMed:11461910). Interacts with NOTCH2 intracellular domain (N2ICD) (By similarity). Interacts with MYC (when phosphorylated) (By similarity). Interacts with USP28, counteracting ubiquitination of MYC (By similarity). Interacts (when phosphorylated at Thr-208) with PIN1, disrupting FBXW7 dimerization and promoting FBXW7 autoubiquitination and degradation (By similarity). Interacts with UBE2QL1 (By similarity). Interacts with FAM83D; promotes FBXW7 degradation (By similarity). Interacts with MYCN; FBXW7 competes with AURKA for binding to unphosphorylated MYCN but not for binding to phosphorylated MYCN (By similarity). Interacts with JUN (By similarity). Found in a complex with JUN and PRR7 (By similarity). Interacts with JUN and PRR7; the interaction inhibits ubiquitination- mediated JUN degradation, promoting its phosphorylation and transcriptional activity (By similarity). Interacts with NFE2L1 (PubMed:21953459). Interacts with NR1D1 (By similarity). Interacts with RICTOR; mediates RICTOR ubiquitination and degradation (By similarity). Interacts with USP38, counteracting ubiquitination of MYC (By similarity).
disruption phenotype: Whole body FBW7 knockout is embryonic lethal. Conditional knockout mice in which FBW7 expression is specifically abolished in osteoclasts display severe bone resorption, bone fragility and low bone mass (PubMed:29149593). Conditional knockout in liver reduces the amplitude of the diurnal expression of many core clock genes and the altered expression of a large number of genes controlling liver metabolic pathways (PubMed:27238018). - FBW7/GSK3β mediated degradation of IGF2BP2 inhibits IGF2BP2-SLC7A5 positive feedback loop and radioresistance in lung cancer.
Zhou, Journal of experimental & clinical cancer research : CR 2024 - GeneRIF: FBW7/GSK3beta mediated degradation of IGF2BP2 inhibits IGF2BP2-SLC7A5 positive feedback loop and radioresistance in lung cancer.
- Selective deletion of E3 ubiquitin ligase FBW7 in VE-cadherin-positive cells instigates diffuse large B-cell lymphoma in mice in vivo.
Cai, Cell death & disease 2024 - GeneRIF: Selective deletion of E3 ubiquitin ligase FBW7 in VE-cadherin-positive cells instigates diffuse large B-cell lymphoma in mice in vivo.
- Deletion of Fbxw7 in oocytes causes follicle loss and premature ovarian insufficiency in mice.
Zhao, Journal of cellular and molecular medicine 2024 - GeneRIF: Deletion of Fbxw7 in oocytes causes follicle loss and premature ovarian insufficiency in mice.
- FBXW7 Enhances Cisplatin-Induced Apoptosis in Oral Cancer Cell Lines.
Yang, International dental journal 2023 - GeneRIF: FBXW7 Enhances Cisplatin-Induced Apoptosis in Oral Cancer Cell Lines.
- MiR-223-3p regulates the eosinophil degranulation and enhances the inflammation in allergic rhinitis by targeting FBXW7.
Wu, International immunopharmacology 2023 (PubMed)- GeneRIF: MiR-223-3p regulates the eosinophil degranulation and enhances the inflammation in allergic rhinitis by targeting FBXW7.
- High-fat diet aggravates the severity of the in vitro posttraumatic osteoarthritis model through macrophagic FBW7.
Duan, Immunity, inflammation and disease 2023 - GeneRIF: High-fat diet aggravates the severity of the in vitro posttraumatic osteoarthritis model through macrophagic FBW7.
- Epigenetic Regulation of IL-23 by E3 Ligase FBXW7 in Dendritic Cells Is Critical for Psoriasis-like Inflammation.
Song, Journal of immunology (Baltimore, Md. : 1950) 2023 (PubMed)- GeneRIF: Epigenetic Regulation of IL-23 by E3 Ligase FBXW7 in Dendritic Cells Is Critical for Psoriasis-like Inflammation.
- Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression in male mice.
Xia, Nature communications 2023 - GeneRIF: Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression in male mice.
- More
PAAG_00103 WD repeat-containing protein from Paracoccidioides lutzii Pb01
25% identity, 37% coverage
- Transcriptional profile of Paracoccidioides spp. in response to itraconazole
da, BMC genomics 2014 - “...Ubiquitin-protein ligase ( UBI ) PAAG_02632 3.7e-11 +2 WD repeat containing protein ( WDR ) PAAG_00103 1.0e-25 +1 Ubiquitin thioesterase ( OTU1 ) PAAG_08841 1.0e-32 -5 Ubiquitin fusion degradation protein ( UFD ) PAAG_01475 1.0e-62 +1 Proteasome component ( PREP6 ) PAAG_07802 6.1e-5 +1 Cellular transport,...”
LIS1_USTMA / Q4P9P9 Nuclear distribution protein PAC1; Lissencephaly-1 homolog; LIS-1; nudF homolog from Ustilago maydis (strain 521 / FGSC 9021) (Corn smut fungus) (see paper)
28% identity, 31% coverage
- function: Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for nuclear migration during vegetative growth as well as development. Required for localization of dynein to the mitotic spindle poles. Recruits additional proteins to the dynein complex at SPBs (By similarity). Required for retrograde early endosome (EE) transport from the hyphal tip.
subunit: Self-associates. Interacts with NDL1 and dynein.
CNG00480 coatomer alpha subunit from Cryptococcus neoformans var. neoformans JEC21
24% identity, 23% coverage
NP_001359172 dynein assembly factor with WD repeat domains 1 isoform b from Mus musculus
26% identity, 35% coverage
SEL10_CAEEL / Q93794 F-box/WD repeat-containing protein sel-10; Egg laying defective protein 41; Suppressor/enhancer of lin-12 protein 10 from Caenorhabditis elegans (see 9 papers)
NP_506421 F-box/WD repeat-containing protein sel-10 from Caenorhabditis elegans
26% identity, 33% coverage
- function: Probable substrate recognition component of SCF (SKP1-CUL-F- box protein) E3 ubiquitin-protein ligase complex, which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:17626846). Regulates synapse elimination in early development in the motor neuron HSNL (PubMed:17626846). Cell autonomous negative regulator of lin-12/Notch-mediated signaling, with respect to lin-12 activity in cell fate decisions and tumorigenesis (PubMed:9389650). May target the intracellular domains of lin-12/Notch proteins for ubiquitin-dependent degradation (PubMed:9389650). Involved in sex determination by promoting female development (PubMed:15306688, PubMed:18718460). Potential regulator of presenilin (PubMed:9861048). May have a role in egg laying (PubMed:15306688, PubMed:8293978). Regulates zyg-1 levels (possibly redundantly with lin-23) to control centrosome duplication during mitosis (PubMed:22623721). Negatively regulates lin-45 activity and protein stability, probably by targeting it for ubiquitination and proteasomal degradation (PubMed:23154983).
subunit: Probable component of the SCF(sel-10) E3 ubiquitin-protein ligase complex which includes skr-1 and F-box domain-containing protein sel-10 as a substrate recognition component (PubMed:17626846). Interacts with fem-1, fem-2, and fem-3 (PubMed:15306688). Interacts with the intracellular domain of glp-1 and sel-12 (PubMed:9861048). Interacts with lin-12 (PubMed:9389650). Interacts with skr-1 (PubMed:18718460). Interacts with zyg-1 (PubMed:22623721).
disruption phenotype: Worms show a weak masculinization phenotype (PubMed:8293978). Moreover sel-10 mutants suppress the egg laying defective (egl) phenotype of the sel-12 mutants (PubMed:8293978). RNAi- mediated knockdown results in increased zyg-1 expression at centrosomes (PubMed:22623721). - Synaptic Protein Degradation Controls Sexually Dimorphic Circuits through Regulation of DCC/UNC-40.
Salzberg, Current biology : CB 2020 - GeneRIF: Synaptic Protein Degradation Controls Sexually Dimorphic Circuits through Regulation of DCC/UNC-40.
- Negative feedback by conserved kinases patterns the degradation of Caenorhabditiselegans Raf in vulval fate patterning.
de, Development (Cambridge, England) 2020 - GeneRIF: Negative feedback by conserved kinases patterns the degradation of Caenorhabditis elegans Raf in vulval fate patterning.
- Notch signaling is antagonized by SAO-1, a novel GYF-domain protein that interacts with the E3 ubiquitin ligase SEL-10 in Caenorhabditis elegans.
Hale, Genetics 2012 - GeneRIF: Combined analysis of the SAO-1-SEL-10 protein interaction and comparisons of sao-1 and sel-10 genetic interactions suggest a possible role for SAO-1 as an accessory protein that participates with SEL-10 in downregulation of Notch signaling.
- The C. elegans F-box proteins LIN-23 and SEL-10 antagonize centrosome duplication by regulating ZYG-1 levels.
Peel, Journal of cell science 2012 - GeneRIF: Data show that a second F-box protein, SEL-10, also contributes to ZYG-1 regulation. Co-depletion of LIN-23 and SEL-10 suggests these proteins function cooperatively.
- Spatial regulation of an E3 ubiquitin ligase directs selective synapse elimination.
Ding, Science (New York, N.Y.) 2007 (PubMed)- GeneRIF: study found stereotyped developmental elimination of synapses in the motor neuron (HSNL) was mediated by a Skp1-cullin-F-box (SCF) complex composed of SKR-1 & SEL-10; SYG-1 bound to SKR-1 & inhibited assembly of the SCF complex, protecting nearby synapses
- The Caenorhabditis elegans F-box protein SEL-10 promotes female development and may target FEM-1 and FEM-3 for degradation by the proteasome.
Jäger, Proceedings of the National Academy of Sciences of the United States of America 2004 - GeneRIF: Results suggest that SEL-10-mediated proteolysis of FEM-1 and FEM-3 is required for normal hermaphrodite development.
NP_001164280 archipelago from Tribolium castaneum
28% identity, 37% coverage
- A coffee berry borer (Hypothenemus hampei) genome assembly reveals a reduced chemosensory receptor gene repertoire and male-specific genome sequences
Navarro-Escalante, Scientific reports 2021 - “...WD-repeat domains. This protein is 53% similar to the T. castaneum Fbox/WD Archipelago protein (Accession: NP_001164280.1). Fbox/WD proteins are part of the SCF (Skp-Cullin-F-box) complex that function as E3 ubiquitin ligases involved in protein degradation and protein functional modifications throughout ubiquitination. To obtain evidence of the...”
- “...[ Tribolium castaneum ] (XP_974381) 6e42 84 HHAM03825 3121 0.001 Archipelago [ Tribolim castaneum ] (NP_001164280) 1e117 45 HHAM06836 1317 0.007 Zinc finger protein 271-like [ Cyprinus carpio ] (XP_018970070) 1e6 43 HHAM04470 2741 0.039 Zinc finger protein 271-like [ Cyprinus carpio ] (XP_018970070) 4e6 43...”
Q22D06 WD domain, G-beta repeat protein from Tetrahymena thermophila (strain SB210)
20% identity, 12% coverage
- CEP104/FAP256 and associated cap complex maintain stability of the ciliary tip
Legal, The Journal of cell biology 2023 - “...catalytic domain protein 1066 Kif16B 29.75 Early endosomes 14.9 0.284 7.7 Decreased at least fourfold Q22D06 WD domain, G-beta repeat protein 2585 Dynein assembly factor with WDR repeat domains 34.2 Cilia 8.55 0.171 13.7 Decreased at least fourfold Q24CF9 WD domain, G-beta repeat protein 2207 Dynein...”
FBXW7_BOVIN / F1MNN4 F-box/WD repeat-containing protein 7; F-box and WD-40 domain-containing protein 7 from Bos taurus (Bovine) (see paper)
24% identity, 47% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes and binds phosphorylated sites/phosphodegrons within target proteins and thereafter brings them to the SCF complex for ubiquitination (By similarity). Identified substrates include cyclin-E (CCNE1 or CCNE2), DISC1, JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NOTCH2, MCL1, MLST8, RICTOR, and probably PSEN1. Acts as a negative regulator of JNK signaling by binding to phosphorylated JUN and promoting its ubiquitination and subsequent degradation (By similarity). SCF(FBXW7) complex mediates the ubiquitination and subsequent degradation of NFE2L1 (By similarity). Involved in bone homeostasis and negative regulation of osteoclast differentiation (By similarity). Also able to promote 'Lys-63'-linked ubiquitination in response to DNA damage (By similarity). The SCF(FBXW7) complex facilitates double-strand break repair following phosphorylation by ATM: phosphorylation promotes localization to sites of double-strand breaks and 'Lys-63'-linked ubiquitination of phosphorylated XRCC4, enhancing DNA non-homologous end joining (By similarity).
subunit: Homodimer; homodimerization plays a role in substrate binding and/or ubiquitination and degradation. Component of the SCF(FBXW7) complex consisting of CUL1, RBX1, SKP1 and FBXW7. Interacts (via F-box domain) with SKP1. Interacts (via F-box domain) with pseudophosphatase STYX; the interaction is direct and prevents FBXW7 interaction with SKP1. Interacts with cyclin-E (CCNE1 or CCNE2). Interacts with PSEN1. Forms a trimeric complex with NOTCH1 and SGK1. Interacts with NOTCH1 intracellular domain/NICD and NOTCH4 intracellular domain/NICD. Interacts with NOTCH2 intracellular domain (N2ICD). Interacts with MYC (when phosphorylated). Interacts with USP28, counteracting ubiquitination of MYC. Interacts with JUN. Found in a complex with JUN and PRR7. Interacts with JUN and PRR7; the interaction inhibits ubiquitination-mediated JUN degradation, promoting its phosphorylation and transcriptional activity. Interacts (when phosphorylated at Thr- 204) with PIN1, disrupting FBXW7 dimerization and promoting FBXW7 autoubiquitination and degradation. Interacts with UBE2QL1. Interacts with FAM83D; promotes FBXW7 degradation. Interacts with MYCN; FBXW7 competes with AURKA for binding to unphosphorylated MYCN but not for binding to phosphorylated MYCN. Interacts with STOML1. Interacts with NFE2L1. Interacts with USP36, counteracting ubiquitination of MYC. Interacts with RICTOR; mediates RICTOR ubiquitination and degradation.l Interacts with USP38, counteracting ubiquitination of MYC (By similarity).
subunit: (Microbial infection) In case of infection, interacts with T.annulata PIN1 (TaPIN1); leading to FBXW7 autoubiquitination and subsequent degradation: FBXW7 degradation promotes stabilization of JUN, which promotes cell transformation (PubMed:25624101).
L8B5P6 F-box and WD-40 domain-containing protein 7 alpha from Xenopus laevis
24% identity, 47% coverage
- The stability of Fbw7α in M-phase requires its phosphorylation by PKC
Zitouni, PloS one 2017 - “...sequences are as follows: Hs-FBW7 alpha (Q969H0), Hs-FBW7 beta (BAA91986.1), Hs-FBW7 gamma (Q969H0-4), Xl-FBW7 alpha (L8B5P6), Xl-FBW7 beta (XP_018105049.2), Xl-FBW7 gamma (XP_018105041.1). Primers for subcloning and PCR amplification of X . laevis FBW7 cDNA isoforms were designed according to the sequences available in databases with the...”
XP_044911707 F-box/WD repeat-containing protein 7 isoform X1 from Felis catus
24% identity, 47% coverage
DAW1_MOUSE / D3Z7A5 Dynein assembly factor with WD repeat domains 1 from Mus musculus (Mouse) (see paper)
26% identity, 35% coverage
- function: Required for axonemal dynein assembly and ciliary motility in ciliated organs, including Kupffer's vesicle, during embryogenesis (By similarity). Facilitates the onset of robust cilia motility during development (By similarity).
subunit: Interacts with IFT46.
CNAG_05294 F-box and WD-40 domain-containing protein CDC4 from Cryptococcus neoformans var. grubii H99
28% identity, 25% coverage
- Multiple F-Box Proteins Collectively Regulate Cell Development and Pathogenesis in the Human Pathogen Cryptococcus neoformans
Cao, Journal of fungi (Basel, Switzerland) 2022 - “...sexual reproduction, and fungal virulence [ 22 ]. We identified a second Cdc4 homolog, Fbp11 (CNAG_05294) and found redundant yet distinct roles of Fbp4 and Fbp11 in regulating cell size and fungal pathogenicity in C. neoformans . Deletion of FBP4 or FBP11 increased cell body size...”
- “...possesses an SDS sensitivity phenotype in the conditions we tested. fbp4 (CNAG_00693) and fbp11 mutants (CNAG_05294) showed multiple phenotypic changes in the virulence and stress response to environment including cell membrane integrity, cell size development, and melanin production. Fbp4 and Fbp11 are two F-box and WD-40...”
- Role of F-box Protein Cdc4 in Fungal Virulence and Sexual Reproduction of Cryptococcus neoformans
Wu, Frontiers in cellular and infection microbiology 2021 - “...and leucine-rich repeat protein Grr1 ( Bailey and Woodword, 1984 ; Liu etal., 2011 ) CNAG_05294 Fbw7 Cdc4 4e-43 ubiquitin-protein ligase, F-box and WD-40 domain-containing protein Cdc4 ( Goh and Surana, 1999 ) CNAG_05450 hypothetical protein CNAG_05454 hypothetical protein CNAG_05773 Met30 Met30 8e-72 F-box and WD-40...”
STRN4_HUMAN / Q9NRL3 Striatin-4; Zinedin from Homo sapiens (Human) (see 2 papers)
NP_037535 striatin-4 isoform 1 from Homo sapiens
25% identity, 37% coverage
- function: Calmodulin-binding scaffolding protein which is the center of the striatin-interacting phosphatase and kinase (STRIPAK) complexes (PubMed:18782753, PubMed:32640226). STRIPAK complexes have critical roles in protein (de)phosphorylation and are regulators of multiple signaling pathways including Hippo, MAPK, nuclear receptor and cytoskeleton remodeling (PubMed:32640226). Different types of STRIPAK complexes are involved in a variety of biological processes such as cell growth, differentiation, apoptosis, metabolism and immune regulation (Probable). Key regulator of the expanded Hippo signaling pathway by interacting and allowing the inhibition of MAP4K kinases by the STRIPAK complex (PubMed:32640226).
subunit: Part of the core of STRIPAK complexes composed of PP2A catalytic and scaffolding subunits, the striatins (PP2A regulatory subunits), the striatin-associated proteins MOB4, STRIP1 and STRIP2, PDCD10 and members of the STE20 kinases, such as STK24 and STK26 (PubMed:18782753, PubMed:32640226). Interacts with CTTNBP2NL (PubMed:18782753). - A WD40 repeat protein regulates fungal cell differentiation and can be replaced functionally by the mammalian homologue striatin
Pöggeler, Eukaryotic cell 2004 - “...which includes striatin (055106), SG2NA (Q13033), and zinedin (NP_037535). These multimodular WD40 repeat and calmodulin binding proteins are thought to act as...”
- “...sapiens SG2NA (Q13033) and H. sapiens zinedin (NP_037535); Dm, Drosophila melanogaster CKA (Q9VLT9); Ce, Caenorhabditis elegans protein encoded by the K07C5.8...”
- Down-regulated TAB1 suppresses the replication of Coxsackievirus B5 via activating the NF-κB pathways through interaction with viral 3D polymerase.
Zhang, Virology journal 2023 - “...Histone H3.1 P68431 0.0114 Down PSMA5 Proteasome subunit alpha type-5 P28066 0.0309 Down STRN4 Striatin-4 Q9NRL3 0.0352 Down TAB1 TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 Q15750 0.0360 Down HBA1 Hemoglobin subunit alpha P69905 0.0007 Up TMEM9 Proton-transporting V-type ATPase complex assembly regulator TMEM9 Q9P0T7 0.0027...”
- Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS.
Zafarullah, International journal of molecular sciences 2023 - “...0.00250122 0.03131584 Calponin-2 174 Q86UT6 NLRX1 0.35 12.84 0.00251982 0.03134018 NLR family member X1 175 Q9NRL3 STRN4 1.43 14.38 0.0025321 0.03134018 Striatin-4 176 Q9NZ45 CISD1 0.42 12.92 0.00257935 0.03174358 CDGSH iron-sulfur domain-containing protein 1 177 P84103 SRSF3 0.54 13.92 0.00270148 0.03305881 Serine/arginine-rich splicing factor 3 178...”
- Transient Receptor Potential Channel A1 (TRPA1) Regulates Sulfur Mustard-Induced Expression of Heat Shock 70 kDa Protein 6 (HSPA6) In Vitro
Lüling, Cells 2018 - “...MS/MS Score Figure 1 C CAPRIN1 Caprin-1 Q14444 78.5 5.0 17 864 STRN4 Striatin 4 Q9NRL3 81.3 5.1 13 787 NCL Nucleolin P19338 76.6 4.5 10 443 GPHN Gephyrin Q9NQX3 80.4 5.1 7 372 Figure 1 D SFXN1 Sideroflexin 1 Q9H9B4 35.9 9.4 10 689 FHL1...”
- Heme-binding-mediated negative regulation of the tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) by IDO2.
Lee, Experimental & molecular medicine 2014 - “...P11021 GRP78 78kDa glucose-regulated protein 1.571 Q9NXE4 SMPD4 Isoform 4 of sphingomyelin phosphodiesterase 4 1.542 Q9NRL3 STRN4 Striatin-4 1.534 Q9NYV4 CDK12 Isoform 1 of cyclin-dependent kinase 12 1.53 Q13610 PWP1 Periodic tryptophan protein 1 homolog 1.521 Q99436 PSMB7 Proteasome subunit beta type-7 1.518 P24390 KDELR1 ER...”
FBXW7_HUMAN / Q969H0 F-box/WD repeat-containing protein 7; Archipelago homolog; hAgo; F-box and WD-40 domain-containing protein 7; F-box protein FBX30; SEL-10; hCdc4 from Homo sapiens (Human) (see 28 papers)
24% identity, 47% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:17434132, PubMed:22748924, PubMed:26976582, PubMed:28727686, PubMed:34741373, PubMed:35395208). Recognizes and binds phosphorylated sites/phosphodegrons within target proteins and thereafter brings them to the SCF complex for ubiquitination (PubMed:17434132, PubMed:22748924, PubMed:26774286, PubMed:26976582, PubMed:28727686, PubMed:34741373). Identified substrates include cyclin-E (CCNE1 or CCNE2), DISC1, JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NFE2L1, NOTCH2, MCL1, MLST8, RICTOR, and probably PSEN1 (PubMed:11565034, PubMed:11585921, PubMed:12354302, PubMed:14739463, PubMed:15103331, PubMed:17558397, PubMed:17873522, PubMed:22608923, PubMed:22748924, PubMed:25775507, PubMed:25897075, PubMed:26976582, PubMed:28007894, PubMed:28727686, PubMed:29149593, PubMed:34102342). Acts as a negative regulator of JNK signaling by binding to phosphorylated JUN and promoting its ubiquitination and subsequent degradation (PubMed:14739463). Involved in bone homeostasis and negative regulation of osteoclast differentiation (PubMed:29149593). Regulates the amplitude of the cyclic expression of hepatic core clock genes and genes involved in lipid and glucose metabolism via ubiquitination and proteasomal degradation of their transcriptional repressor NR1D1; CDK1-dependent phosphorylation of NR1D1 is necessary for SCF(FBXW7)-mediated ubiquitination (PubMed:27238018). Also able to promote 'Lys-63'-linked ubiquitination in response to DNA damage (PubMed:26774286). The SCF(FBXW7) complex facilitates double-strand break repair following phosphorylation by ATM: phosphorylation promotes localization to sites of double-strand breaks and 'Lys-63'-linked ubiquitination of phosphorylated XRCC4, enhancing DNA non-homologous end joining (PubMed:26774286).
subunit: Homodimer; homodimerization plays a role in substrate binding and/or ubiquitination and degradation (PubMed:17434132, PubMed:22608923, PubMed:28007894). Component of the SCF(FBXW7) complex consisting of CUL1, RBX1, SKP1 and FBXW7 (PubMed:11565034, PubMed:15103331, PubMed:22748924, PubMed:26774286, PubMed:26976582, PubMed:28007894, PubMed:28727686, PubMed:34741373). Interacts (via F- box domain) with SKP1 (PubMed:11585921, PubMed:17434132, PubMed:26976582, PubMed:28007894, PubMed:28727686). Interacts (via F- box domain) with pseudophosphatase STYX; the interaction is direct and prevents FBXW7 interaction with SKP1 (PubMed:28007894). Interacts with cyclin-E (CCNE1 or CCNE2) (PubMed:11565034, PubMed:17434132). Interacts with PSEN1 (PubMed:12354302). Forms a trimeric complex with NOTCH1 and SGK1 (PubMed:21147854). Interacts with NOTCH1 intracellular domain/NICD and NOTCH4 intracellular domain/NICD (PubMed:11585921). Interacts with NOTCH2 intracellular domain (N2ICD) (PubMed:29149593). Interacts with MYC (when phosphorylated) (PubMed:17873522, PubMed:25775507, PubMed:28007894). Interacts with USP28, counteracting ubiquitination of MYC (PubMed:17873522). Interacts with JUN (PubMed:14739463, PubMed:22608923). Found in a complex with JUN and PRR7 (PubMed:27458189). Interacts with JUN and PRR7; the interaction inhibits ubiquitination-mediated JUN degradation, promoting its phosphorylation and transcriptional activity (PubMed:27458189). Interacts (when phosphorylated at Thr-205) with PIN1, disrupting FBXW7 dimerization and promoting FBXW7 autoubiquitination and degradation (PubMed:22608923). Interacts with UBE2QL1 (PubMed:24000165). Interacts with FAM83D; promotes FBXW7 degradation (PubMed:24344117). Interacts with MYCN; FBXW7 competes with AURKA for binding to unphosphorylated MYCN but not for binding to phosphorylated MYCN (PubMed:27837025). Interacts with STOML1 (PubMed:23082202). Interacts with NFE2L1 (By similarity). Interacts with USP36, counteracting ubiquitination of MYC (PubMed:25775507). Interacts with NR1D1 (PubMed:27238018). Interacts with RICTOR; mediates RICTOR ubiquitination and degradation (PubMed:25897075). Interacts with USP38, counteracting ubiquitination of MYC (PubMed:34102342).
subunit: (Microbial infection) Interacts (via WD repeats) with SV40 large T antigen (via CPD region). - Profiling of differentially expressed MicroRNAs in familial hypercholesterolemia via direct hybridization.
Cione, Non-coding RNA research 2024 - “...ATRX P46100 3 2 3 2 10 KSR2 Q6VAB6 3 1 5 1 10 FBXW7 Q969H0 3 1 2 4 10 ERBB4 Q15303 3 0 6 1 10 IRGQ Q8WZA9 3 0 6 1 10 RSBN1 Q5VWQ0 3 0 5 2 10 CREBRF Q8IUR6 3 0...”
- The role of HR-HPV integration in the progression of premalignant lesions into different cancer types.
Catalán-Castorena, Heliyon 2024 - “...NFKBIA (P25963) NSD1 (Q96L73) ASAP1 (Q9ULH1) BBX (Q8WY36) SLTM (Q9NWH9) STAT1 (P42224) ZNF750 (Q32MQ0) FBXW7 (Q969H0) NSD1 (Q96L73) TGFBR2 (P37173) [ 161 ] 36 head and neck tumors positive HPV 16 and 18 DIPS-PCR E1, L1, E2 y L2 Intergenic regions, introns, and exons PTPRN2 (Q92932)...”
- “...viral genome Introns and exons PIK3CA (P42336) MLL2 (O14686) PTEN ( P60484) SOX2 (P48431) FBXW7 (Q969H0) TP53 (P04637) MYC (P01106) RICTOR (Q6R327) FGF10 (O15520) FGF3 (P11487) CCND1 (P24385) FBXW7 (Q969H0) STK11 (Q15831) AKT1 (P31749) AKT2 (P31751) AKT3 (Q9Y243) [ 160 ] 40 anal squamous cell carcinoma...”
- Recognition and reprogramming of E3 ubiquitin ligase surfaces by α-helical peptides.
Tokareva, Nature communications 2023 - “...SOCS2, and FBWX7 For protein used in phage display screens and SPR: FBXW7 (Uniprot ID: Q969H0, residues 263706) with an N-terminal GST-TEV tag and C-terminal AVI tag were co-expressed with full-length SKP1 (Uniprot ID: P63208, residues 1163) in the pETDuet-1 plasmid(Novagen). SOCS2 (Uniprot ID: O14508, residues...”
- Degron masking outlines degronons, co-degrading functional modules in the proteome.
Guharoy, Communications biology 2022 - “...Degronon components a (Gene name, UniProt ID) G1/S-specific cyclin-E1 (CCNE1, P24864) 393 LLTPPQS 399 FBXW7 (Q969H0) GSK3B (P49841), CDK2 (P24941) Numb-like protein (NUMBL, Q9Y6R0) 577 FEAQWAAL 584 MDM2 (Q00987) EPS15 (P42566), EPS15L1 (Q9UBC2) Cellular tumor antigen p53 (TP53, P04637) 19 FSDLWKLL 26 MDM2 (Q00987) PIN1 (Q13526),...”
- “...(P78527), ATM (Q13315), b CREBBP (Q92793) Myc proto-oncogene protein (MYC, P01106) 55 LLPTPPLS 62 FBXW7 (Q969H0) PIN1 (Q13526), BIN1 (O00499), GSK3B (P49841), MAPK1 (P28482), b DYRK2 (Q92630), b PPP2R5D (Q14738) Mitotic checkpoint serine/threonine-protein kinase BUB1 (BUB1, O43683) 534 NKENY 538 FZR1 (Q9UM11) CDC20 (Q12834) Claspin (CLSPN,...”
- The AlphaFold Database of Protein Structures: A Biologist's Guide.
David, Journal of molecular biology 2022 - “...52.0 1126 66.7 373 22.1 BRAF P15056 766 447 58.4 421 55.0 295 38.5 FBXW7 Q969H0 707 444 62.8 471 66.6 443 62.7 VHL P40337 213 160 75.1 155 72.8 150 70.4 RB1 P06400 928 698 75.2 592 63.8 763 82.2 LDLR P01130 860 705 82.0...”
- MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction.
Zhang, Acta pharmaceutica Sinica. B 2021 - “...(A) The search interface; (B) The result page. Figure7 For example, after inputting UniProt Accession Q969H0, the first row of Fig.7 B shows that UniProt Accession is Q969H0, Gene Name is FBXW7, Confidence Level is 2 (described in Table 1 ), PDB Code is 2OVP, Released...”
- Identification of Candidate Biomarkers for Idiopathic Thrombocytopenic Purpura by Bioinformatics Analysis of Microarray Data.
Gilanchi, Iranian journal of pharmaceutical research : IJPR 2020 - “...O43684 BUB3 85 0.058294 6 O94913 PCF11 77 0.037986 7 Q9Y243 PCF12 62 0.03668 8 Q969H0 FBXW7 53 0.025345 9 P15170 GSPT1 49 0.037137 10 P30622 CLIP1 46 0.012378 11 P42684 ABL2 42 0.023944 Down-regulated 1 P49407 ARRB1 125 0.121072* 2 P52292 KPNA2 81 0.066201 3...”
- Merkel cell polyomavirus small T antigen induces genome instability by E3 ubiquitin ligase targeting.
Kwun, Oncogene 2017 - “...pLKO.1 vector 6 were used for the knockdown study. shRNAs for human Fbw7 (UniProtKB ID: Q969H0) were described previously, 10 and a control shRNA construct was obtained from Addgene (#1864). Lentiviral and retroviral particles were generated in 293FT (Invitrogen) cells maintained in Dulbeccos modified Eagles medium...”
- More
KTNB1_DANRE / Q7ZUV2 Katanin p80 WD40 repeat-containing subunit B1; Katanin p80 subunit B1; p80 katanin from Danio rerio (Zebrafish) (Brachydanio rerio) (see 2 papers)
27% identity, 30% coverage
- function: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation.
subunit: Interacts with katna1. This interaction enhances the microtubule binding and severing activity of katna1 and also targets this activity to the centrosome.
disruption phenotype: Results in a significant reduction in midbrain size. A wide spectrum of defects in gastrulation and formation of anterior structures are noticed, ranging from milder microcephaly to more severe anencephaly and early embryonic death.
Ava_0039 Peptidase C14, caspase catalytic subunit p20 from Anabaena variabilis ATCC 29413
24% identity, 22% coverage
- The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria
Bhattacharjee, Journal of experimental botany 2020 - “...p20-like sub-domain in the predicted cytoplasmic portion. This presumed topology prevailed in six true OCAs: Ava_0039, Ava_3079, Cri9333_3253, GEI7407_1667, GEI7407_1667, and Glo7428_1095. Among these, the presence of NACHT in the predicted cytoplasmic portion of GEI7407_1667 implies its activity during PCD. Moreover, Ava_0039, Ava_3079, and GEI7407_1667 have...”
XP_005171005 F-box/WD repeat-containing protein 7 isoform X3 from Danio rerio
24% identity, 46% coverage
NP_079921 U5 small nuclear ribonucleoprotein 40 kDa protein from Mus musculus
Q6PE01 U5 small nuclear ribonucleoprotein 40 kDa protein from Mus musculus
25% identity, 36% coverage
Tery_3681 serine/threonine protein kinase with WD40 repeats from Trichodesmium erythraeum IMS101
26% identity, 36% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...(5) Tery_1030 cbSTKII FHA Tery_3423 cbSTKI-other Tery_1036 cbSTKII DUF323 Tery_3510 cbSTKI Tery_1627 cbSTKII WD40 (7) Tery_3681 cbSTKII TPR (7) Tery_1668 cbSTKI-other Tery_3863 cbSTKII GAF Tery_1722 cbSTKII GUN4 Tery_4060 cbSTKII WD40 (7) Tery_1723 cbSTKII GUN4 Tery_4351 cbSTKII DUF323 (2) Tery_2033 cbSTKII WD40 (7) Tery_4411 cbSTKI-TM Tery_2051 cbSTKI-other...”
DDB_G0287961 DENN domain-containing protein from Dictyostelium discoideum AX4
25% identity, 16% coverage
FBXW7_DROME / Q9VZF4 F-box/WD repeat-containing protein 7; F-box and WD-40 domain-containing protein 7; Protein archipelago from Drosophila melanogaster (Fruit fly) (see 5 papers)
NP_523922 archipelago, isoform C from Drosophila melanogaster
27% identity, 21% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity). Probably recognizes and binds to phosphorylated target proteins (By similarity). In the wing and eye, negatively regulates cell growth and proliferation by mediating the degradation of Myc and cyclin E, respectively (PubMed:11565033, PubMed:15182669). Required for endocycles, but not mitosis in follicle cell epithelium (PubMed:15175253).
subunit: Part of a SCF E3 ubiquitin-protein ligase complex. Interacts with Myc and puf (PubMed:15182669, PubMed:24173801). Interacts with CycE (PubMed:11565033).
disruption phenotype: RNAi-mediated knockdown in the posterior compartment of the larval wing disk increases cell size in the posterior compartment of the adult wing, resulting in an increase in the size of the posterior compartment as well as an increase in the ratio between the posterior and anterior areas. Knockdown of the gene is embryonic lethal. Neuronal-specific knockdown results in deficits in habituation learning, as demonstrated by the light-off reflex habituation assay. - A Drosophila genetic screen for suppressors of S6kinase-dependent growth identifies the F-box subunit Archipelago/FBXW7.
Zahoor, Molecular genetics and genomics : MGG 2019 (PubMed)- GeneRIF: Findings indicate that Archipelago (Ago)/FBXW7 controls S6kinase (dS6K) protein levels, but do not impinge on the transcript level.
- The archipelago ubiquitin ligase subunit acts in target tissue to restrict tracheal terminal cell branching and hypoxic-induced gene expression.
Mortimer, PLoS genetics 2013 - GeneRIF: these findings identify Ago as a required element of a circuit that suppresses the tracheogenic activity of larval muscle cells by antagonizing the Sima-mediated transcriptional response to hypoxia.
- Notch-dependent expression of the archipelago ubiquitin ligase subunit in the Drosophila eye.
Nicholson, Development (Cambridge, England) 2011 - GeneRIF: Notch-archipelago-cyclin E link represents a significant new cell cycle regulatory mechanism in the developing eye.
- dp53 Restrains ectopic neural stem cell formation in the Drosophila brain in a non-apoptotic mechanism involving Archipelago and cyclin E.
Ouyang, PloS one 2011 - GeneRIF: p53-mediated regulation of ectopic neural stem cells (NSC) self-renewal through the Ago/Cyc E axis becomes particularly important when NSC homeostasis is perturbed.
- The archipelago tumor suppressor gene limits rb/e2f-regulated apoptosis in developing Drosophila tissues.
Nicholson, Current biology : CB 2009 - GeneRIF: Ago loss induces hyperplasia of some organs but paradoxically reduces the size of the adult eye.
- The Drosophila F-box protein Archipelago controls levels of the Trachealess transcription factor in the embryonic tracheal system.
Mortimer, Developmental biology 2007 - GeneRIF: novel function for the ago ubiquitin-ligase in tracheal morphogenesis via Trh and its target breathless, and suggest that ago has distinct functions in mitotic and post-mitotic cells that influence its role in development and disease
- The Drosophila F box protein archipelago regulates dMyc protein levels in vivo.
Moberg, Current biology : CB 2004 (PubMed)- GeneRIF: archipelago is an important inhibitor of Drosophila Myc in developing tissues, and can regulate Cyclin E levels and Notch activity.
XP_002517787 notchless protein homolog from Ricinus communis
24% identity, 36% coverage
WDS_DROME / Q9V3J8 Protein will die slowly from Drosophila melanogaster (Fruit fly) (see 7 papers)
NP_001245503 will die slowly, isoform B from Drosophila melanogaster
27% identity, 35% coverage
- function: Contributes to histone modification. May position the N- terminus of histone H3 for efficient trimethylation at 'Lys-4' (PubMed:25310983). In neurons and together with DNA N6-methyl adenine demethylase Tet, plays a role in the maintenance of transcriptional activation for specific sets of genes (PubMed:30078725).
subunit: Core component of several methyltransferase-containing complexes. Component of the SET1 complex, composed at least of the catalytic subunit Set1, wds/WDR5, Wdr82, Rbbp5, ash2, Cfp1/CXXC1, hcf and Dpy-30L1 (PubMed:21694722). Interacts with Set1 (PubMed:21694722, PubMed:21875999, PubMed:22048023). Component of the MLL3/4 complex composed at least of the catalytic subunit trr, ash2, Rbbp5, Dpy-30L1, wds, hcf, ptip, Pa1, Utx, Lpt and Ncoa6 (PubMed:21875999). Component of the Ada2a-containing (ATAC) complex composed of at least Ada2a, Atac1, Hcf, Ada3, Gcn5, Mocs2B, Charac-14, Atac3, Atac2, NC2beta and wds (PubMed:18327268). Interacts with Nup98 (PubMed:25310983). Interacts (via WD repeats) with Tet (via C-terminus) (PubMed:30078725).
disruption phenotype: Larval lethal (PubMed:12471440). Conditional RNAi-mediated knockdown in larval wing imaginal disks results in reduced levels of trimethylated 'Lys-4' in histone H3 (PubMed:25310983). RNAi-mediated knockdown in neurons, does not affect mushroom bodies alpha lobe development (PubMed:30078725). Simultaneous RNAi-mediated knockdown of wds and Tet results in enhanced mushroom body alpha lobe development defects compared to the single Tet knockdown (PubMed:30078725). - A clustering of heterozygous missense variants in the crucial chromatin modifier WDR5 defines a new neurodevelopmental disorder.
Snijders, HGG advances 2023 - GeneRIF: A clustering of heterozygous missense variants in the crucial chromatin modifier WDR5 defines a new neurodevelopmental disorder.
- A genetic screen in Drosophila implicates Sex comb on midleg (Scm) in tissue overgrowth and mechanisms of Scm degradation by Wds.
Guo, Mechanisms of development 2015 (PubMed)- GeneRIF: Wds promotes Scm degradation through ubiquitination in vitro in Drosophila.
- The essential Drosophila melanogaster gene wds (will die slowly) codes for a WD-repeat protein with seven repeats.
Hollmann, Molecular genetics and genomics : MGG 2002 (PubMed)- GeneRIF: The essential Drosophila melanogaster gene wds (will die slowly) codes for a WD-repeat protein with seven repeats.
SNR40_HUMAN / Q96DI7 U5 small nuclear ribonucleoprotein 40 kDa protein; U5 snRNP 40 kDa protein; U5-40K; 38 kDa-splicing factor; Prp8-binding protein; hPRP8BP; U5 snRNP-specific 40 kDa protein; WD repeat-containing protein 57 from Homo sapiens (Human) (see 13 papers)
NP_004805 U5 small nuclear ribonucleoprotein 40 kDa protein from Homo sapiens
25% identity, 36% coverage
- function: Required for pre-mRNA splicing as component of the activated spliceosome (PubMed:11991638, PubMed:28076346, PubMed:28502770, PubMed:28781166, PubMed:29301961, PubMed:29360106, PubMed:30315277, PubMed:30705154). Component of the U5 small nuclear ribonucleoprotein (snRNP) complex and the U4/U6-U5 tri-snRNP complex, building blocks of the spliceosome (PubMed:16723661, PubMed:26912367, PubMed:9774689). As a component of the minor spliceosome, involved in the splicing of U12- type introns in pre-mRNAs (Probable).
subunit: Component of the pre-catalytic and catalytic spliceosome complexes (PubMed:11991638, PubMed:28076346, PubMed:28502770, PubMed:28781166, PubMed:29301961, PubMed:29360106, PubMed:30315277, PubMed:9731529). Component of the postcatalytic spliceosome P complex (PubMed:30705154). Part of the U5 snRNP complex. Interacts with PRPF8. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39 (PubMed:16723661). Component of the minor spliceosome, which splices U12-type introns (PubMed:33509932). - The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Reduced symmetric dimethylation stabilizes vimentin and promotes metastasis in MTAP-deficient lung cancer.
Chang, EMBO reports 2022 - “...repair crosscomplementing protein 6 69.8 1.2E+07 2.5E+00 4.7E+06 P25311 AZGP1 Zincalpha2glycoprotein 34.2 1.6E+06 3.1E+00 3.2E+06 Q96DI7 SNRNP40 U5 small nuclear ribonucleoprotein 40kDa protein 39.3 5.3E+00 1.4E+06 7.0E+07 P81605 DCD Dermcidin 11.3 2.8E+07 3.4E+00 2.3E+00 P04406 GAPDH Glyceraldehyde3phosphate dehydrogenase 36.0 6.0E+06 5.5E+00 2.4E+00 P19338 NCL Nucleolin 76.6...”
- The use of proteomics for blood biomarker research in premature infants: a scoping review.
Letunica, Clinical proteomics 2021 - “...Antioxidant activity/ haemoglobin binding Acute inflammatory response [ 12 ] U5 small nuclear ribonucleoprotein SNRNP40 Q96DI7 RNA binding RNA splicing and processing [ 12 ] Lysophospholipid acyltransferase 7 MBOAT7 Q96N66 Lysophospholipid acyltransferase activity Lipid modification/regulation of triglyceride metabolic process [ 17 ] Apolipoprotein L1 APOL1 O14791...”
- Redox modifications of cysteine-containing proteins, cell cycle arrest and translation inhibition: Involvement in vitamin C-induced breast cancer cell death.
El, Redox biology 2019 - “...histone-binding protein RBBP4 (Q09028), ATP-dependent RNA helicase DHX8 (Q14562), U5 small nuclear ribonucleoprotein 40-kDa protein (Q96DI7), tRNA-splicing ligase RtcB homolog (Q9Y3I0), 26S proteasome non-ATPase regulatory subunit 3 (O43242), Cullin-4A (Q13619), E3 ubiquitin-protein ligase RING2 (Q99496), E3 ubiquitin-protein ligase UBR4 (Q5T4S7), E3 ubiquitin-protein ligase XIAP (P98170), and...”
- Breaking up the C complex spliceosome shows stable association of proteins with the lariat intron intermediate.
Coltri, PloS one 2011 - “...25 O75643 U5200 kD Brr2p 244 56 18 Q15029 U5116 kD Snu114p 109 13 10 Q96DI7 U540 kD 39 2 3 Recruited to B complex: Q9HCG8 CWC22 Cwc22p 105 3 3 P23246 PSF 76 13 1 NTC: Q9UMS4 PRP19 Prp19p 55 26 7 Q99459 CDC5L Cef1p...”
- Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
Kan, Placenta 2023 (PubMed)- GeneRIF: Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
- Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness.
Nguyen, Nature communications 2016 - GeneRIF: Clinically, low SNRNP40 expression is associated with metastatic relapse.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_009611 DDB0219950 U5-100 kDa (Prp28p) DDX23 NP_004809 NP_609888 NP_180929 NP_010529 DDB0233518 U5-40 kDa (na) SNRNP40 NP_004805 NP_608501 NP_181905 No hit DDB0233510 U5-15 kDa (Dib1p) TXNL4A NP_006692 NP_608830 NP_196446 NP_015407 DDB0233538 d U5-52 kDa (na) CD2BP2 NP_006101 NP_609404 NP_568211 No hit d 2E. U4/U6 snRNP-specific proteins DDB0233224...”
AT1G11160 nucleotide binding from Arabidopsis thaliana
27% identity, 20% coverage
- KTN80 confers precision to microtubule severing by specific targeting of katanin complexes in plant cells
Wang, The EMBO journal 2017 - “...genome has four loci encoding katanin p80 subunits, At1G11160, At1G61210, At5G08390, and At5G23430, which we designated the encoded katanin subunits KTN80.1, 2,...”
- “...knock out the four KTN80-encoding genes KTN80.1 (At1g11160), KTN80.2 (At1g61210), KTN80.3 (At5g08390), and KTN80.4 (At5g23430), we first generated the ktn80.12...”
POP2_SCHPO / O14170 WD repeat-containing protein pop2; Proteolysis factor sud1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 4 papers)
pop2 / RF|NP_594956.1 F-box/WD repeat protein Pop2 from Schizosaccharomyces pombe (see 3 papers)
NP_594956 F-box/WD repeat protein Pop2 from Schizosaccharomyces pombe
SPAC4D7.03 F-box/WD repeat protein Pop2 from Schizosaccharomyces pombe
23% identity, 36% coverage
KTN81_ARATH / A0A1P8AW69 Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.1 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
27% identity, 20% coverage
- function: May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity). Microtubule severing may promote rapid reorganization of cellular microtubule arrays (By similarity). Confers precision to microtubule (MT) severing by specific targeting of KTN1 to MT cleavage sites such as crossover or branching nucleation sites (PubMed:28978669). Together with other KTN80s, regulates cell elongation by modulating MT organization (PubMed:28978669).
subunit: Component of KTN80-KTN1 complexes composed of a hexamer of KTN1-KTN80 heterodimers that sense microtubule (MT) geometry to confer precise MT severing (PubMed:28978669). Interacts directly with AAA1/KTN1 and KTN80.3, and weakly with KTN80.4 (PubMed:28978669).
disruption phenotype: The double mutant ktn80.1 ktn80.2 exhibits normal growth, but the quadruple mutant ktn80.1 ktn80.2 ktn80.3 ktn80.4 has a severe dwarf phenotype, with small and round dark-green rosette leaves as well as wide and short petioles, probably due to cell elongation defects, and associated with a complex cortical microtubule (MT) network with stable entanglements (PubMed:28978669). Plants missing KTN80s have a disruption of KTN1 recruitment at MT crossover or branching nucleation sites, leading to an abolishment of MT severing (PubMed:28978669).
SPCC16A11.02 U3 snoRNP-associated protein Utp13 (predicted) from Schizosaccharomyces pombe
25% identity, 37% coverage
- The cell cycle-regulated genes of Schizosaccharomyces pombe
Oliva, PLoS biology 2005 - “...processing), SPBC13G1.09 (bystin family protein, associated with U3 and U14 snoRNAs, involved in rRNA processing); SPCC16A11.02 (WD-repeat protein, processome component, involved in rRNA processing); SPAC23C4.17 (tRNA methyltransferase of the NOL1/NOP2/sun family involved in methylation of cytidine to 5-methyl-cytidine [m5C] at several positions in different tRNAs); SPBC11G11.03...”
NCU03244 WD repeat protein from Neurospora crassa OR74A
32% identity, 29% coverage
- Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability
Kelliher, PLoS biology 2023 - “...Fig ) despite its arrhythmic phenotype by race tube [ 70 ]. set-1 and swd3 (NCU03244) mutants each had approximately 24-hour long period phenotypes by luciferase assay ( S7 Fig ). To investigate whether the long period phenotype of set-1 was exclusively due to loss of...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...11225 two-component system response regulator Morph/Hyph NCU03206 11486 zinc finger transcription factor-22 znf-22 Transc Factors NCU03244 11360 WD repeat protein Transc Factors NCU03281 11276 transport of copper-2 tcu-2 Morph/Hyph NCU03320 11058 all development altered-4 ada-4 Transc Factors NCU03479 12931 endoribonuclease ysh-1 paa-5 Morph/Hyph Binding/Catalytic Activity Metabolic...”
- Involvement of the adaptor protein 3 complex in lignocellulase secretion in Neurospora crassa revealed by comparative genomic screening
Pei, Biotechnology for biofuels 2015 - “...factor FlbC 419.0852.77 27.31 86 20306 NCU08380 jgi|Trire2|122050| Plasma membrane phosphatase 416.518.07 27.57 87 11360 NCU03244 jgi|Trire2|62053| WD repeat protein 346.4727.22 39.81 a N. crassa orthologs: locus selected according to the N. crassa database (v7) ( https://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html ). b RUTC30 targets: locus selected according to the...”
- “...such pathways. In addition, our screening identified several deletion strains, namely, NCU02152, NCU03184, NCU08380, and NCU03244, with decreased secretion capacities, which suggests that they play positive roles in regulating lignocellulase secretion. All four strains were found to have secretion that was decreased by more than 25%...”
- Methylation of histone H3 on lysine 4 by the lysine methyltransferase SET1 protein is needed for normal clock gene expression
Raduwan, The Journal of biological chemistry 2013 - “...( swd1 ):: hph, A FGSC FGSC13701 ncu07885 ( swd2 ):: hph, a FGSC FGSC11360 ncu03244 ( swd3 ):: hph, a FGSC FGSC14862 ncu03037 ( sdc1 ):: hph, a FGSC FGSC11914 ncu06266 ( dot1 ):: hph, a FGSC XB140-10 set1 :: hph, A This study 9440...”
HPODL_01497 Guanine nucleotide-binding protein subunit beta-like protein from Ogataea parapolymorpha DL-1
28% identity, 27% coverage
Tery_4060 serine/threonine protein kinase with WD40 repeats from Trichodesmium erythraeum IMS101
26% identity, 24% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...cbSTKII WD40 (7) Tery_3681 cbSTKII TPR (7) Tery_1668 cbSTKI-other Tery_3863 cbSTKII GAF Tery_1722 cbSTKII GUN4 Tery_4060 cbSTKII WD40 (7) Tery_1723 cbSTKII GUN4 Tery_4351 cbSTKII DUF323 (2) Tery_2033 cbSTKII WD40 (7) Tery_4411 cbSTKI-TM Tery_2051 cbSTKI-other Tery_4467 cbSTKII WD40 (7) Tery_2064 cbSTKII Pentapeptide (3) Tery_4781 cbSTKII TPR (11)...”
CND05450 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
26% identity, 36% coverage
K7EN33 Notchless homolog 1 (Fragment) from Homo sapiens
25% identity, 35% coverage
Cri9333_3253 caspase family protein from Crinalium epipsammum PCC 9333
25% identity, 21% coverage
- The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria
Bhattacharjee, Journal of experimental botany 2020 - “...in the predicted cytoplasmic portion. This presumed topology prevailed in six true OCAs: Ava_0039, Ava_3079, Cri9333_3253, GEI7407_1667, GEI7407_1667, and Glo7428_1095. Among these, the presence of NACHT in the predicted cytoplasmic portion of GEI7407_1667 implies its activity during PCD. Moreover, Ava_0039, Ava_3079, and GEI7407_1667 have an AAA_16...”
C1GAF5 Coatomer subunit alpha from Paracoccidioides brasiliensis (strain Pb18)
PADG_04241 coatomer subunit alpha from Paracoccidioides brasiliensis Pb18
24% identity, 23% coverage
- Transcriptional profiling of a fungal granuloma reveals a low metabolic activity of Paracoccidioides brasiliensis yeasts and an actively regulated host immune response
Borges, Frontiers in cellular and infection microbiology 2023 - “...b-c1 complex subunit 2 DOWN(D) -4,10832 0,000135 Transport C1FZ88 importin subunit alpha-6/7 DOWN(8) -4,36192 0,003272 C1GAF5 Coatomer subunit alpha DOWN(8) -2,60008 0,001756 C1GJS2 Phosphatidylinositol transfer protein SFH5 (PITP SFH5) DOWN(D) -7,21769 1,52E-05 Amino acid metabolism C1G3V5 Aspartate aminotransferase (EC 2.6.1.1) DOWN(12) -5,05193 7,6E-05 C1GBD8 3-oxoacid CoA-transferase...”
- “...pre-mRNA-splicing helicase BRR2 (C1G5P0). Finally, proteins involved in vesicle transport, such as coatomer subunit alpha (C1GAF5), importin subunit alpha-6/7 (C1FZ88) and phosphatidylinositol transfer protein SFH5 (C1GJS2) have also been decrease in abundance. We hypothesize that the fungi inside the granulomas avoid energy loss by lowering protein...”
- Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis
Navarro, Frontiers in microbiology 2020 - “...C1GB16 Uncharacterized protein 89.27 PADG_03203 C1G7P8 Uncharacterized protein 87.67 PADG_01328 C1G312 Ornithine aminotransferase 75.75 PADG_04241 C1GAF5 Coatomer subunit alpha 71.14 PADG_04250 C1GAG4 Uncharacterized protein 65.74 PADG_00608 C1G168 Uncharacterized protein 57.93 PADG_00379 C1G0I9 Uncharacterized protein 53.39 PADG_01745 C1G479 Mannose-1-phosphate guanyltransferase 36.45 PADG_01083 C1FZ57 60S ribosomal protein L32...”
- Effect of Nitrosative Stress on the S-Nitroso-Proteome of Paracoccidioides brasiliensis
Navarro, Frontiers in microbiology 2020 - “...PADG_04452 C1GB16 Uncharacterized protein 89.27 PADG_03203 C1G7P8 Uncharacterized protein 87.67 PADG_01328 C1G312 Ornithine aminotransferase 75.75 PADG_04241 C1GAF5 Coatomer subunit alpha 71.14 PADG_04250 C1GAG4 Uncharacterized protein 65.74 PADG_00608 C1G168 Uncharacterized protein 57.93 PADG_00379 C1G0I9 Uncharacterized protein 53.39 PADG_01745 C1G479 Mannose-1-phosphate guanyltransferase 36.45 PADG_01083 C1FZ57 60S ribosomal protein...”
B7Z2C8 cDNA FLJ55681, highly similar to F-box/WD repeat protein 7 from Homo sapiens
24% identity, 47% coverage
K1PPW8 Coatomer subunit beta from Magallana gigas
22% identity, 37% coverage
KTNB1_STRPU / O61585 Katanin p80 WD40 repeat-containing subunit B1; Katanin p80 subunit B1; p80 katanin from Strongylocentrotus purpuratus (Purple sea urchin) (see 3 papers)
27% identity, 28% coverage
- function: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation.
subunit: Interacts with KATNA1. This interaction enhances the microtubule binding and severing activity of KATNA1 and also targets this activity to the centrosome.
MHCK A / AAA66070.1 myosin heavy chain kinase A from Dictyostelium discoideum (see paper)
25% identity, 27% coverage
MHCKA_DICDI / P42527 Myosin heavy chain kinase A; MHCK-A; EC 2.7.11.7 from Dictyostelium discoideum (Social amoeba) (see paper)
P42527 myosin-heavy-chain kinase (EC 2.7.11.7) from Dictyostelium discoideum (see 11 papers)
XP_635119 Alpha kinase family protein from Dictyostelium discoideum AX4
25% identity, 27% coverage
- function: Catalyzes its autophosphorylation, which is needed for enzymatic activity and phosphorylates myosin II heavy chain at a threonine in the C-terminal tail region (PubMed:7822274). This phosphorylation is critical for regulating the assembly and disassembly of myosin II filament, affecting myosin localization during an array of cellular contractile events, including cytokinesis and capping of cell surface receptors as well as chemotactic cell locomotion (PubMed:7822274).
catalytic activity: L-threonyl-[myosin heavy-chain] + ATP = O-phospho-L-threonyl- [myosin heavy-chain] + ADP + H(+) (RHEA:11424)
cofactor: Mg(2+) Mn(2+)
subunit: Oligomer - Combined treatment of mitoxantrone sensitizes breast cancer cells to rapalogs through blocking eEF-2K-mediated activation of Akt and autophagy.
Guan, Cell death & disease 2020 - “...107326) was retrieved from the National Center for Biotechnology Institute (NCBI) with UniProtKB accession number (P42527). The protein modeling online server SWISS-MODEL ( https://swissmodel.expasy.org/ ) was employed for the template searching, then the eEF-2K model construction was performed in Molecular Operating Environment (MOE, version 2018). As...”
- Autophosphorylation at Thr279 of Entamoeba histolytica atypical kinase EhAK1 is required for activity and regulation of erythrophagocytosis
Mansuri, Scientific reports 2016 - “...TRPM7. The kinase domains of EhAK1, MHCK-A, MHCK-B, EF2K, and TRPM7 (UniprotKB accession codes C4M9G9, P42527, P90648, 000918 and Q923J1, respectively) were aligned on the basis of similarities in their sequence. Sequences representing P-loop, N/D loop, G-rich region and Zinc finger motif are indicated. Invariant K85...”
- Myosin heavy-chain kinase A from Dictyostelium possesses a novel actin-binding domain that cross-links actin filaments
Russ, The Biochemical journal 2006 - “...in this text refers to the GenBankTM accession number P42527 for MHCK A [13]. The recombinant plasmid for bacterial expression of the entire coiled-coil domain...”
- “...acid numbering indicated corresponds to GenBankTM accession number P42527 for MHCK A. (B) The graph shows the probability (y -axis) of each residue contributing...”
- Autophosphorylation activates Dictyostelium myosin II heavy chain kinase A by providing a ligand for an allosteric binding site in the alpha-kinase domain
Crawley, The Journal of biological chemistry 2011 - “...C-tail sequences. The NCBI accession numbers are: MHCK A, XP_635119; MHCK B, XP_636368; MHCK C, XP_635600; MHCK D, XP_640080; and AK1, XP_629868. B, the kinase...”
- Crystal structure of the alpha-kinase domain of Dictyostelium myosin heavy chain kinase A.
Ye, Science signaling 2010 - GeneRIF: when crystallized in the presence of ATP and a peptide substrate, which does not appear in the structure, adenosine diphosphate (ADP) was found at the active site and an invariant aspartic acid residue (Asp(766)) at the active site was phosphorylated
8r09E / Q96DI7 8r09E (see paper)
25% identity, 36% coverage
NCU02966 pre-mRNA splicing factor prp46 from Neurospora crassa OR74A
26% identity, 27% coverage
LIS1_CHICK / Q9PTR5 Lissencephaly-1 homolog from Gallus gallus (Chicken) (see paper)
XP_015151147 lissencephaly-1 homolog isoform X1 from Gallus gallus
23% identity, 41% coverage
- function: Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in PAF inactivation. Regulates the PAF-AH (I) activity in a catalytic dimer composition- dependent manner (By similarity). Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule- dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. May be required for proliferation of neuronal precursors and neuronal migration.
subunit: Can self-associate. Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity (By similarity). Interacts with dynein, dynactin, NDE1 and NDEL1. - Cytoplasmic dynein and LIS1 are required for microtubule advance during growth cone remodeling and fast axonal outgrowth.
Grabham, The Journal of neuroscience : the official journal of the Society for Neuroscience 2007 - GeneRIF: LIS1/PAFAH1B1 plays a prominent role in microtubule advance during growth cone remodeling associated with axonogenesis.
NP_001300561 F-box domain-containing protein from Caenorhabditis elegans
25% identity, 41% coverage
LIN23_CAEEL / Q09990 F-box/WD repeat-containing protein lin-23; Abnormal cell lineage protein 23 from Caenorhabditis elegans (see paper)
25% identity, 41% coverage
- function: Functions cell autonomously to negatively regulate cell cycle progression. Required to restrain cell proliferation in response to developmental cues. Probably recognizes and binds to some proteins and promotes their ubiquitination and degradation (By similarity).
subunit: Part of a SCF (SKP1-cullin-F-box) protein ligase complex.
alr0671 WD-repeat protein from Nostoc sp. PCC 7120
27% identity, 33% coverage
NP_001278731 uncharacterized protein LOC100282591 from Zea mays
25% identity, 36% coverage
- Rapid Birth or Death of Centromeres on Fragmented Chromosomes in Maize
Liu, The Plant cell 2020 - “...under number GSE124242. The sequences used for FISH can be found under accession numbers Zm00001d039211 (NP_001278731), Zm00001d018596 (XP_008651903) and Zm00001d008176 (XP_008655451). Supplemental Data Supplemental Figure 1. Examples of other types of translocations. Supplemental Figure 2. Analysis of a terminal translocation. Supplemental Figure 3. Examples of altered...”
2ovqB / Q969H0 Structure of the skp1-fbw7-cyclinedegc complex (see paper)
24% identity, 47% coverage
NP_566557 Transducin/WD40 repeat-like superfamily protein from Arabidopsis thaliana
AT3G16650 PP1/PP2A phosphatases pleiotropic regulator 2 (PRL2) from Arabidopsis thaliana
24% identity, 21% coverage
- Pleiotropic regulatory locus 2 exhibits unequal genetic redundancy with its homolog PRL1.
Weihmann, Plant & cell physiology 2012 (PubMed)- GeneRIF: Identification and characterization of a dominant suppressor of prl1 revealed a regulatory, gain-of-function mutation in PLEIOTROPIC REGULATORY LOCUS 2 (PRL2), a close homolog of PRL1.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_612033 NP_172448 NP_013940 DDB0233387-f Prp5 DDX46 NP_055644 NP_573020 NP_187573 NP_009796 DDB0233530 Prp46 PLRG1 NP_002660 NP_572778 NP_566557 NP_015174 DDB0233583 fSap33 ISY1 NP_065752 NP_649768 NP_188509 NP_012584 DDB0233121 Prp19 PRPF19 NP_055317 NP_523783 NP_850206 NP_013064 DDB0233480 Crn CRNKL1 NP_057736 NP_477118 NP_198992 NP_013218 DDB0233461 SYF1 XAB2 NP_064581 NP_610891 NP_198226 NP_010704 3C....”
- Transcript Profiling Analysis and ncRNAs' Identification of Male-Sterile Systems of Brassica campestris Reveal New Insights Into the Mechanism Underlying Anther and Pollen Development
Zhou, Frontiers in plant science 2022 - “...Homologous genes in Arabidopsis Gene annotation ID in TAIR Gene name Bra021188 2.043 0.345 Down AT3G16650 Pleiotropic regulatory locus 2 ( PRL2 ) RNA processing and modification Bra029913 56.944 6.537 Down AT3G48690 Carboxylesterase 12 ( CXE12 ) Serine hydrolases hydrolyzing 2,4-D-methyl Bra002042 8.613 3.164 Down AT2G16720...”
- The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host
Diaz-Granados, Molecular plant pathology 2020 - “...AT4G39740 0.47864 1.61E04 Thioredoxin superfamily protein HCC2 AT3G27070 0.41832 5.61E05 Translocase outer membrane 201 TOM201 AT3G16650 0.34724 9.37E05 Transducin/WD40 repeatlike superfamily protein AT3G09940 0.34616 9.86E05 Monodehydroascorbate reductase MDHAR Upregulated in upl35 AT4G07820 1.63498 1.25E04 CAP (cysteinerich secretory proteins, antigen 5 and pathogenesisrelated 1 protein) superfamily protein...”
- Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression
Fonseca, Frontiers in plant science 2019 - “...; Jia et al., 2017 ; Li et al., 2018 ; Wiborg et al., 2008 AT3G16650 PRL2 yes nd miRNA biogenesis MAC complex Jia et al., 2017 ; Li et al., 2018 AT2G33340 MAC3B yes nd miRNA biogenesis; CRL4 E3 ubiquitin ligase activity; plant innate immunity...”
- Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana
Chang, Proteomics 2009 - “...Cell cycle protein FtsH homolog 1 (1) At1g50250 100 37 PP1/PP2A phosphatase pleiotropic regulator (1) At3g16650 100 35 Ubiquitin ligase SINAT2 (1) At3g58040 99.9 32 FRIGIDA (1) At4g00650 99.8 30 Cysteine synthase (1) At4g14880 99.9 30 Cysteine synthase (1) At3g59760 100 49 Katanin like protein (1)...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...1 12 SANT, 2; [104] PRL1* Prp46p atPRL1 At4g15900 4 14 WD-40, 2;WD40like, 1; atPRL2 At3g16650 3 6 WD-40, 2;WD40like, 1; AD-002* Cwc15p atAD-002 At3g13200 3 22 Cwf_Cwc_15, 1; HSP73/HSPA8* HSP73-1 At3g12580 3 35 Hsp70, 1; HSP73-2 At5g42020 5 51 IntronR (1); Hsp70, 1; HSP73-3 At5g02500...”
AT3G21540 transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
36% identity, 12% coverage
- Pospiviroid Infection of Tomato Regulates the Expression of Genes Involved in Flower and Fruit Development
Aviña-Padilla, Viruses 2018 - “...in the pathogenicity (P) domain of the pospiviroid genome targeted a WD40 repeat family gene (At3g21540) conserved in tomato ( SlWD40-repeat ; SGN_U563134) and that is proposed to play a role in signal transduction, plant growth, and pollen viability. Expression of this gene was down-regulated in...”
- The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana
Lange, PLoS genetics 2014 - “...Mascot score #Spectra Mascot score #Spectra AT1G59760 MTR4 (bait) 7666.5 1332 7928.1 1352 8755.6 1999 AT3G21540 Transducin family/WD-40 repeat protein Ribo. bio. 537.8 26 606.2 29 720.0 28 AT1G15440 Periodic tryptophan protein 2 Ribo. bio. 718.5 27 863.7 27 857.8 26 AT3G61620 RRP41 EXO9 548.2 21...”
- Transcriptome-mining for single-copy nuclear markers in ferns
Rothfels, PloS one 2013 - “...6 3 10 transducin transducin family protein / WD-40 repeat family protein 2868 -- a AT3G21540 11 3 For each gene, we list its length in ferns and in Arabidopsis , provide the TAIR accession number for the Arabidopsis sequence (as well as its number of...”
- Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions
Pendle, Molecular biology of the cell 2005 - “...WDrepeat- containing protein of unknown function encoded by At3g21540 is a homologue of Utp12p found in the yeast SSU processome, along with U3snoRNP proteins,...”
EX895_005820 hypothetical protein from Sporisorium graminicola
27% identity, 31% coverage
- Molecular Mechanisms Involved in the Multicellular Growth of Ustilaginomycetes
Martínez-Soto, Microorganisms 2020 - “...filament organization UMAG_04613 UHOR_06638 UBRO_06638 sr15500 EX895_002183 BCV70DRAFT_202237 LIS1 Nuclear migration UMAG_03164 UHOR_04938 UBRO_04938 sr14206 EX895_005820 BCV70DRAFT_200264 Actin regulating Ser/Thr kinase UMAG_03081 UHOR_04824 UBRO_04824 sr14140 EX895_002483 - Formin; actin nucleation UMAG_12254 UHOR_06202 UBRO_06202 sr15020 EX895_001591 BCV70DRAFT_205747 Formin; actin nucleation. Functionally redundant with Bni1 UMAG_01141 UHOR_01723 UBRO_01723...”
LIS1_RAT / P63004 Platelet-activating factor acetylhydrolase IB subunit alpha; Lissencephaly-1 protein; LIS-1; PAF acetylhydrolase 45 kDa subunit; PAF-AH 45 kDa subunit; PAF-AH alpha; PAFAH alpha from Rattus norvegicus (Rat) (see 8 papers)
LIS1_MOUSE / P63005 Platelet-activating factor acetylhydrolase IB subunit beta; Lissencephaly-1 protein; LIS-1; PAF acetylhydrolase 45 kDa subunit; PAF-AH 45 kDa subunit; PAF-AH alpha; PAFAH alpha from Mus musculus (Mouse) (see 30 papers)
NP_038653 platelet-activating factor acetylhydrolase IB subunit beta from Mus musculus
23% identity, 41% coverage
- function: Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in PAF inactivation. Regulates the PAF-AH (I) activity in a catalytic dimer composition- dependent manner (By similarity). Required for proper activation of Rho GTPases and actin polymerization at the leading edge of locomoting cerebellar neurons and postmigratory hippocampal neurons in response to calcium influx triggered via NMDA receptors. Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule- dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. Required during brain development for the proliferation of neuronal precursors and the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Neuronal migration involves a process called nucleokinesis, whereby migrating cells extend an anterior process into which the nucleus subsequently translocates. During nucleokinesis dynein at the nuclear surface may translocate the nucleus towards the centrosome by exerting force on centrosomal microtubules. May also play a role in other forms of cell locomotion including the migration of fibroblasts during wound healing. Required for dynein recruitment to microtubule plus ends and BICD2-bound cargos (By similarity). May modulate the Reelin pathway through interaction of the PAF-AH (I) catalytic dimer with VLDLR (By similarity).
subunit: Can self-associate. Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity. Interacts with the catalytic dimer of PAF-AH (I) heterotetrameric enzyme: interacts with PAFAH1B2 homodimer (alpha2/alpha2 homodimer), PAFAH1B3 homodimer (alpha1/alpha1 homodimer) and PAFAH1B2-PAFAH1B3 heterodimer (alpha2/alpha1 heterodimer) (By similarity). Interacts with DCX, dynactin, IQGAP1, KATNB1, NDE1, NUDC and RSN. Interacts with DISC1, and this interaction is enhanced by NDEL1. Interacts with DAB1 when DAB1 is phosphorylated in response to RELN/reelin signaling. Interacts with dynein and NDEL1 (PubMed:11163260, PubMed:16481446). Interacts with INTS13. Interacts with DCDC1 (By similarity). - function: Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in PAF inactivation. Regulates the PAF-AH (I) activity in a catalytic dimer composition- dependent manner (By similarity). Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule- dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. Required during brain development for the proliferation of neuronal precursors and the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Neuronal migration involves a process called nucleokinesis, whereby migrating cells extend an anterior process into which the nucleus subsequently translocates. During nucleokinesis dynein at the nuclear surface may translocate the nucleus towards the centrosome by exerting force on centrosomal microtubules. Also required for proper activation of Rho GTPases and actin polymerization at the leading edge of locomoting cerebellar neurons and postmigratory hippocampal neurons in response to calcium influx triggered via NMDA receptors. May also play a role in other forms of cell locomotion including the migration of fibroblasts during wound healing. Non-catalytic subunit of an acetylhydrolase complex which inactivates platelet-activating factor (PAF) by removing the acetyl group at the SN-2 position. Required for dynein recruitment to microtubule plus ends and BICD2-bound cargos (By similarity). May modulate the Reelin pathway through interaction of the PAF-AH (I) catalytic dimer with VLDLR (PubMed:17330141).
subunit: Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity. Interacts with the catalytic dimer of PAF-AH (I) heterotetrameric enzyme: interacts with PAFAH1B2 homodimer (alpha2/alpha2 homodimer), PAFAH1B3 homodimer (alpha1/alpha1 homodimer) and PAFAH1B2-PAFAH1B3 heterodimer (alpha2/alpha1 heterodimer) (PubMed:11344260, PubMed:12885786, PubMed:16481446). Can self-associate (PubMed:11163259, PubMed:11344260, PubMed:12885786, PubMed:15572112). Interacts with DCX, dynein, dynactin, IQGAP1, KATNB1, NDE1, NDEL1, NUDC, and RSN (PubMed:11001923, PubMed:11056530, PubMed:11163258, PubMed:11163259, PubMed:11163260, PubMed:11231056, PubMed:11940666, PubMed:12885786, PubMed:15173193, PubMed:15473966, PubMed:15473967, PubMed:15572112, PubMed:16203747, PubMed:16291865, PubMed:16369480, PubMed:16481446). Interacts with DAB1 when DAB1 is phosphorylated in response to RELN/reelin signaling (PubMed:14578885). Interacts with INTS13 (PubMed:23097494). Interacts with DCDC1 (By similarity). Interacts with DISC1, and this interaction is enhanced by NDEL1 (By similarity).
disruption phenotype: Double heterozygous PAFAH1B1 and homozygous VLDLR knockout mice present no obvious cortical layering defects (PubMed:17330141). Double heterozygous PAFAH1B1 and homozygous LRP8 knockout mice display a reeler-like phenotype in the forebrain consisting of the inversion of cortical layers and hippocampal disorganization (PubMed:17330141). - LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways.
Kshirsagar, Nature communications 2023 - GeneRIF: LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways.
- Lis1 mutation prevents basal radial glia-like cell production in the mouse.
Penisson, Human molecular genetics 2022 (PubMed)- GeneRIF: Lis1 mutation prevents basal radial glia-like cell production in the mouse.
- Properties of the epileptiform activity in the cingulate cortex of a mouse model of LIS1 dysfunction.
Domínguez-Sala, Brain structure & function 2022 - GeneRIF: Properties of the epileptiform activity in the cingulate cortex of a mouse model of LIS1 dysfunction.
- A selective LIS1 requirement for mitotic spindle assembly discriminates distinct T-cell division mechanisms within the T-cell lineage.
Argenty, eLife 2022 - GeneRIF: A selective LIS1 requirement for mitotic spindle assembly discriminates distinct T-cell division mechanisms within the T-cell lineage.
- Emergence of non-canonical parvalbumin-containing interneurons in hippocampus of a murine model of type I lissencephaly.
Ekins, eLife 2020 - GeneRIF: Emergence of non-canonical parvalbumin-containing interneurons in hippocampus of a murine model of type I lissencephaly.
- Mature Hippocampal Neurons Require LIS1 for Synaptic Integrity: Implications for Cognition.
Sudarov, Biological psychiatry 2018 - GeneRIF: This study demonstrated that LIS1 supports synaptic function and plasticity of mature CA1 neurons.
- Lis1 dysfunction leads to traction force reduction and cytoskeletal disorganization during cell migration.
Jheng, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: Lis1 dysfunction reduces migration and traction force production in fibroblasts.
- Hepatic loss of Lissencephaly 1 (Lis1) induces fatty liver and accelerates liver tumorigenesis in mice.
Li, The Journal of biological chemistry 2018 - GeneRIF: genetic deletion of Lis1 in the mouse liver increases lipid accumulation and inflammation in this organ. Further analysis revealed that loss of Lis1 triggers endoplasmic reticulum (ER) stress and reduces triglyceride secretion.
- More
- Proteomic Analysis of Retinal Tissue in an S100B Autoimmune Glaucoma Model.
Reinehr, Biology 2021 - “...10 0.005 33% 5 P56574 Isocitrate dehydrogenase [NADP], mitochondrial 7.62 10 4 0.006 53% 6 P63004 Platelet-activating factor acetylhydrolase IB subunit alpha 3.21 10 5 0.007 45% 7 P12785 Fatty acid synthase 2.00 10 6 0.007 57% 8 P49432 Pyruvate dehydrogenase e1 component subunit beta, mitochondrial...”
- Identification of Differential Protein Expression in Hepatocellular Carcinoma Induced Wistar Albino Rats by 2D Electrophoresis and MALDI-TOF-MS Analysis
Vedarethinam, Indian journal of clinical biochemistry : IJCB 2016 - “...19 27 27644.5 5.31 73.49 59.46 -0.642 P63004 Platelet-activating factor acetylhydrolase 31 46670.0 6.97 34.71 70.78 -0.514 Up-regulated proteins of rat...”
- Improved spatial learning and memory by perilla diet is correlated with immunoreactivities to neurofilament and α-synuclein in hilus of dentate gyrus.
Lee, Proteome science 2012 - “...P46462 8.33E+16 40.3 Transitional endoplasmic reticulum ATPase 0 + P70566 3.88E+06 31.9 Tropomodulin-2 - - P63004 8881 21 Platelet-activating factor acetylhydrolase IB subunit beta - 0 O88989 743497 27.2 Malate dehydrogenase, cytoplasmic - 0 P61158 1.10E+07 24.4 Actin-related protein 3 - - P04764 2.91E+09 39.6 Alpha-enolase...”
- High-throughput identification of IMCD proteins using LC-MS/MS.
Pisitkun, Physiological genomics 2006 - Non-targeted proteomic analysis of Asian elephant (Elephas maximus) seminal plasma using an in-solution digestion technique and liquid chromatography tandem-mass spectrometry
Wattananit, Frontiers in veterinary science 2023 - “...(Human) Male gonad development Q8IZA3 Oocyte-specific histone H1 (H1FOO) Homo sapiens (Human) Meiotic cell cycle P63005 Platelet-activating factor acetylhydrolase IB subunit alpha (PAFAH1B1) Mus musculus (Mouse) Acrosome assembly Q9NQI0 Probable ATP-dependent RNA helicase DDX4 (DDX4) Homo sapiens (Human) Spermatogenesis P51531 Probable global transcription activator SNF2L2 (SMARCA2)...”
- Urinary Metabolomic and Proteomic Analyses in a Mouse Model of Prostatic Inflammation.
Wei, Urine (Amsterdam, Netherlands) 2019 - “...3.07 3.3E-03 P12961 Neuroendocrine protein 7B2 7B2 5.14 4.2E-03 Q9ESB3 Histidine-rich glycoprotein HRG 2.62 4.7E-03 P63005 Platelet-activating factor acetylhydrolase IB subunit alpha LIS1 8.02 4.8E-03 O70251 Elongation factor 1-beta EF1B 13.10 4.8E-03 P16675 Lysosomal protective protein PPGB 2.86 4.9E-03 P01132 Pro-epidermal growth factor EGF 2.31 5.1E-03...”
- A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model
Deslyper, PLoS neglected tropical diseases 2016 - “...cell migration; Negative regulation of angiogenesis; Tissue regeneration Pafah1b1 Platelet-activating factor acetylhydrolase IB subunit alpha P63005 C57 0.7 Actin cytoskeleton organization; Negative regulation of JNK cascade; Positive regulation of cytokine-mediated signaling; Regulation of microtubule motor activity Serpinf2 Alpha-2-antiplasmin Q61247 C57 0.6 Acute-phase response; Positive regulation of...”
- Doublecortin (Dcx) family proteins regulate filamentous actin structure in developing neurons.
Fu, The Journal of neuroscience : the official journal of the Society for Neuroscience 2013 - “...Filamin-A 13.7 13.5 (6) 20 (13) 0.7 P13020 Gelsolin 7 1.4 (2.4) 1.3 (2.3) 1.1 P63005 LIS1 15.4 11 (4) 11 (3.4) 1 P62962 Profilin-1 47 24 (7) 16 ( 1.7) 1.5 Q9JJV2 Profilin-2 40 3.9 (2.5) 3.9 (1.8) 1 P60764 Ras-related C3 botulinum toxin substrate...”
LIS1_CAEEL / Q9NDC9 Lissencephaly-1 homolog; Pronuclear migration abnormal protein 1 from Caenorhabditis elegans (see 6 papers)
NP_499755 Lissencephaly-1 homolog from Caenorhabditis elegans
26% identity, 36% coverage
- function: Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as nuclear migration during cell division (PubMed:11685578, PubMed:15331665). Part of a complex with nud-2, which is recruited to the nuclear envelope by unc-83, where, in turn, it recruits dynein to the nuclear surface and regulates nuclear migration in hypodermal precursor cells (PubMed:20005871). Plays a role in GABAergic synaptic vesicle localization in the ventral nerve cord (PubMed:16996038). Required for neuronal cell differentiation (PubMed:15254012).
subunit: Component of a dynein-regulating complex composed of at least lis-1 and nud-2 (PubMed:20005871). Interacts with nud-2; the interaction is direct (PubMed:16996038).
disruption phenotype: Defects lead to convulsions mimicking epilepsy, possibly due to altered neurotransmitter function (PubMed:15254012). RNAi-mediated knockdown results in arrest at the 50-100 cell stage, whereby egg and sperm pronuclei fails to migrate (PubMed:11685578). RNAi-mediated knockdown prevents the sperm-donated centrosome from leaving the posterior cortex in 1-cell embryos (PubMed:20599902). RNAi- mediated knockdown results in an abnormal distribution of GABAergic synaptic vesicles at synaptic termini of the ventral nerve cord (PubMed:16996038). RNAi-mediated knockdown results in nuclear migration defects in hyp7 hypodermal precursor cells, but only in a small number of animals (PubMed:20005871). RNAi-mediated knockdown in a pam-1 mutant background restores anterior-posterior polarity (PubMed:20599902). - NudE regulates dynein at kinetochores but is dispensable for other dynein functions in the C. elegans early embryo.
Simões, Journal of cell science 2018 - GeneRIF: The C. elegans NudE homolog NUD-2 is dispensable for dynein- and LIS-1-dependent mitotic spindle assembly in the zygote. This facilitates functional characterization of kinetochore-localized NUD-2, which is recruited by the CENP-F-like proteins HCP-1 and HCP-2 independently of RZZ-Spindly and dynein-LIS-1.
- Progression from mitotic catastrophe to germ cell death in Caenorhabditis elegans lis-1 mutants requires the spindle checkpoint.
Buttner, Developmental biology 2007 - GeneRIF: lis-1 induces a spindle checkpoint-dependent mitotic arrest in the germline and an increase in germ-cell apoptosis.
- Epileptic-like convulsions associated with LIS-1 in the cytoskeletal control of neurotransmitter signaling in Caenorhabditis elegans.
Williams, Human molecular genetics 2004 (PubMed)- GeneRIF: The convulsions mimicking epilepsy can be induced by a mutation in a C. elegans lis-1 allele (pnm-1), in combination with a chemical antagonist of gamma-aminobutyric acid (GABA) neurotransmitter signaling.
- lis-1 is required for dynein-dependent cell division processes in C. elegans embryos.
Cockell, Journal of cell science 2004 (PubMed)- GeneRIF: Dynein and Lis1, albeit functioning in identical processes, are targeted partially independently of one another.
LIS1_BOVIN / P43033 Platelet-activating factor acetylhydrolase IB subunit beta; Lissencephaly-1 protein; LIS-1; PAF acetylhydrolase 45 kDa subunit; PAF-AH 45 kDa subunit; PAF-AH alpha; PAFAH alpha from Bos taurus (Bovine) (see 4 papers)
NP_777088 platelet-activating factor acetylhydrolase IB subunit beta from Bos taurus
23% identity, 41% coverage
- function: Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in the PAF inactivation (PubMed:10542206). Regulates the PAF-AH (I) activity in a catalytic dimer composition-dependent manner (PubMed:10542206). Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. Required during brain development for the proliferation of neuronal precursors and the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Neuronal migration involves a process called nucleokinesis, whereby migrating cells extend an anterior process into which the nucleus subsequently translocates. During nucleokinesis dynein at the nuclear surface may translocate the nucleus towards the centrosome by exerting force on centrosomal microtubules. Also required for proper activation of Rho GTPases and actin polymerization at the leading edge of locomoting cerebellar neurons and postmigratory hippocampal neurons in response to calcium influx triggered via NMDA receptors. May also play a role in other forms of cell locomotion including the migration of fibroblasts during wound healing (By similarity). Required for pronuclear migration during fertilization. Required for dynein recruitment to microtubule plus ends and BICD2-bound cargos (By similarity). May modulate the Reelin pathway through interaction of the PAF-AH (I) catalytic dimer with VLDLR (By similarity).
subunit: Can self-associate. Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity (PubMed:10542206). Interacts with the catalytic dimer of PAF-AH (I) heterotetrameric enzyme: interacts with PAFAH1B2 homodimer (alpha2/alpha2 homodimer), PAFAH1B3 homodimer (alpha1/alpha1 homodimer) and PAFAH1B2-PAFAH1B3 heterodimer (alpha2/alpha1 heterodimer) (PubMed:10940388). Interacts with DCX, IQGAP1, KATNB1, NDEL1, NUDC and RSN. Interacts with DISC1, and this interaction is enhanced by NDEL1. Interacts with DAB1 when DAB1 is phosphorylated in response to RELN/reelin signaling (By similarity). Interacts with dynein and NDE1 (PubMed:10940388, PubMed:11056532). Interacts with dynactin (PubMed:11056532, PubMed:14584027). - PAFAH Ib phospholipase A2 subunits have distinct roles in maintaining Golgi structure and function.
Bechler, Biochimica et biophysica acta 2013 - GeneRIF: PAFAH Ib phospholipase A2 subunits have distinct roles in maintaining Golgi structure and function.
- LIS1 association with dynactin is required for nuclear motility and genomic union in the fertilized mammalian oocyte.
Payne, Cell motility and the cytoskeleton 2003 (PubMed)- GeneRIF: Results suggest that LIS1 is essential to mediate genomic union in a process that involves the dynein-dynactin complex.
LIS1_HUMAN / P43034 Platelet-activating factor acetylhydrolase IB subunit beta; Lissencephaly-1 protein; LIS-1; PAF acetylhydrolase 45 kDa subunit; PAF-AH 45 kDa subunit; PAF-AH alpha; PAFAH alpha from Homo sapiens (Human) (see 16 papers)
XP_016880190 platelet-activating factor acetylhydrolase IB subunit beta isoform X2 from Homo sapiens
23% identity, 41% coverage
- function: Regulatory subunit (beta subunit) of the cytosolic type I platelet-activating factor (PAF) acetylhydrolase (PAF-AH (I)), an enzyme that catalyzes the hydrolyze of the acetyl group at the sn-2 position of PAF and its analogs and participates in PAF inactivation. Regulates the PAF-AH (I) activity in a catalytic dimer composition- dependent manner (By similarity). Required for proper activation of Rho GTPases and actin polymerization at the leading edge of locomoting cerebellar neurons and postmigratory hippocampal neurons in response to calcium influx triggered via NMDA receptors (By similarity). Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. Required during brain development for the proliferation of neuronal precursors and the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Neuronal migration involves a process called nucleokinesis, whereby migrating cells extend an anterior process into which the nucleus subsequently translocates. During nucleokinesis dynein at the nuclear surface may translocate the nucleus towards the centrosome by exerting force on centrosomal microtubules. May also play a role in other forms of cell locomotion including the migration of fibroblasts during wound healing. Required for dynein recruitment to microtubule plus ends and BICD2-bound cargos (PubMed:22956769). May modulate the Reelin pathway through interaction of the PAF-AH (I) catalytic dimer with VLDLR (By similarity).
subunit: Component of the cytosolic PAF-AH (I) heterotetrameric enzyme, which is composed of PAFAH1B1 (beta), PAFAH1B2 (alpha2) and PAFAH1B3 (alpha1) subunits. The catalytic activity of the enzyme resides in the alpha1 (PAFAH1B3) and alpha2 (PAFAH1B2) subunits, whereas the beta subunit (PAFAH1B1) has regulatory activity. Trimer formation is not essential for the catalytic activity. Interacts with the catalytic dimer of PAF-AH (I) heterotetrameric enzyme: interacts with PAFAH1B2 homodimer (alpha2/alpha2 homodimer), PAFAH1B3 homodimer (alpha1/alpha1 homodimer) and PAFAH1B2-PAFAH1B3 heterodimer (alpha2/alpha1 heterodimer) (By similarity). Interacts with IQGAP1, KATNB1 and NUDC. Interacts with DAB1 when DAB1 is phosphorylated in response to RELN/reelin signaling (By similarity). Can self-associate. Interacts with DCX, dynein, dynactin, NDE1, NDEL1 and RSN. Interacts with DISC1, and this interaction is enhanced by NDEL1. Interacts with INTS13. Interacts with DCDC1 (PubMed:22159412). - Proteomic Analysis Reveals Cadherin, Actin, and Focal Adhesion Molecule-Mediated Formation of Cervical Cancer Spheroids
Molika, Cells 2024 - “...P09382 2.542 0.008 3 BMS1 Q14692 2.490 0.023 4 MYH9 P35579 2.470 0.002 5 LIS1 P43034 2.285 0.049 6 COF1 P23528 2.262 0.028 7 VINC P18206 2.239 0.039 8 TOIP1 Q5JTV8 2.215 0.020 9 GSTP1 P09211 2.200 0.003 10 MBB1A Q9BQG0 2.130 0.038 11 ANXA2 P07355...”
- Transgenic Drosophila melanogaster Carrying a Human Full-Length DISC1 Construct (UAS-hflDISC1) Showing Effects on Social Interaction Networks.
Samardžija, Current issues in molecular biology 2024 - “...A-kinase anchor protein 9 Q99996 Lissencephaly-1 CG8440 2R (16,178,82616,185,103) Platelet-activating factor acetylhydrolase IB subunit alpha P43034 CG30291 CG30291 2R (21,007,75521,009,576) CDK5 regulatory subunit-associated protein 3 Q96JB5 Zipper sti CG15792 2R (24,990,57025,011,965) Centrosomal protein of 63 kDa Q96MT8 Cell division cycle 5 ortholog CG6905 3L (357,851361,383) Cell...”
- Structure and Function of Dynein's Non-Catalytic Subunits.
Rao, Cells 2024 - “...predicated by ColabFold to interact with Nde1 (Uniprot Q9NXR1, amino acids 1189) and Lis1 (Uniprot P43034, full-length). Predictions were performed using ColabFold v1.5.5, employing AlphaFold2 with MMseqs2, and conducted without a template. ( b ) The structure of IC2s SAH and H2 (Uniprot Q13409, amino acids...”
- Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Singh, Science (New York, N.Y.) 2024 - “...domain to the CC1B segment and of DCTN1 (557-987) for the ICD-CC2 segment. LIS1 (UniProt P43034) was predicted by running ColabFold 1.3.0 using two copies of this protein. Interaction between CC1B-DIC-N-LIS1-N was predicted by running ColabFold 1.3.0 on two copies each of DCTN1 (350-547), DIC (1-34)...”
- Fluconazole-Induced Protein Changes in Osteogenic and Immune Metabolic Pathways of Dental Pulp Mesenchymal Stem Cells of Osteopetrosis Patients.
Alkhayal, International journal of molecular sciences 2023 - “...Q96AY3 FKBP10 0.0030 5.92 OP-Rx OP-NoRx Oste Imperfata P38159 RBMX 0.0020 979.35 OP-Rx OP-NoRx Osteoblast P43034 PAFAH1B1 0.0085 39.22 OP-Rx OP-NoRx Osteoclast...”
- Comprehensive proteomic profiling of plasma and serum phosphatidylserine-positive extracellular vesicles reveals tissue-specific proteins
Muraoka, iScience 2022 - “...ADH5 5.64 30.80 Q70IA8 MOB3C 5.66 9.97 P23526 AHCY 5.66 21.91 P10075 GLI4 5.76 34.21 P43034 PAFAH1B1 5.88 32.33 P35579 MYH9 5.92 35.31 P60660 MYL6 5.95 34.30 Table 3 Top 10 stably identified proteins in six serum-derived EV samples UniProt ID Genes CV (%) in plasma...”
- Proteomic analysis and miRNA profiling of human testicular endothelial cell-derived exosomes: the potential effects on spermatogenesis.
Song, Asian journal of andrology 2022 - “...Spermatogenesis Spermatid nucleus differentiation Ronfani et al . 65 Platelet-activating factor acetylhydrolase IB subunit alpha P43034 PAFAH1B1 Acrosome assembly Yao et al . 66 Phosphoglycerate mutase 2 P15259 PGAM2 Spermatogenesis Fundele et al . 67 Peroxiredoxin-4 Q13162 PRDX4 Spermatogenesis Shi et al . 68 60S ribosomal...”
- Identification of COPA as a potential prognostic biomarker and pharmacological intervention target of cervical cancer by quantitative proteomics and experimental verification.
Bao, Journal of translational medicine 2022 - “...AK1 0.90 5.27E01 1.23 3.65E01 1.37 5.33E02 Q9UIJ7 AK3 0.96 7.95E01 0.95 8.07E01 0.99 9.55E01 P43034 PAFAH1B1 1.31 1.26E01 1.27 1.12E01 0.97 7.92E01 Q14624 ITIH4 0.48 7.14E05 0.56 1.23E03 1.16 2.92E01 P01860 IGHG3 0.46 2.71E05 0.44 1.32E04 0.95 7.86E01 Q9H223 EHD4 1.22 2.67E01 1.33 1.35E01 1.09...”
- More
- Clinical analysis of PAFAH1B1 gene variants in pediatric patients with epilepsy.
Feng, Seizure 2024 (PubMed)- GeneRIF: Clinical analysis of PAFAH1B1 gene variants in pediatric patients with epilepsy.
- Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Singh, Science (New York, N.Y.) 2024 - GeneRIF: Molecular mechanism of dynein-dynactin complex assembly by LIS1.
- Lis1-dynein drives corona compaction and limits erroneous microtubule attachment at kinetochores.
Mitevska, Journal of cell science 2023 (PubMed)- GeneRIF: Lis1-dynein drives corona compaction and limits erroneous microtubule attachment at kinetochores.
- Prenatal diagnosis of Miller-Dieker syndrome/PAFAH1B1-related lissencephaly: Ultrasonography and genetically investigative results.
Zhang, European journal of obstetrics, gynecology, and reproductive biology 2022 (PubMed)- GeneRIF: Prenatal diagnosis of Miller-Dieker syndrome/PAFAH1B1-related lissencephaly: Ultrasonography and genetically investigative results.
- NudCD1 as a prognostic marker in colorectal cancer and its role in the upregulation of cellular spindle assembly checkpoint genes and LIS1 pathways.
Feng, BMC cancer 2022 - GeneRIF: NudCD1 as a prognostic marker in colorectal cancer and its role in the upregulation of cellular spindle assembly checkpoint genes and LIS1 pathways.
- Prenatal diagnosis of Miller-Dieker syndrome by chromosomal microarray.
Shi, Annals of human genetics 2021 (PubMed)- GeneRIF: Prenatal diagnosis of Miller-Dieker syndrome by chromosomal microarray.
- Human cytomegalovirus infection is associated with increased expression of the lissencephaly gene PAFAH1B1 encoding LIS1 in neural stem cells and congenitally infected brains.
Rolland, The Journal of pathology 2021 (PubMed)- GeneRIF: Human cytomegalovirus infection is associated with increased expression of the lissencephaly gene PAFAH1B1 encoding LIS1 in neural stem cells and congenitally infected brains.
- LIS1 promotes the formation of activated cytoplasmic dynein-1 complexes.
Htet, Nature cell biology 2020 - GeneRIF: LIS1 binding at these sites functions in multiple stages of assembling the motile dynein-dynactin-activating adaptor complex.
- More
CCM_02300 WD repeat-containing protein from Cordyceps militaris CM01
29% identity, 37% coverage
- milR4 and milR16 Mediated Fruiting Body Development in the Medicinal Fungus Cordyceps militaris
Shao, Frontiers in microbiology 2019 - “...transcripts encode fungal transcriptional regulatory protein (CCM_08428), frequency clock protein (CCM_01014), and WD repeat-containing protein (CCM_02300). Whereas, milR16 was predicted to target a transcript encode putative glycosyltransferase (CCM_ 09558). miRNAs directly degrade their target mRNA in plants and mediate suppressed mRNA translation in plants and animals...”
PF3D7_0302000 pre-mRNA-splicing factor PRP46, putative from Plasmodium falciparum 3D7
31% identity, 27% coverage
- Genome-Wide Collation of the Plasmodium falciparum WDR Protein Superfamily Reveals Malarial Parasite-Specific Features
Chahar, PloS one 2015 - “...homolog PF3D7_1220100 Pre-mRNA splicing factor, putative NP_056975.1-Pre-mRNA-processing factor 17 (PRP17) (YDR364C-Pre-mRNA-processing factor 17) Pf PRP17 PF3D7_0302000 Golgi organization and biogenesis factor, putative NP_002660.1-Pleiotropic regulator 1 (PLRG1) (YPL151C-Pre-mRNA-splicing factor PRP46) Pf PRP46 Pre-mRNA-splicing factor PF3D7_1241100 Conserved Plasmodium protein, unknown function NP_060853.3-Pre-mRNA 3' end processing protein WDR33 (YNL317W-Polyadenylation...”
MGG_08829 transcriptional repressor rco-1 from Pyricularia oryzae 70-15
28% identity, 31% coverage
Tery_1627 serine/threonine protein kinase with WD40 repeats from Trichodesmium erythraeum IMS101
25% identity, 42% coverage
- Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes
Xu, BMC genomics 2009 - “...slr1950 slr1400 slr1805 slr0484 sll1708 sll1371 slr1489 IMS101 Tery_4669 Tery_2879 Tery_1324 Tery_4986 Tery_3858 Tery_0199 Tery_2779 Tery_1627 Tery_3423 Tery_2051 Tery_4912 Tery_1557 BP-1 tsr0033 tlr1171 tll0330 tlr2000 tlr2001 tlr2002 tlr2003 tll0559 tlr0335 tlr2000 tlr2001 tlr2002 tlr2003 tll0328 4.1. Photosynthesis and carbon fixation Various numbers of genes involved in...”
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...(3) Tery_3400 cbSTKII Pentapeptide (5) Tery_1030 cbSTKII FHA Tery_3423 cbSTKI-other Tery_1036 cbSTKII DUF323 Tery_3510 cbSTKI Tery_1627 cbSTKII WD40 (7) Tery_3681 cbSTKII TPR (7) Tery_1668 cbSTKI-other Tery_3863 cbSTKII GAF Tery_1722 cbSTKII GUN4 Tery_4060 cbSTKII WD40 (7) Tery_1723 cbSTKII GUN4 Tery_4351 cbSTKII DUF323 (2) Tery_2033 cbSTKII WD40 (7)...”
Q7PMU5 Coatomer subunit beta' from Anopheles gambiae
24% identity, 27% coverage
Q4DKP1 Uncharacterized protein from Trypanosoma cruzi (strain CL Brener)
24% identity, 38% coverage
- Proteome-Wide Analysis of Trypanosoma cruzi Exponential and Stationary Growth Phases Reveals a Subcellular Compartment-Specific Regulation
Avila, Genes 2018 - “...was the WD40 domain G repeat (pfam00400) with 12 domain hits belonging to four proteins (Q4DKP1, Q4DCC3, Q4DEL9, and Q4DCC3) ( Table S4 ). Proteins with the WD (tryptophan/aspartic acid) domain play diverse biological functions, including cell division, gene transcription, transmembrane signaling, mRNA modification, apoptosis, cytoskeleton...”
POP1_SCHPO / P87060 WD repeat-containing protein pop1; WD repeat-containing protein ste16 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 6 papers)
pop1 / RF|XP_001713146.1 cullin 1 adaptor protein Pop1 from Schizosaccharomyces pombe (see 6 papers)
27% identity, 36% coverage
- function: Involved in maintenance of ploidy through proteasome dependent degradation of CDK inhibitor rum1 and S-phase initiator cdc18. Functions as a recognition factor for rum1 and cdc18, which are subsequently ubiquitinated and targeted to the 26S proteasome for degradation. Together with pop2, required for cig2 instability during G2 and M phase and cig2 degradation in exponentially growing cells. Regulates cell-cycle progression under starvation through the rum1 protein.
subunit: Homodimer and heterodimer with pop2. Binds to cdc18, phosphorylated cig2, cul1, pip1 and skp1. - CharProtDB Source (per GeneDB): GeneDB_Spombe
SCONB_EMENI / Q00659 Probable E3 ubiquitin ligase complex SCF subunit sconB; Sulfur controller B; Sulfur metabolite repression control protein B from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see paper)
28% identity, 31% coverage
WDR5B_ARATH / Q9SY00 COMPASS-like H3K4 histone methylase component WDR5B; AtWDR5B from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT4G02730 transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
22% identity, 41% coverage
- subunit: Unlike WDR5A, does not interact with RBL or TRO.
disruption phenotype: No visible phenotype. - The complexity of vesicle transport factors in plants examined by orthology search
Paul, PloS one 2014 - “...for At2g43770, we predict cytosolic localization ( Table 8 ). Furthermore, At3g49660 as well as At4g02730 have been described as components of the H3K4 methyltransferase complexes localized in the nucleus [149] . Similarly, one of the (co-)orthologue of Sec13 in yeast (YBR175W) is assigned to perform...”
- Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris
Abou-Elwafa, Journal of experimental botany 2011 - “...BQ489608 7.4e-17 FPA At2g19520 FVE EG550040 4.4e-85 FVE BQ592158 2.4e-62 FVE At5g13480 FY BQ588779 1.3e-15 At4g02730 At4g02560 LD BQ589018 4.0e-27 LD BQ594506 1.6e-18 LD a Beta vulgaris ESTs or TCs (tentative consensus sequences) were identified by tblastn sequence similarity searches in BvGI 3.0 ( http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=beet )....”
E9HMX3 F-box domain-containing protein from Daphnia pulex
26% identity, 35% coverage
RCO1_NEUCR / P78706 Transcriptional repressor rco-1 from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see paper)
NCU06205, XP_962921 transcriptional repressor rco-1 from Neurospora crassa OR74A
28% identity, 31% coverage
- function: Represses transcription by RNA polymerase II. May be involved at several stages of conidiation and other growth and development processes. Appears to regulate genes that are expressed in asexual and sexual spore pathways
disruption phenotype: Mutant are aconidial, female sterile, have reduced growth rates and form hyphae that coil in a counterclockwise direction, opposite to that of the wild-type. - Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast
Fagerström-Billai, Molecular and cellular biology 2005 - “...Tup1 (AACUO1001716.1); Neurospora crassa, Tup1 (P78706); Emericella nidulans, Tup1 (AAB63194); Yarrowia lipolytica, Tup1 (CAC81004); Dictostelium discodeum,...”
- Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast.
Sprague, The EMBO journal 2000 (no snippet) - VE-1 regulation of MAPK signaling controls sexual development in <i>Neurospora crassa</i>
Cea-Sánchez, mBio 2024 - “...membrane phosphatase required for sodium stress response YES YES NO NO YES ( 64 ) NCU06205 rco-1 TUP1 PP / P / A Transcriptional repressor rco-1 YES NO NO YES YES ( 65 ) Other signaling pathways NCU09123 camk-1 CMK1/CMK2 PP / P / A Ca/CaM-dependent...”
- Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability
Kelliher, PLoS biology 2023 - “...with APA events: ck-1a (NCU00685), frq (NCU02265), upf1 prd-6 (NCU04242), ckb-1 ( NCU05485 ), rco-1 (NCU06205), pkac-1 (NCU06240), NCU06565, prd-1 (NCU07839), and nab2 (NCU16397) ( S3 Table ). Given the strict cutoff for consensus APA, we added 7 additional genes after visual inspection: set-2 (NCU00269), wc-2...”
- Proteomic Shifts Reflecting Oxidative Stress and Reduced Capacity for Protein Synthesis, and Alterations to Mitochondrial Membranes in Neurospora crassa Lacking VDAC
Shuvo, Microorganisms 2022 - “...showing differential expression are linked to hyphal morphology. Two regulatory proteins involved in conidiation, Rco-1 (NCU06205), and Nrc-2 (NCU01797) were detected only in Por-1, suggesting that they are upregulated in this mutant ( Table S4 ). Intriguingly, the null mutants of rco-1 (regulator of conidiation-1) [...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...Organization or Biogenisis/Cellular Process/Metabolic Process NCU06028 11034 fail quinic acid utilization activator qa-1F Transc Factors NCU06205 11372 fail regulator of conidiation-1 rco-1 Morph/Hyph NCU06145 12557 fail RING-6 RING-6 Morph/Hyph NCU02214 11068 fail TAH-2 tah-2 Transc Factors NCU10008 22177 fail tricarboxylic acid-14 tca-14 E. coli CS Orth...”
- “...Transc Factors NCU06175 11244 Peroxisomal membrane protein pex3 Morph/Hyph NCU06186 11369 hypothetical protein Transc Factors NCU06205 11371 transcriptional repressor rco-1 rco-1 Transc Factors NCU06213 11373 zinc finger transcription factor-9 znf-9 Transc Factors NCU06265 11245 Hyphal anastamosis-13 protein ham-13 Morph/Hyph NCU06407 11017 zinc finger transcription factor 1...”
- Functional Profiling of Transcription Factor Genes in Neurospora crassa
Carrillo, G3 (Bethesda, Md.) 2017 - “...contained representation from several transcription factor classes, with loss of the WD40 gene, rco -1/ NCU06205 ( Yamashiro et al. 1996 ), resulting in the slowest growth rate observed in our study ( Figure 3A and Table S1 ). Only two mutants grew faster than wild...”
- “.../ NCU08726 ; ( Bailey and Ebbole 1998 )] and the transcriptional adapter rco-1 / NCU06205 ( Yamashiro et al. 1996 ) are blocked at distinct points in the process. Other work has demonstrated transcription factors that influence conidiation under different environmental conditions or the extent...”
- Regulation of glycogen metabolism by the CRE-1, RCO-1 and RCM-1 proteins in Neurospora crassa. The role of CRE-1 as the central transcriptional regulator.
Cupertino, Fungal genetics and biology : FG & B 2015 (PubMed)- GeneRIF: Glycogen content is misregulated in the rco-1(KO) strain, and the glycogen synthase phosphorylation is decreased, showing that RCO-1 is involved in glycogen accumulation and in the regulation of GSN activity by phosphorylation.
- Neurospora crassa female development requires the PACC and other signal transduction pathways, transcription factors, chromatin remodeling, cell-to-cell fusion, and autophagy
Chinnici, PloS one 2014 - “...et al. [45] . We also found that deletion mutants for the transcription factor rco-1 (NCU06205) and 3 calcium signaling genes, cnb-1 (NCU03833), camk-1 (NCU09123), and ham-10 (NCU02833) were affected in ascogonia formation. This suggests that Ca++ signaling may be required for the initiation of female...”
- “...previously identified by Aramayo et al. [85] as being needed for protoperithecium development. The rco-1 (NCU06205), rcm-1 (NCU06842) and adv-1 (NCU07392) genes had been previously identified as encoding transcription factors needed for cell-to-cell fusion [35] . The rco-1 (NCU06205) and rcm-1 (NCU06842) genes are homologs of...”
- Suppression of WC-independent frequency transcription by RCO-1 is essential for Neurospora circadian clock
Zhou, Proceedings of the National Academy of Sciences of the United States of America 2013 - “...created an rco-1KO strain, in which the rco-1 gene (NCU06205) was deleted from a Neurospora ras-1bd strain by gene replacement with a hygromycin resistance gene...”
- More
L7M0T0 F-box domain-containing protein from Rhipicephalus pulchellus
25% identity, 35% coverage
MHCKB_DICDI / P90648 Myosin heavy chain kinase B; MHCK-B; EC 2.7.11.7 from Dictyostelium discoideum (Social amoeba) (see paper)
P90648 myosin-heavy-chain kinase (EC 2.7.11.7) from Dictyostelium discoideum (see 5 papers)
DDB_G0289115 Alpha kinase family protein from Dictyostelium discoideum AX4
26% identity, 38% coverage
- function: Catalyzes its autophosphorylation, which is needed for enzymatic activity and phosphorylates myosin II heavy chain at a threonine in the C-terminal tail region (PubMed:9115238). This phosphorylation is critical in regulating the assembly and disassembly of myosin II filament (PubMed:9115238). Participates in control of myosin localization (PubMed:9115238).
catalytic activity: L-threonyl-[myosin heavy-chain] + ATP = O-phospho-L-threonyl- [myosin heavy-chain] + ADP + H(+) (RHEA:11424) - A Proteomics Analysis of Calmodulin-Binding Proteins in Dictyostelium discoideum during the Transition from Unicellular Growth to Multicellular Development
Kim, International journal of molecular sciences 2021 - “...phosphatase 2B catalytic subunit Q7YSW8 DDB_G0276883 DDB0185021 No Yes mhkB Myosin heavy chain kinase B P90648 DDB_G0289115 DDB0191333 No Yes rgaA Ras GTPase-activating-like protein rgaA Q54K32 DDB_G0287585 DDB0191437 No Yes rpl19 60S ribosomal protein L19 P14329 DDB_G0281565 DDB0214854 Yes Yes CaMBPs with Non-Canonical CaMBDs [ 6...”
- Autophosphorylation at Thr279 of Entamoeba histolytica atypical kinase EhAK1 is required for activity and regulation of erythrophagocytosis
Mansuri, Scientific reports 2016 - “...The kinase domains of EhAK1, MHCK-A, MHCK-B, EF2K, and TRPM7 (UniprotKB accession codes C4M9G9, P42527, P90648, 000918 and Q923J1, respectively) were aligned on the basis of similarities in their sequence. Sequences representing P-loop, N/D loop, G-rich region and Zinc finger motif are indicated. Invariant K85 that...”
- A Proteomics Analysis of Calmodulin-Binding Proteins in Dictyostelium discoideum during the Transition from Unicellular Growth to Multicellular Development
Kim, International journal of molecular sciences 2021 - “...2B catalytic subunit Q7YSW8 DDB_G0276883 DDB0185021 No Yes mhkB Myosin heavy chain kinase B P90648 DDB_G0289115 DDB0191333 No Yes rgaA Ras GTPase-activating-like protein rgaA Q54K32 DDB_G0287585 DDB0191437 No Yes rpl19 60S ribosomal protein L19 P14329 DDB_G0281565 DDB0214854 Yes Yes CaMBPs with Non-Canonical CaMBDs [ 6 ]...”
TRCB_XENLA / Q91854 Beta-TrCP; Beta-transducin repeat-containing protein from Xenopus laevis (African clawed frog) (see paper)
NP_001081064 beta-TrCP from Xenopus laevis
25% identity, 36% coverage
B3KPF6 cDNA FLJ31732 fis, clone NT2RI2006856, highly similar to Striatin-4 from Homo sapiens
24% identity, 37% coverage
- Protein Profiling of a Cellular Model of NAFLD by Advanced Bioanalytical Approaches.
Altomare, International journal of molecular sciences 2022 - “...expression-enhancing protein REEP6 2 20,733 0.87 Q53G72 B-cell receptor-associated protein 31 BCAP31 4 27,931 1.11 B3KPF6 Striatin-4 STRN4 3 38,960 1.20 Q96IF1 LIM domain-containing protein ajuba AJUBA 5 56,933 1.46 B4DZM3 Ribosomal RNA processing protein 1 RRP1 3 46,150 ijms-23-09025-t002_Table 2 Table 2 Canonical pathways modulated...”
F7D3K4 Platelet-activating factor acetylhydrolase IB subunit alpha from Equus caballus
26% identity, 31% coverage
NP_524430 supernumerary limbs, isoform A from Drosophila melanogaster
Q9VDE3 LD08669p from Drosophila melanogaster
26% identity, 35% coverage
- Gotta Go Slow: Two Evolutionarily Distinct Annelids Retain a Common Hedgehog Pathway Composition, Outlining Its Pan-Bilaterian Core
Platova, International journal of molecular sciences 2022 - “...Kif27 ++ Kif27 + Costal2 O16844 Mouse KIF7 B7ZNG0 Mouse KIF27 Q7M6Z4 Slimb/-TrCP ++ + NP_524430 Human NP_378663 IFT25/HSPB11 ++ + x Human NP_001303864 IFT27 ++ + x Human NP_001171172 IFT38/CLUAP1 ++ ? NP_608470 Human NP_055856 IFT52 ++ + NP_609045 Human NP_001290387 IFT54/TRAF3IP1 ++ + NP_650353...”
- SCF-Slimb is critical for Glycogen synthase kinase-3β-mediated suppression of TAF15-induced neurotoxicity in Drosophila.
Choi, Journal of neurochemistry 2021 (PubMed)- GeneRIF: SCF-Slimb is critical for Glycogen synthase kinase-3beta-mediated suppression of TAF15-induced neurotoxicity in Drosophila.
- Wnt regulation: exploring Axin-Disheveled interactions and defining mechanisms by which the SCF E3 ubiquitin ligase is recruited to the destruction complex.
Schaefer, Molecular biology of the cell 2020 - GeneRIF: Wnt regulation: exploring Axin-Disheveled interactions and defining mechanisms by which the SCF E3 ubiquitin ligase is recruited to the destruction complex.
- The E3 ubiquitin ligase Slimb/β-TrCP is required for normal copper homeostasis in Drosophila.
Zhang, Biochimica et biophysica acta. Molecular cell research 2020 (PubMed)- GeneRIF: The E3 ubiquitin ligase Slimb/beta-TrCP is required for normal copper homeostasis in Drosophila.
- Casein kinase 1 family proteins promote Slimb-dependent Expanded degradation.
Fulford, eLife 2019 - GeneRIF: Here, the authors show that the Casein Kinase 1 (CKI) family is required for Expanded phosphorylation. CKI expression promotes Expanded phosphorylation and interaction with Slimb/beta-TrCP.
- The SCF ubiquitin ligase Slimb controls Nerfin-1 turnover in Drosophila.
Lin, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: Our data revealed a new link to understand the underlying mechanism for Nerfin-1 turnover in post-translational level, and provided useful insights in animal development and disease treatment by manipulating the activity of Slimb and Nerfin-1.
- The Drosophila F-box protein Slimb controls dSmurf protein turnover to regulate the Hippo pathway.
Hu, Biochemical and biophysical research communications 2017 (PubMed)- GeneRIF: Interaction with Slimb leads to the ubiquitination and degradation of dSmurf, resulting in negative regulation of dSmurf-mediated Yki phosphorylation and activity in the Hippo pathway. Thus our study revealed a new regulatory mechanism of the Hippo pathway which may provide implications for developing tumor treatment.
- Asterless Reduction during Spermiogenesis Is Regulated by Plk4 and Is Essential for Zygote Development in Drosophila.
Khire, Current biology : CB 2015 - GeneRIF: When Asl reduction is attenuated by Asl overexpression, plk4 mutations, Plk4 RNAi, or Slimb overexpression, Asl levels are higher in spermatozoa, resulting in embryos with reduced viability.
- More
- Identification of putative circadian clock genes in the American horseshoe crab, Limulus polyphemus
Chesmore, Comparative biochemistry and physiology. Part D, Genomics & proteomics 2016 (secret) - Apocrine secretion in Drosophila salivary glands: subcellular origin, dynamics, and identification of secretory proteins
Farkaš, PloS one 2014 - “...Src42A) Q9V9J3 59.1 signaling enzyme cytoplasmic Stromal interaction molecule P83094 64.8 transport membrane Supernumerary limbs Q9VDE3 59.0 proteosomal degradation cytoplasmic Synaptojanin Q5U0V7 134.6 enzyme Syndecan P49415 42.1 signaling membrane Tetraspanin 42Ef Q7K010 24.7 scaffolding/anchoring membrane Thioredoxin Q9W022 15.9 enzyme cytoplasmic Thioredoxin reductase-1 P91938 64.3 metabolism mitochondrial...”
NCU06483 F-box and WD repeat-containing protein from Neurospora crassa OR74A
24% identity, 40% coverage
An15g00140 uncharacterized protein from Aspergillus niger
29% identity, 31% coverage
- Genome-wide transcription landscape of citric acid producing Aspergillus niger in response to glucose gradient
Zheng, Frontiers in bioengineering and biotechnology 2023 - “...various An03g04720 snfA n.d. 35.88 0.52 36.72 0.43 39.94 3.65 43.82 3.44 40.81 2.41 various An15g00140 rcoA n.d. 128.79 3.00 137.71 3.76 145.13 1.36 144.03 3.05 129.23 1.16 various An02g03940 ssnF n.d. 60.18 1.84 62.65 5.65 67.63 5.94 62 4.45 56.29 0.84 various An07g06080 ckiA n.d....”
- The transcriptional repressor TupA in Aspergillus niger is involved in controlling gene expression related to cell wall biosynthesis, development, and nitrogen source availability
Schachtschabel, PloS one 2013 - “...and show that the mutant is mutated in the A. niger TupA homolog. The tupA (An15g00140) mutant in A. niger displays in addition to induced expression of agsA a strongly reduced radial growth rate, increased branching, and abundant secretion of an unknown pigment into the medium....”
- “...III subclone giving complementation was subject to further analysis and sequencing. For complementation studies the An15g00140 locus, including approximately 2.3-kb promoter and 1.4-kb terminator regions, was PCR-amplified using N402 genomic DNA as template and the Not I site-containing primers P1_0140_For and P2_0140_Rev ( Table 2 )....”
- Casein phosphopeptides drastically increase the secretion of extracellular proteins in Aspergillus awamori. Proteomics studies reveal changes in the secretory pathway
Kosalková, Microbial cell factories 2012 - “...28 ], is only detected under control conditions but not in CPPs-supplemented cultures (spot IC57, An15g00140) (Figure 7 ). Another transcriptional NmrA-like repressor (spot IC60, An15g02410) was found underrepresented in CPPs-supplemented cells. NmrA is an Aspergillus nidulans negative transcriptional regulator involved in modulating the activity of...”
6rxtUL / G0RZL9 6rxtUL (see paper)
25% identity, 39% coverage
NLE1_SCHPO / O74855 Ribosome assembly protein 4; Notchless protein homolog 1; Ribosome biogenesis factor rsa4 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
24% identity, 36% coverage
- function: Involved in ribosome biogenesis. Required for processing and efficient intra-nuclear transport of pre-60S ribosomal subunits. Interacts with the AAA-ATPase Midasin, which is essential for the ATP- dependent dissociation of a group of nonribosomal factors from the pre- 60S particle.
subunit: Associates with the pre-60S ribosomal particle. Interacts (via WD repeats) with uL18 (rpl501/rpl502). Interacts (via UBL domain) with mdn1 (via VWFA/MIDAS domain). Interacts (via WD repeats) with nsa2.
4j8gB / Q96WV5 Crystal structure of alpha-cop/e19 complex (see paper)
24% identity, 35% coverage
P46800 Small ribosomal subunit protein RACK1 from Dictyostelium discoideum
DDB_G0275045 hypothetical protein from Dictyostelium discoideum AX4
25% identity, 32% coverage
- The Dictyostelium discoideum RACK1 orthologue has roles in growth and development
Omosigho, Cell communication and signaling : CCS 2014 - “...accession numbers from H. sapiens (P63244), D. melanogaster (O18640), A. thaliana (O24456), D. discoideum (DdRACK1) (P46800) and S. cerevisiae (P38011). The WD40 repeats and -propeller blade positions are written above the sequences. Alignment was done with the ClustalW program and processed through ESPript for representation. All...”
- “...H. sapiens (P63244), D. melanogaster (O18640), A. thaliana (O24456), S. cerevisiae (P38011), and D. discoideum (P46800) were retrieved from Uniprot protein database and aligned using ClustalW program with Blosum 62 matrix. The aligned sequences were processed through EsPript for representation. The structural coordinates of S. cerevisiae...”
- The Dictyostelium discoideum RACK1 orthologue has roles in growth and development
Omosigho, Cell communication and signaling : CCS 2014 - “...blades 6 and 7 of the propeller. Results Characterization of D. discoideum RACK1 (DdRACK1) gpbB (DDB_G0275045) is located on chromosome 2 of the D. discoideum genome and has 2 exons. The open reading frame encompasses 1136bp which encodes a protein of 329 amino acids migrating as...”
- Azidoblebbistatin, a photoreactive myosin inhibitor
Képiró, Proceedings of the National Academy of Sciences of the United States of America 2012 - “...domain-containing protein Elongation factor 1 Hypothetical protein DDB_G0275045 Malate dehydrogenase 244 120 89 69 63 50 37 38 9406 |...”
- A Dictyostelium chalone uses G proteins to regulate proliferation
Bakthavatsalam, BMC biology 2009 - “...the transport of AprA receptors to the plasma membrane. A second g -like gene (gpbB, DDB_G0275045) is encoded by the Dictyostelium genome [ 15 ], so G9 may possibly interact with this other G to regulate growth. Despite having very low extracellular levels of AprA and...”
CPAR2_503400 uncharacterized protein from Candida parapsilosis
29% identity, 22% coverage
TOZ_ARATH / Q9LFE2 Protein TORMOZ EMBRYO DEFECTIVE from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G16750 TOZ (TORMOZEMBRYO DEFECTIVE); nucleotide binding from Arabidopsis thaliana
NP_568338 Transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
23% identity, 26% coverage
- function: Essential protein involved in the regulation of cell division planes during embryogenesis which defines cell patterning, especially longitudinal division planes of the proembryo, probably via the regulation of embryo patterning genes expression patterns.
disruption phenotype: Defective embryo arrested at preglobular stage characterized by aberrant cell division planes leading to an abnormal cell patterning; longitudinal division planes of the proembryo are frequently replaced by transverse divisions and less frequently by oblique divisions (PubMed:17616738). Altered embryo patterning genes expression patterns (PubMed:17616738). - Arabidopsis ribosomal RNA processing meerling mutants exhibit suspensor-derived polyembryony due to direct reprogramming of the suspensor
Wang, The Plant cell 2024 - “...), IAA12/BDL ( AT1G04550 ), TWN2 ( AT1G14610 ), IYO ( AT4G38440 ), TOZ ( AT5G16750 ), and PCN ( AT4G07410 ). Supplementary Material koae087_Supplementary_Data Acknowledgments We thank the Lausanne Genomic Technology Facility (LTGF, University of Lausanne) for performing the genome sequencing. HCN seeds were kindly...”
- “...Read Archive SRA Araport: Sequence Read Archive bHLH49 Gramene: AT1G68920 bHLH49 Araport: AT1G68920 TOZ Gramene: AT5G16750 TOZ Araport: AT5G16750 References Aubert M , ODonohue M-F , Lebaron S , Gleizes P-E . Pre-ribosomal RNA processing in human cells: from mechanisms to congenital diseases . Biomolecules ....”
- The root-knot nematode effector Mi2G02 hijacks a host plant trihelix transcription factor to promote nematode parasitism
Zhao, Plant communications 2024 - “...Y1H assay revealed that GT-3a bound directly to the promoters of TORMOZ ( TOZ ; AT5G16750), RADIATION SENSITIVE 23C ( RAD23C ; AT3G02540), and a WRKY TF ( WRKY2 ; AT5G56270) ( Figure5 B and Supplemental Figure6 ). We investigated the ability of GT-3a to repress...”
- “...), GT-3a ( AT5G01380 ), LBD41 ( AT3G02550 ), UBQ1 ( AT3G52590 ), TOZ ( AT5G16750 ), RAD23C ( AT3G02540 ), WRKY2 ( AT5G56270 ), UBP22 ( AT5G10790 ), SRP34 ( AT1G02840 ), DVL4 ( AT1G13245 ), SKP2 ( AT1G21410 ), FEI1 ( AT1G31420 ), FEI2...”
- Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
Kumar, Frontiers in plant science 2020 - “...Potri.001G394200 AT4G20010 PTAC9 PLASTID TRANSCRIPTIONALLY ACTIVE 9- a single-stranded DNA binding protein. Cell division Potri.013G079600 AT5G16750 TOZ TORMOZ -rRNA processing required for cell division Cell division Potri.015G048000 AT5G08130 BIM1 + BES1-INTERACTING MYC-LIKE 1-a BHLH TF involved in brassinosteroid signaling BR signaling All genes from network analyses...”
- Plant Nucleolar Stress Response, a New Face in the NAC-Dependent Cellular Stress Responses
Ohbayashi, Frontiers in plant science 2017 - “...severe loss of leaf abaxialadaxial polarity in as1 and as2 Huang et al., 2014 TOZ At5g16750 WD40 repeat protein Nucleolus toz Ds insertion Enlargement Impairment of pre-rRNA processing Embryonic lethality (aberrant cell division) Griffith et al., 2007 ATLa1 At4g32720 La motif protein Nucleoplasm and nucleolar cavity...”
- Evolution of Daily Gene Co-expression Patterns from Algae to Plants
de, Frontiers in plant science 2017 - “...day 935 Photosynthesis AT4G10340 1,060 Signal transduction ostta04g01810 1,467 Photosynthesis Cre16.g673650 Trough night Ribosome biogenesis AT5G16750 DNA replication ostta01g02580 Carbohydrate derivative Cre12.g508700 Photosynthesis ostta14g00150 Biosynthetic process Peak dusk 907 DNA metabolic process AT2G42120 1,620 DNA metabolic process ostta02g00690 3,751 DNA metabolic process Cre01.g017450 Trough dawn Carbohydrate...”
- The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana
Lange, PLoS genetics 2014 - “...14 639.3 21 AT3G57940 unknown protein, DUF1726 Nuc. bind. 491.5 11 577.3 19 737.6 19 AT5G16750 TORMOZ EMBRYO DEFECTIVE Ribo. bio. 486.4 8 611.3 13 728.9 19 AT5G22100 RNA cyclase family protein Ribo. bio. 443.5 12 441.1 16 518.3 17 AT2G25355 RRP40 EXO9 429.7 15 363.8...”
- Populus tremula (European aspen) shows no evidence of sexual dimorphism
Robinson, BMC plant biology 2014 - “...contains WD40 domains and shows highest sequence similarity based homology to the A. thaliana gene AT5G16750 (TORMOZEMBRYO DEFECTIVE, TOZ). In A. thaliana this gene is required for regulated division planes and embryo development [ 35 ] and is thought to be involved in 18S rRNA biogenesis...”
- Bidirectional promoters in seed development and related hormone/stress responses
Kourmpetli, BMC plant biology 2013 - “...membrane cytosol AT5G10745 AT5G10740 275 unknown protein Protein phosphatase 2C family protein membrane nucleus AT5G16760 AT5G16750 331 inositol-trisphosphate 5/6-kinase TORMOZEMBRYO DEFECTIVE (TOZ) cytosol nucleolus AT5G37350 AT5G37340 232 RIO1 kinase ZPR1 zinc-finger domain protein nucleus cytosol AT5G51540 AT5G51530 529 Zincin-like metalloproteases Ubiquitin c-terminal hydrolase plastid cytosol AT5G54062...”
- “...gametophyte development, in an RNase P/MRP complex [ 59 ]. The TORMOZ and AURORA genes (At5g16750 and At2g25880) are involved in embryo development [ 60 , 61 ]; SYN1 (At5g05490) is essential for meiosis [ 62 ]; SD3 and DWF5 are membrane proteins involved in seedling...”
- More
- The TORMOZ gene encodes a nucleolar protein required for regulated division planes and embryo development in Arabidopsis.
Griffith, The Plant cell 2007 - GeneRIF: Mutation of the TORMOZ (TOZ) gene yields embryos with aberrant cell division planes and arrested embryos that appear not to have established normal patterning.
3v7dB / P07834 Crystal structure of scskp1-sccdc4-psic1 peptide complex (see paper)
25% identity, 34% coverage
NLE1_ARATH / Q9FLX9 Notchless protein homolog from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_200094 WD-40 repeat family protein / notchless protein from Arabidopsis thaliana
AT5G52820 WD-40 repeat family protein / notchless protein, putative from Arabidopsis thaliana
25% identity, 36% coverage
- function: Required for female gametophyte development.
subunit: Associates with the pre-60S ribosomal particle.
disruption phenotype: Female semisterility due to strongly delayed development of female gametophyte. - Arabidopsis NOTCHLESS plays an important role in root and embryo development.
Li, Plant signaling & behavior 2023 - GeneRIF: Arabidopsis NOTCHLESS plays an important role in root and embryo development.
- Arabidopsis NOTCHLESS plays an important role in root and embryo development
Li, Plant signaling & behavior 2023 - “...XP_001700359.1 ( C. reinhardtii ). Arabidopsis genes accession numbers were deposited in the TAIR10: NLE (AT5G52820) and MDN1 (AT1G67120). Disclosure statement No potential conflict of interest was reported by the author(s). Authors contributions Ke Li and Pengfei Wang designed the study. Ke Li, Qingtian Zhang, Huiping...”
- Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes
de, International journal of genomics 2022 - “...Gene module Gene name Description AT1G27120 3327 Turquoise AT1G27120 ( GALT4 ) Galactosyltransferase family protein AT5G52820 2853 Blue NOTCHLESS ( NLE ) WD-40 repeat family protein/notchless protein AT5G56090 2348 Brown CYTOCHROME C OXIDASE 15 ( COX15 ) Encodes a homolog of COX15 AT2G43100 2134 Yellow ISOPROPYLMALATE...”
- Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression
Fonseca, Frontiers in plant science 2019 - “...cycle PeBoW (PES, BOP, WDR12) complex Zografidis et al., 2014 ; Ahn et al., 2016 AT5G52820 NLE (NOTCHLESS) yes nd 60 S ribosomal subunit maturation and assembly; cell growth and proliferation; female gametophyte development Chantha and Matton, 2007 ; Chantha et al., 2010 The table summarizes...”
- Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis
Zhu, Journal of experimental botany 2016 - “...contrast, the first intron retention rate of EMBRYO SAC DEVELOPMENT ARREST 32 (AT3G62210) and NOTCHLESS (AT5G52820) was obviously higher in the gfa1-1/+ mutant and lower in the rid1-2 /+ mutant, compared with the wild-type retention rate. Of these genes, three (AT2G47430, AT3G62210, and AT5G52820) are known...”
- Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction
Amil-Ruiz, Frontiers in plant science 2016 - “...Haloacid dehalogenase-like hydrolase 2.02 3.95E-02 M7B2 gene10408 AT3G03890 Flavin mononucleotide binding 1.94 3.95E-02 M14A10 gene29476 AT5G52820 WD-40 repeat CUL4 RING ubiquitin ligase complex 1.94 3.95E-02 M5B7 gene09169 AT1G48380 DNA binding protein ROOT HAIRLESS 1, component of the topoisomerase VI complex 1.92 3.95E-02 M18D12 gene20804 AT2G22530 Alkaline-phosphatase-like...”
- The MIDASIN and NOTCHLESS genes are essential for female gametophyte development in Arabidopsis thaliana
Chantha, Physiology and molecular biology of plants : an international journal of functional plant biology 2010 - “...ecotype (corresponding to positions 322-1089 in the At5g52820 cDNA sequence) was PCR amplified from cloned cDNA with the NLEWS3 primer...”
- “...At1g67120 and the AtNLE gene corresponds to locus At5g52820. Accession numbers for ClustalW protein sequence analyses of AtMDN1 orthologues are as follows:...”
sll0163 beta transducin-like protein from Synechocystis sp. PCC 6803
23% identity, 20% coverage
- Genomic analysis of parallel-evolved cyanobacterium Synechocystis sp. PCC 6803 under acid stress
Uchiyama, Photosynthesis research 2015 (PubMed)- “...acid stress in the P strain, whereas sll0162, sll0163, slr0623, and slr0529 expressions decreased. There were no differences in the SNP genes expression levels...”
- “...and 4.00 0.66, respectively). In contrast, of sll0162, sll0163, slr0623, and slr0529 expression levels decreased under acid conditions in the P strain (0.09...”
- Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803
Chen, Biotechnology for biofuels 2014 - “...Transport and binding proteins Sll0064 -1.91 15.8 -1.96 15.8 Putative polar amino acid transport system Sll0163 -1.643 5.7 WD-repeat protein Sll0834 -2.36 11.7 -1.944 11.7 Low affinity sulfate transporter Slr0559 -2.07 40.7 Branched chain amino acid ABC transporter Slr0864 -1.51 10.8 ATP-binding protein of ABC transporter...”
- “...also found in Synechocystis treated with ethanol [ 27 ]. In addition, a WD-repeat protein (Sll0163) was down-regulated in the slr1037 mutant (Table 2 ). Synechocystis possesses several open reading frames encoding putative WD-repeat proteins, one of which, the Hat protein, has been found to be...”
- A noncanonical WD-repeat protein from the cyanobacterium Synechocystis PCC6803: structural and functional study
Hisbergues, Protein science : a publication of the Protein Society 2001 - “...such potential proteins present in the latter strain, one (Sll0163 in Cyanobase [Kaneko et al. 1996]) would contain 16 WD repeats, the highest number known...”
rcoA transcriptional corepressor (Eurofung) from Emericella nidulans (see 3 papers)
28% identity, 31% coverage
- CharProtDB Description: WD40 repeat protein; required for sexual development and for sterigmatocystin production; Source:AspGD
FGSG_05038 nuclear distribution protein nudF from Fusarium graminearum PH-1
28% identity, 27% coverage
NP_572778 transport and golgi organization 4 from Drosophila melanogaster
23% identity, 47% coverage
NP_608501 uncharacterized protein, isoform A from Drosophila melanogaster
Q9VPL0 GM13767p from Drosophila melanogaster
26% identity, 38% coverage
F7FZQ6 Platelet-activating factor acetylhydrolase IB subunit alpha from Monodelphis domestica
23% identity, 41% coverage
Ava_3079 Peptidase C14, caspase catalytic subunit p20 from Anabaena variabilis ATCC 29413
25% identity, 15% coverage
- The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria
Bhattacharjee, Journal of experimental botany 2020 - “...sub-domain in the predicted cytoplasmic portion. This presumed topology prevailed in six true OCAs: Ava_0039, Ava_3079, Cri9333_3253, GEI7407_1667, GEI7407_1667, and Glo7428_1095. Among these, the presence of NACHT in the predicted cytoplasmic portion of GEI7407_1667 implies its activity during PCD. Moreover, Ava_0039, Ava_3079, and GEI7407_1667 have an...”
- “...distant positioning of several p20-like sub-domains of a single strain, such as Ava_2184, Ava_3246, and Ava_3079 from A. variabilis ATCC 2943 or Tery_2471, Tery_1841, and Tery_2760 from T. erythraeum IMS101, is apparently explained by multiple independent HGT events during the course of evolution. However, the tree...”
FBW1A_HUMAN / Q9Y297 F-box/WD repeat-containing protein 1A; E3RSIkappaB; Epididymis tissue protein Li 2a; F-box and WD repeats protein beta-TrCP; pIkappaBalpha-E3 receptor subunit from Homo sapiens (Human) (see 44 papers)
NP_378663 F-box/WD repeat-containing protein 1A isoform 1 from Homo sapiens
24% identity, 36% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:10066435, PubMed:10497169, PubMed:10644755, PubMed:10835356, PubMed:11158290, PubMed:11238952, PubMed:11359933, PubMed:11994270, PubMed:12791267, PubMed:12902344, PubMed:14603323, PubMed:14681206, PubMed:14988407, PubMed:15448698, PubMed:15917222, PubMed:16371461, PubMed:22017875, PubMed:22017876, PubMed:22017877, PubMed:22087322, PubMed:25503564, PubMed:25704143, PubMed:36608670, PubMed:9859996, PubMed:9990852). Recognizes and binds to phosphorylated target proteins (PubMed:10066435, PubMed:10497169, PubMed:10644755, PubMed:10835356, PubMed:11158290, PubMed:11238952, PubMed:11359933, PubMed:11994270, PubMed:12791267, PubMed:12902344, PubMed:14603323, PubMed:14681206, PubMed:14988407, PubMed:15448698, PubMed:15917222, PubMed:16371461, PubMed:22017875, PubMed:22017876, PubMed:22017877, PubMed:22087322, PubMed:25503564, PubMed:25704143, PubMed:36608670, PubMed:9859996, PubMed:9990852). SCF(BTRC) mediates the ubiquitination of CTNNB1 and participates in Wnt signaling (PubMed:12077367, PubMed:12820959). SCF(BTRC) mediates the ubiquitination of phosphorylated NFKB1, ATF4, CDC25A, DLG1, FBXO5, PER1, SMAD3, SMAD4, SNAI1 and probably NFKB2 (PubMed:10835356, PubMed:11238952, PubMed:14603323, PubMed:14681206). SCF(BTRC) mediates the ubiquitination of NFKBIA, NFKBIB and NFKBIE; the degradation frees the associated NFKB1 to translocate into the nucleus and to activate transcription (PubMed:10066435, PubMed:10497169, PubMed:10644755, PubMed:9859996). Ubiquitination of NFKBIA occurs at 'Lys-21' and 'Lys- 22' (PubMed:10066435). The SCF(FBXW11) complex also regulates NF-kappa- B by mediating ubiquitination of phosphorylated NFKB1: specifically ubiquitinates the p105 form of NFKB1, leading to its degradation (PubMed:10835356, PubMed:11158290, PubMed:14673179). SCF(BTRC) mediates the ubiquitination of CEP68; this is required for centriole separation during mitosis (PubMed:25503564, PubMed:25704143). SCF(BTRC) mediates the ubiquitination and subsequent degradation of nuclear NFE2L1 (By similarity). Has an essential role in the control of the clock- dependent transcription via degradation of phosphorylated PER1 and PER2 (PubMed:15917222). May be involved in ubiquitination and subsequent proteasomal degradation through a DBB1-CUL4 E3 ubiquitin-protein ligase. Required for activation of NFKB-mediated transcription by IL1B, MAP3K14, MAP3K1, IKBKB and TNF. Required for proteolytic processing of GLI3 (PubMed:16371461). Mediates ubiquitination of REST, thereby leading to its proteasomal degradation (PubMed:18354482, PubMed:21258371). SCF(BTRC) mediates the ubiquitination and subsequent proteasomal degradation of KLF4; thereby negatively regulating cell pluripotency maintenance and embryogenesis (By similarity). SCF(BTRC) acts as a regulator of mTORC1 signaling pathway by catalyzing ubiquitination and subsequent proteasomal degradation of phosphorylated DEPTOR, TFE3 and MITF (PubMed:22017875, PubMed:22017876, PubMed:22017877, PubMed:33110214, PubMed:36608670). SCF(BTRC) directs 'Lys-48'-linked ubiquitination of UBR2 in the T-cell receptor signaling pathway (PubMed:38225265).
subunit: Homodimer. Self-associates. Component of the SCF(BTRC) complex formed of CUL1, SKP1, RBX1 and a BTRC dimer (PubMed:10066435, PubMed:22017875, PubMed:22017876, PubMed:22017877, PubMed:36608670, PubMed:9990852). Direct interaction with SKP1 occurs via the F-box domain. Interacts with phosphorylated ubiquitination substrates SMAD3 and SMAD4. Interacts with phosphorylated ubiquitination substrates CTNNB1, NFKBIA, NFKBIB, NFKBIE, NFKB1/nuclear factor NF-kappa-B p105 subunit, ATF4, CDC25A, DLG1, FBXO5 and SNAI1; the interaction requires the phosphorylation of the 2 serine residues in the substrate destruction motif D-S-G-X(2,3,4)-S. Binds UBQLN1. Interacts with CDC34 and UBE2R2. Interacts with FBXW11. Interacts with CUL4A and DDB1. Part of a SCF(BTRC)-like complex lacking CUL1, which is associated with phosphorylated NKBIA and RELA; RELA interacts directly with NFKBIA. Interacts with the phosphorylated form of GLI3. Interacts with CLU. Interacts with PER1 (phosphorylated), PER2 (phosphorylated) and PER3. Interacts with phosphorylated ubiquitination substrate CEP68 (PubMed:25503564, PubMed:25704143). Interacts with ZC3H12A; this interaction occurs when ZC3H12A is phosphorylated in a IKBKB/IKKB- dependent manner (By similarity). Interacts with HSF1; this interaction occurs during mitosis and induces HSF1 ubiquitin-dependent degradation, a process inhibited by CDC20 (PubMed:18794143). Interacts with NFE2L1 (By similarity). Interacts with INAVA (PubMed:29420262). Interacts with IL10RA; this interaction leads to IL10RA ubiquitination and subsequent degradation (PubMed:22087322). Interacts with REST (PubMed:18354482). Interacts with KLF4; this interaction leads to KLF4 ubiquitination and subsequent degradation (By similarity). Interacts with UBR2, as part of a SCF(BTRC) complex; the interaction mediates 'Lys-48'-linked ubiquitination of UBR2 and is regulated by DUSP22 in the T-cell receptor signaling pathway (PubMed:38225265).
subunit: (Microbial infection) Interacts with vaccinia virus A49; this interaction inhibits NF-kappa-B activation.
subunit: (Microbial infection) Interacts with HIV-1 Vpu. - The EIF3H-HAX1 axis increases RAF-MEK-ERK signaling activity to promote colorectal cancer progression.
Jin, Nature communications 2024 - “...HAX1 O00165 HAX1 87 23 589 1.00510 11 P04049 RAF1 31 14 15 8.31010 7 Q9Y297 TrCP 9 4 4 1.06610 7 PSMs peptide-spectrum matches. Fig. 3 E3 ubiquitin ligase TrCP promotes HAX1 ubiquitination through binding phosphodegron of HAX1. a 293T cells were transfected with Flag-tagged...”
- Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers
Ershov, International journal of molecular sciences 2023 - “...partners of ORF proteins: ADRM1 (Q16186), APEX1 (P27695), ARHGEF1 (Q92888), BCL2L1 (Q07817), BCR (P11274), BTRC (Q9Y297), CALM3 (P0DP25), CDH1 (P12830), EIF3L (Q9Y262), EZR (P15311), FBXW8 (Q8N3Y1), GAPDHS (O14556), GPR161 (Q8N6U8), JUN (P05412), KPNA1 (P52294), MDM2 (Q00987), MEIS2 (O14770), NDFIP2 (Q9NV92), NUP214 (P35658), OPTN (Q96CV9), PBX1 (P40424),...”
- Arecoline promotes proliferation and migration of human HepG2 cells through activation of the PI3K/AKT/mTOR pathway.
Xie, Hereditas 2022 - “...assembly CDKN1B Cyclin-dependent kinase inhibitor 1B p46527 (CDN1B_HUMAN) Cell cycle BTRC F-box/WD repeat-containing protein 1A Q9Y297 (FBW1A_HUMAN) Biological rhythms, Host-virus interaction, Ubl conjugation pathway, Wnt pathway Effects of hub gene expression on hepatocellular cancer prognosis We investigated the potential effects of the expression of the top...”
- Degron masking outlines degronons, co-degrading functional modules in the proteome.
Guharoy, Communications biology 2022 - “...O43683) 534 NKENY 538 FZR1 (Q9UM11) CDC20 (Q12834) Claspin (CLSPN, Q9HAW4) 29 DSGQGS 34 BTRC (Q9Y297) PLK1 (P53350), CASP3 (P42574) Cyclin-dependent kinase inhibitor 1B (CDKN1B, P46527) 183 SVEQTPKK 190 SKP2 (Q13309), CKS1B (P61024) CCNE1 (P24864), CDK2 (P24941), PIN1 (Q13526), YWHAQ (P27348), b AKT1 (P31749) Cyclin-dependent kinase...”
- “...CDK2 (P24941) FYVE, RhoGEF and PH domain-containing protein 3 (FGD3, Q5JSP0) 75 DSGIDS 80 BTRC (Q9Y297) GSK3B (P49841) Catenin beta-1 (CTNNB1, P35222) 32 DSGIHS 37 BTRC (Q9Y297) GSK3B (P49841), b CSNK1A1 (P48729), b AXIN1 (O15169) FYVE, RhoGEF and PH domain-containing protein 1 (FGD1, P98174) 282 DSGIDS...”
- Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants
González-Sánchez, Nucleic acids research 2021 - “...( B ) Network view of CTNNB1 (UniProtKB: P35222), GSK3B (UniProtKB: P49841) and BTRC (UniProtKB: Q9Y297), displaying protein domains, domain-motif interactions from ELM (purple lines), phosphorylation sites (small yellow flags), and cancer missense variants from COSMIC (blue t-shaped lines, heights are proportional to number of samples)....”
- “...and PhosphositePlus). Moreover, these phosphorylations are required for the recognition of CTNNB1 by BTRC (UniProtKB: Q9Y297), a component of E3 ubiquitin-protein ligase complex, through a diphospho-dependent degron DEG_SCF_TRCP1_1 (ELM accession: ELME000269) that interacts with its WD40 -propeller. Therefore, these variants ultimately prevent ubiquitination of CTNNB1 and...”
- Virus-Host Protein-Protein Interactions between Human Papillomavirus 16 E6 A1 and D2/D3 Sub-Lineages: Variances and Similarities.
Dayer, International journal of molecular sciences 2020 - “...kinase HCK (P08631) (AAE6), cyclin-dependent kinase 9 CDK9 (P50750), and F-box/WD repeat-containing protein 1A FBW1A (Q9Y297) (EPE6). 2.2. Protein-Pathway Method: AAE6 Is More Successful than EPE6 in the Malignant Transformation Process We also designed the more inclusive Protein-Pathway Method to select additional potential E6 targets. We...”
- Merkel cell polyomavirus small T antigen induces genome instability by E3 ubiquitin ligase targeting.
Kwun, Oncogene 2017 - “...as referenced. shRNA-targeting sequences of CDC20 (TRCN0000003790, UniProtKB ID: Q12834) and BTRC (TRCN0000006541, UniProtKB ID: Q9Y297) cloned in pLKO.1 vector 6 were used for the knockdown study. shRNAs for human Fbw7 (UniProtKB ID: Q969H0) were described previously, 10 and a control shRNA construct was obtained from...”
- Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface.
Gorelik, Proceedings of the National Academy of Sciences of the United States of America 2016 - More
- Gotta Go Slow: Two Evolutionarily Distinct Annelids Retain a Common Hedgehog Pathway Composition, Outlining Its Pan-Bilaterian Core
Platova, International journal of molecular sciences 2022 - “...Kif27 + Costal2 O16844 Mouse KIF7 B7ZNG0 Mouse KIF27 Q7M6Z4 Slimb/-TrCP ++ + NP_524430 Human NP_378663 IFT25/HSPB11 ++ + x Human NP_001303864 IFT27 ++ + x Human NP_001171172 IFT38/CLUAP1 ++ ? NP_608470 Human NP_055856 IFT52 ++ + NP_609045 Human NP_001290387 IFT54/TRAF3IP1 ++ + NP_650353 Human NP_056465...”
AT2G43770 transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
NP_181905 Transducin/WD40 repeat-like superfamily protein from Arabidopsis thaliana
25% identity, 32% coverage
- Arabinosylation of cell wall extensin is required for the directional response to salinity in roots
Zou, The Plant cell 2024 - “...was carried out using Bio-Rad CFX96 system. Relative expression was calculated using the reference gene AT2G43770 ( MAC17 ) and AT2G28390 ( MON1 ) individually, and the average was used. Values represent means SEs from 9 tubes from 3 plates, each tube containing 2 seedlings. For...”
- “...CFX Opus 384 Real-Time PCR System (Bio-Rad). Relative expression was calculated using the reference gene AT2G43770 . Primers used for gene expression analysis are listed in Supplementary Table S4 . Sequential extraction and CoMPP analysis The 5-d-old Col-0, exad1-1 , and exad1-3 mutant seedlings were transferred...”
- Root branching under high salinity requires auxin-independent modulation of LATERAL ORGAN BOUNDARY DOMAIN 16 function
Zhang, The Plant cell 2024 - “...Expression values were fold changes normalized by mock treatment under 0 mM. The housekeeping gene At2g43770 was used for normalization in D) and E) . Statistical analyses in B) and C) were done using a 2-sided t test. Statistical analyses in D) and E) were done...”
- “...represent fold changes of ZAT6 expression normalized by the expression levels of the housekeeping gene At2g43770 and the expression of Col-0 at the 0-h time point ( n = 4 to 5, Supplementary Data Set 5 ). Statistical analysis in D) was done using 2-way ANOVA...”
- MOS4-associated complex contributes to proper splicing and suppression of ER stress under long-term heat stress in Arabidopsis
Endo, PNAS nexus 2023 - “...to a D284N substitution in sloh3 , and a nonsense mutation in the exon of At2g43770 led to W299X (X, stop codon) and a truncated protein in sloh63 (Fig. 3 A). To perform a complementation test, we transformed sloh3 and sloh63 with At5g22350 and At2g43770 ,...”
- “...and that of the transgene (Fig. 3 B). The introduction of At5g28740 into sloh3 and At2g43770 into sloh63 restored the L-heat tolerance to that of WT, indicating that these genes were the causal genes of interest (Fig. 3 B). To understand whether SLOH3 and SLOH63 are...”
- ABA signaling prevents phosphodegradation of the SR45 splicing factor to alleviate inhibition of early seedling development in Arabidopsis
Albuquerque-Martins, Plant communications 2023 - “...etal., 2013 ). SR45 has also been reported to interact with the products of the At2g43770 and At1g10580 genes ( Zhang etal., 2014 ), which are predicted to contain WD40 domains ( Zhang etal., 2008 ). WD40 proteins function as potential substrate receptors of CUL4 E3...”
- Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction
Liu, BMC plant biology 2022 - “...the synergid cells, affect the female gametophyte a UMSL129_0009 N/A N/A MYB 1.85 N/A UMSL039_0026 AT2G43770 CR12G01870 DEAD 2.21 FAP 52: flagellar associated protein b UMSL054_0061 N/A N/A DEAD 2.81 N/A UMSL003_0532 AT5G58080 CR02G02460 GARP_G2-like 1.08 ARR18: member of response regulator a UMSL103_0003 AT5G43990 N/A SET...”
- A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes involved in cuticular wax biosynthesis in Brassica napus
Jin, BMC plant biology 2020 - “...NAD-dependent Glycerol-3-Phosphate Dehydrogenase (GPDHc1) Bn-A05-p2030789 BnaA05g03470D-BnaA05g36470D (47) BnaA05g03540D BnaA05g03570D BnaA05g03920D BnaA05g04000D 2.47 2.19 2.59 3.42 AT2G43770 AT2G43800 AT2G44220 AT2G44450 WD40 repeat-like superfamily protein FORMIN HOMOLOGY 2 DUF239 BGLU15 Bn-scaff_15798_1-p733219 BnaC04g35190D-BnaC04g36140D (3) BnaC04g35220D BnaC04g35860D 7.51 4.97 AT1G13080 AT2G23200 CYP71B2 Protein kinase superfamily protein Bn-A08-p16793918 BnaA08g17640D-BnaA08g18370D (3) BnaA08g17780D...”
- Seed traits are pleiotropically regulated by the flowering time gene PERPETUAL FLOWERING 1 (PEP1) in the perennial Arabis alpina
Hughes, Molecular ecology 2019 - “...seeds, AaKU70 (an ortholog of At1g16970 in A. alpina ) and AaWU40 (an ortholog of At2g43770; Dekkers et al., 2012 ). These genes were selected for their stability and efficiency based on a preliminary assessment of a range of housekeeping genes. Relative expression was determined using...”
- WD40-Repeat Proteins in Plant Cell Wall Formation: Current Evidence and Research Prospects
Guerriero, Frontiers in plant science 2015 - “...al., 2007 ; Zhou et al., 2010 ). The study identified three WDR proteins, AT1G04510, AT2G43770, and AT4G34460, among the 42 most likely cell wall-related candidate proteins. Other studies show that AT1G04510 codes for MAC3A, a WDR protein with roles in plant immunity and activation of...”
- “...), although this remains to be shown experimentally. The second predicted cell wall-related WDR protein, AT2G43770, is the plant homolog of SNRNP40, also a spliceosome component, and is predicted to interact with a UDP-D-xylose synthase, UXS6 (AT2G28760). Finally, the third predicted cell wall WDR protein, AT4G34460,...”
- More
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...U5-100 kDa (Prp28p) DDX23 NP_004809 NP_609888 NP_180929 NP_010529 DDB0233518 U5-40 kDa (na) SNRNP40 NP_004805 NP_608501 NP_181905 No hit DDB0233510 U5-15 kDa (Dib1p) TXNL4A NP_006692 NP_608830 NP_196446 NP_015407 DDB0233538 d U5-52 kDa (na) CD2BP2 NP_006101 NP_609404 NP_568211 No hit d 2E. U4/U6 snRNP-specific proteins DDB0233224 U4/U6-90 kDa...”
F2Z521 Platelet-activating factor acetylhydrolase IB subunit alpha from Sus scrofa
31% identity, 16% coverage
KTN84_ARATH / Q8H0T9 Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.4 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G23430 transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
26% identity, 32% coverage
- function: May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity). This activity may promote rapid reorganization of cellular microtubule arrays (By similarity). Confers precision to microtubule (MT) severing by specific targeting of KTN1 to MT cleavage sites such as crossover or branching nucleation sites (PubMed:28978669). Together with other KTN80s, regulates cell elongation by modulating MT organization (PubMed:28978669).
subunit: Component of KTN80-KTN1 complexes composed of a hexamer of KTN1-KTN80 heterodimers that sense microtubule (MT) geometry to confer precise MT severing (PubMed:28978669). Interacts directly with AAA1/KTN1, and weakly with KTN80.1 and KTN80.3 (PubMed:28978669).
disruption phenotype: The double mutant ktn80.3 ktn80.4 exhibits normal growth, but the quadruple mutant ktn80.1 ktn80.2 ktn80.3 ktn80.4 has a severe dwarf phenotype, with small and round dark-green rosette leaves as well as wide and short petioles, probably due to cell elongation defects, and associated with a complex cortical microtubule (MT) network with stable entanglements (PubMed:28978669). Plants missing KTN80s have a disruption of KTN1 recruitment at MT crossover or branching nucleation sites, leading to an abolishment of MT severing (PubMed:28978669). - Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana
Soto-Cardinault, Genes 2023 - “...S5 ). The first group of genes in the Darkmagenta module consisted of seven genes (AT5G23430, AT3G13340, AT3G18060, AT5G51980, AT1G79990, VPS and VSC) that contained the WD40/YVTN repeat-like domain (IPR015943). In A. thaliana , 237 proteins have been reported to contain four or more copies of...”
- “...cell death [ 77 ]. In this group, we identified at least 3 G-type genes (AT5G23430, AT5G51980, AT1G79990) ( Table 4 ). In the second group, we identified three CPG for key enzymes in sterol biosynthesis, SMT1, SMO1-1, and 3BETAHSD/D1 ( Table 4 ). Sterols are...”
- Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole
Abu-Zaitoon, Plants (Basel, Switzerland) 2023 - “...of flowering time in Arabidopsis thaliana [ 31 ]. The authors identified a novel gene, At5g23430, which was significantly coexpressed with multiple known flowering time regulators, and demonstrated its role in the regulation of flowering time. In this study, version 11 of ATTED-II database released in...”
- KTN80 confers precision to microtubule severing by specific targeting of katanin complexes in plant cells
Wang, The EMBO journal 2017 - “...katanin p80 subunits, At1G11160, At1G61210, At5G08390, and At5G23430, which we designated the encoded katanin subunits KTN80.1, 2, 3, and 4, respectively....”
- “...(At1g11160), KTN80.2 (At1g61210), KTN80.3 (At5g08390), and KTN80.4 (At5g23430), we first generated the ktn80.12 double mutants and the ktn80.34 double mutants...”
- Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination
Srivastava, PloS one 2015 - “...encompass more than 200 putative WD40 domain containing proteins [ 57 ]. Arabidopsis At5g08390 and At5g23430 displayed protein similarity with corresponding S . cerevisiae SPT8. However, in plant genome, a large number of plant proteins comprising either Bromo-domain or WD40 domain, exhibited a substantial level of...”
- Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana
Chang, Proteomics 2009 - “...synthase (1) At4g14880 99.9 30 Cysteine synthase (1) At3g59760 100 49 Katanin like protein (1) At5g23430 99.6 26 Cell division protein 48 homolog E (1) At5g03340 99.8 26 GIGANTEA protein (1) At1g22770 99.7 26 Serpin (1) At1g62170 99.9 21 Lyase (1) At3g25810 99.9 68 Putative unconventional...”
- Regulon organization of Arabidopsis
Mentzen, BMC plant biology 2008 - “...= -0.73) is At1g06650 (2-oxoglutarate-dependent dioxygenase similar to tomato ethylene synthesis regulatory protein E8) and At5g23430 (transducin family protein with nucleotide binding WD-40 repeat). Another example is At3g11910 (DNA binding ubiquitin-specific protease) and At4g12800 (photosystem I reaction center subunit XI) (R = -0.73). A testable hypothesis...”
AFUA_2G14110 sulfur metabolite repression control protein SconB, putative from Aspergillus fumigatus Af293
30% identity, 31% coverage
- RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
Irmer, BMC genomics 2015 - “...transcriptional regulator of adherence, host cell interactions and virulence; required for wild-type levels of conidiation AFUA_2G14110 sulfur metabolite repression control protein, ortholog(s) have protein binding, bridging, ubiquitin binding activity AFUA_2G14680 flbB Bzip developmental regulator; role in asexual development, gliotoxin production AFUA_2G16230 C2H2 finger domain protein, has...”
- Conservation of nucleosome positions in duplicated and orthologous gene pairs
Nishida, TheScientificWorldJournal 2012 - “...AFUA_2G07570 0.469287567 YOL156W AFUA_7G00950 0.46726022 YGL201C AFUA_5G10890 0.462753539 YKR086W AFUA_1G03820 0.461061937 YPL157W AFUA_6G08610 0.460257721 YIL046W AFUA_2G14110 0.45798838 YGL048C AFUA_4G04660 0.457664607 YHR216W AFUA_2G03610 0.456902272 YDR424C AFUA_1G04850 0.455530713 YPR141C AFUA_2G14280 0.452133975 YLR427W AFUA_1G07150 0.444534443 YHL004W AFUA_1G06570 0.439699159 YLL002W AFUA_5G09540 0.431520497 YKR052C AFUA_6G12550 0.429429023 YNL260C AFUA_1G09000 0.425937756 YNL112W AFUA_2G10750...”
CG3909, NP_649969 uncharacterized protein from Drosophila melanogaster
24% identity, 36% coverage
- EGFR signaling activates intestinal stem cells by promoting mitochondrial biogenesis and β-oxidation
Zhang, Current biology : CB 2022 - “...). Between these binding sites and the mtTFB2 coding sequence, there is another gene ( CG3909 ) on the same strand, which was also up-regulated by PntP1 and PntP2 ( Figures 6B and 6C ). These observations suggest that Pnt activates an enhancer up-stream of mtTFB2....”
- “...PntP1 and PntP2 upstream of mtTFB2 gene. (C-D) PntP1 and PntP2 up-regulated the expression of CG3909 and mtTFB2 by RNASeq. (E-F) mtTFB2 is sufficient to mildly induce ISC proliferation. Confocal images of posterior midgut. Guts were stained for GFP (green), PH3 (red), mtTFB2-HA (white), and with...”
- RNA degradation is required for the germ-cell to maternal transition in Drosophila
Blatt, Current biology : CB 2021 - “...found that ski3 ( CG8777 ) mutant and germline depletion of ski3 and ski8 ( CG3909 ) phenocopied tst mutants ( Figure 1J 1N , S1H S1J ). The conserved GTPase, Hsp70 subfamily B Suppressor (HBS1), is thought to fulfill the role of SKI7 in Drosophila...”
- “...w*;P{UAS-tkv.Q253D.Nb}3/TM3,Sb 1 Ser 1 Bloomington Drosophila Stock Center BDSC: 36536 D. melanogaster : RNAi for CG3909 (Ski8): y 1 sc*v 1 sev 21 ;P{TRiP.HMC04664}attP40 Bloomington Drosophila Stock Center BDSC: 57377 D. melanogaster : RNAi for bam : y 1 v 1 ;P{TRiP.HMJ22155}attP40 Bloomington Drosophila Stock Center...”
- The genetic makeup of the Drosophila piRNA pathway
Handler, Molecular cell 2013 - “...be involved in aspects of RNA Polymerase II biology. For example, the identified factors Atu, CG3909, CG9915, CG40228, and TfIIS are either annotated Paf1 complex members or are linked to TfIIS, a key factor required to rescue backtracked RNA Pol II ( Sims etal., 2004 )....”
- Identification of genetic suppressors of the Sin3A knockdown wing phenotype
Swaminathan, PloS one 2012 - “...Pbp95 CG10488 eyg CG10704 toe CG10390 mia CG43662 Rpb4 CG9461 FBX011 CG7467 osa CG4107 Pcaf CG3909 CG3909 CG5358 Art4 CG1070 Alh CG11033 Kdm2 Signaling CG5974 pII CG11848 Bili CG31110 5PtaseI CG12876 ALiX CG7910 CG7910 Cell Proliferation and Division CG2669 hd CG10061 Sas-4 CG6875 asp CG5814 CycB3...”
- “...chromatin remodeling ( osa ) and histone modification, such as histone acetylation ( Pcaf and CG3909 ) and histone methylation. Interestingly, multiple genes ( Arginine methyltransferase 4 (Art4), Alhambra ( Alh) and Lysine (K)-specific demethylase 2 (Kdm2 )) involved in methylation, including both methyltransferases and demethylases,...”
- Comprehensively surveying structure and function of RING domains from Drosophila melanogaster
Ying, PloS one 2011 - “...Human NP_001121684 is provided with a typical RING/U-box domain (E-value: 1.02e-23); however, its putative ortholog (NP_649969) from Drosophila melanogaster lacks the corresponding domain, resulting in RING/U-box proteins from Drosophila melanogaster having one less than the human ( Table S1 ). With a similar percentage of assignments,...”
- A genomic response to the yeast transcription factor GAL4 in Drosophila
Liu, Fly 2008 - “...bowl + 10/6.87/7.56 0.00623 C2H2 Zn-finger 0027524 CG3909 - 20/26/6.54 0.00750 transcription factor www.landesbioscience.com Fly 95 GAL4-responsive genes in...”
- Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters
Shippy, Development genes and evolution 2008 - “...Tc_00887 , Tc_00664 , Tc_00665 , and Tc_00666 ) and the ortholog of D. melanogaster CG3909 ( Tc_00886 ). We identified the orthologs of these genes in D. melanogaster , Anopheles gambiae , and Apis mellifera and determined their map positions. None of these genes map...”
- Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome
Orban, RNA (New York, N.Y.) 2005 - “...encoded by the uncharacterized Drosophila genes CG8777 and CG3909, respectively. In yeast, the interaction between the exosome and the Ski complex is thought to...”
- “...homolog of Ski7p. In cells depleted of CG8777 or CG3909, but not of HBS1, the adh 5 decay intermediate increased in abundance relative to the full-length...”
- More
XP_006231593 F-box/WD repeat-containing protein 1A isoform X2 from Rattus norvegicus
25% identity, 39% coverage
C6KSR5 Coatomer alpha subunit, putative from Plasmodium falciparum (isolate 3D7)
25% identity, 18% coverage
orf19.3778 putative uncharacterized protein from Candida albicans (see paper)
25% identity, 33% coverage
- CharProtDB CGD description: Predicted ORF in Assemblies 19, 20 and 21; mutation confers hypersensitivity to 5-fluorocytosine (5-FC), 5-fluorouracil (5-FU); downregulated in core stress response; decreased expression in response to prostaglandins
D6WA15 Supernumerary limbs from Tribolium castaneum
24% identity, 39% coverage
Afu6g13030 cell division control protein Cdc4, putative from Aspergillus fumigatus Af293
28% identity, 23% coverage
- The bZIP Transcription Factor HapX Is Post-Translationally Regulated to Control Iron Homeostasis in Aspergillus fumigatus
López-Berges, International journal of molecular sciences 2021 - “...we identified two previously uncharacterized interactors related to protein post-translational modification. The F-box protein Fbx22 (Afu6g13030) and the small ubiquitin-related modifier SumO (Afu1g10850) co-immunoprecipitated with M HapX to different extents ( Figure 4 ). F-box proteins, as part of the SCF complex (Skp, Cullin, F-box containing...”
- “...replace the hapX coding sequence [ 17 ]. For the generation of A. fumigatus fbx22 (Afu6g13030) and sumO (Afu1g10850) deletion mutant strains, targeted replacement cassettes were constructed amplifying DNA fragments flanking both coding sequences and fusing them with the pyrithiamine resistance marker by Gibson assembly [...”
LIS1_DROME / Q7KNS3 Lissencephaly-1 homolog; DLis-1; Dlis1; Lissencephaly1 from Drosophila melanogaster (Fruit fly) (see 6 papers)
NP_477160 Lissencephaly-1, isoform A from Drosophila melanogaster
32% identity, 16% coverage
- function: Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as nuclear migration during cell division, mitotic spindle formation and the removal of mitotic checkpoint proteins from kinetochores at the metaphase to anaphase transition. Required for several aspects of neurogenesis including neuroblast proliferation, neuronal cell differentiation, dendritic growth, branching and maturation and axonal transport. Required for synchronized cell divisions in the germline, fusome integrity and oocyte differentiation. Acts together with BicD, Egl, dynein and microtubules to determine oocyte identity during oogenesis. Also required for nurse cell to oocyte transport during oocyte growth and for the positioning of the nucleus in the oocyte.
subunit: Interacts with dynein and dynactin. Does not interact with Paf-A-Halpha. - Reducing Lissencephaly-1 levels augments mitochondrial transport and has a protective effect in adult Drosophila neurons.
Vagnoni, Journal of cell science 2016 - GeneRIF: lowering levels of Lissencephaly-1 (Lis1), a dynein motor co-factor, augments axonal mitochondrial transport in ageing wing neurons.
- Lissencephaly-1 promotes the recruitment of dynein and dynactin to transported mRNAs.
Dix, The Journal of cell biology 2013 - GeneRIF: The data reveal a critical role for Lis1 within the mRNA localization machinery and suggest a model in which Lis1 facilitates motor complex association with cargos by promoting the interaction of dynein with dynactin.
- Regulation of dynein localization and centrosome positioning by Lis-1 and asunder during Drosophila spermatogenesis.
Sitaram, Development (Cambridge, England) 2012 - GeneRIF: present a model in which Lis-1 and asun cooperate to regulate dynein localization and centrosome positioning during spermatogenesis
- Microtubules and Lis-1/NudE/dynein regulate invasive cell-on-cell migration in Drosophila.
Yang, PloS one 2012 - GeneRIF: A general role of Lis-1/NudE, Dynein and microtubules, in cell-on-cell migration, is reported.
- Lissencephaly-1 controls germline stem cell self-renewal through modulating bone morphogenetic protein signaling and niche adhesion.
Chen, Proceedings of the National Academy of Sciences of the United States of America 2010 - GeneRIF: Lis1, which is widely expressed in adult mammalian tissues, could regulate adult tissue stem cells through modulating niche signaling and adhesion.
- The Drosophila cell adhesion molecule Neuroglian regulates Lissencephaly-1 localisation in circulating immunosurveillance cells.
Williams, BMC immunology 2009 - GeneRIF: Neuroglian regulates the localisation of the nucleokinesis complex protein lissencephaly-1.
- Lis1/dynactin regulates metaphase spindle orientation in Drosophila neuroblasts.
Siller, Developmental biology 2008 - GeneRIF: Mutants in the Lis1/dynactin complex strongly decrease maximum and average spindle velocity, consistent with this motor complex mediating spindle/cortex forces.
- Live imaging of Drosophila brain neuroblasts reveals a role for Lis1/dynactin in spindle assembly and mitotic checkpoint control.
Siller, Molecular biology of the cell 2005 - GeneRIF: We conclude that Lis1/dynactin act together to regulate multiple, independent functions in mitotic cells, including spindle formation and cell cycle checkpoint release.
- Analysis of insect nuclear small heat shock proteins and interacting proteins
Moutaoufik, Cell stress & chaperones 2021 - “...M9PJE4 DmHsp27 P02518 Two-hybrid Giot et al. (2003) Lis1 Q7KNS3 DmHsp27 P02518 Two-hybrid Giot et al. (2003) Lk6 Q9VGI4 DmHsp27 P02518 Two-hybrid Giot et al....”
- Mass spectrometry reveals specific and global molecular transformations during viral infection
Go, Journal of proteome research 2006 - “...(EC 6.3.2.19) O46037 Vinculin Q9VTU3 CG6811-PA(LD02491p) Q7KNS3 Lissencephaly-1 homolog (Lissencephalyl) (Dlis1) (DLis-1) P29845 Heat shock 70 kDa protein...”
all0284 WD-40 repeat protein from Nostoc sp. PCC 7120
24% identity, 16% coverage
NP_001263303 WD repeat-containing protein 38 isoform 1 from Homo sapiens
24% identity, 37% coverage
FBW1A_MOUSE / Q3ULA2 F-box/WD repeat-containing protein 1A; Beta-TrCP protein E3RS-IkappaB; Beta-transducin repeat-containing protein; Beta-TrCP; E3RSIkappaB; mE3RS-IkappaB; F-box and WD repeats protein beta-TrCP; HOS; Ubiquitin ligase FWD1; pIkappaB-E3 receptor subunit from Mus musculus (Mouse) (see 13 papers)
NP_001032847 F-box/WD repeat-containing protein 1A isoform a from Mus musculus
24% identity, 35% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:10097128, PubMed:16371461, PubMed:18782782, PubMed:21911472, PubMed:29593216, PubMed:9859996, PubMed:9990853). Recognizes and binds to phosphorylated target proteins (PubMed:10097128, PubMed:16371461, PubMed:18782782, PubMed:21911472, PubMed:9859996, PubMed:9990853). SCF(BTRC) mediates the ubiquitination of phosphorylated NFKB, ATF4, CDC25A, DLG1, FBXO5, PER1, SMAD3, SMAD4, SNAI1 and probably NFKB2. SCF(BTRC) mediates the ubiquitination of CTNNB1 and participates in Wnt signaling (By similarity). SCF(BTRC) mediates the ubiquitination of NFKBIA, NFKBIB and NFKBIE; the degradation frees the associated NFKB1 to translocate into the nucleus and to activate transcription (PubMed:10097128, PubMed:9859996). Ubiquitination of NFKBIA occurs at 'Lys-21' and 'Lys-22' (PubMed:10097128, PubMed:9859996). The SCF(FBXW11) complex also regulates NF-kappa-B by mediating ubiquitination of phosphorylated NFKB1: specifically ubiquitinates the p105 form of NFKB1, leading to its degradation (By similarity). SCF(BTRC) mediates the ubiquitination of CEP68; this is required for centriole separation during mitosis (By similarity). SCF(BTRC) mediates the ubiquitination and subsequent degradation of nuclear NFE2L1 (PubMed:21911472). Has an essential role in the control of the clock-dependent transcription via degradation of phosphorylated PER1 and PER2 (PubMed:18782782). May be involved in ubiquitination and subsequent proteasomal degradation through a DBB1- CUL4 E3 ubiquitin-protein ligase (By similarity). Required for activation of NFKB-mediated transcription by IL1B, MAP3K14, MAP3K1, IKBKB and TNF (By similarity). Required for proteolytic processing of GLI3 (PubMed:16371461). Mediates ubiquitination of REST, thereby leading to its proteasomal degradation (By similarity). SCF(BTRC) mediates the ubiquitination and subsequent proteasomal degradation of KLF4; thereby negatively regulating cell pluripotency maintenance and embryogenesis (PubMed:29593216). SCF(BTRC) acts as a regulator of mTORC1 signaling pathway by catalyzing ubiquitination and subsequent proteasomal degradation of phosphorylated DEPTOR, TFE3 and MITF (By similarity). SCF(BTRC) directs 'Lys-48'-linked ubiquitination of UBR2 in the T-cell receptor signaling pathway (By similarity).
subunit: Homodimer. Self-associates. Component of the SCF(BTRC) complex, composed of SKP1, CUL1 and BTRC. Direct interaction with SKP1 with SKP1 occurs via the F-box domain. Interacts with phosphorylated ubiquitination substrates SMAD3 and SMAD4. Interacts with phosphorylated ubiquitination substrates CTNNB1, NFKBIA, NFKBIB, NFKBIE, NFKB1/nuclear factor NF-kappa-B p105 subunit, ATF4, CDC25A, DLG1, FBXO5 and SNAI1; the interaction requires the phosphorylation of the 2 serine residues in the substrate destruction motif D-S-G- X(2,3,4)-S. Binds UBQLN1. Interacts with CDC34 and UBE2R2. Interacts with FBXW11. Interacts with CUL4A and DDB1. Part of a SCF(BTRC)-like complex lacking CUL1, which is associated with phosphorylated NKBIA and RELA; RELA interacts directly with NFKBIA. Interacts with the phosphorylated form of GLI3. Interacts with CLU. Interacts with PER1 (phosphorylated), PER2 (phosphorylated) and PER3. Interacts with phosphorylated ubiquitination substrate CEP68 (By similarity). Interacts with ZC3H12A; this interaction occurs when ZC3H12A is phosphorylated in a IKBKB/IKKB-dependent manner (PubMed:22037600). Interacts with HSF1; this interaction occurs during mitosis and induces HSF1 ubiquitin-dependent degradation, a process inhibited by CDC20 (By similarity). Interacts with NFE2L1 (PubMed:21911472). Interacts with INAVA (By similarity). Interacts with IL10RA; this interaction leads to IL10RA ubiquitination and subsequent degradation (By similarity). Interacts with REST (By similarity). Interacts with KLF4; this interaction leads to KLF4 ubiquitination and subsequent degradation (PubMed:29593216). Interacts with UBR2, as part of a SCF(BTRC) complex; the interaction mediates 'Lys-48'-linked ubiquitination of UBR2 and is regulated by DUSP22 in the T-cell receptor signaling pathway (By similarity).
disruption phenotype: Mutants have normal circadian behavior with normal PER2 expression in the suprachiasmatic nucleus. - Novel targets of β-TrCP cooperatively accelerate carbohydrate and fatty acid consumption.
Joo, Journal of cellular physiology 2024 (PubMed)- GeneRIF: Novel targets of beta-TrCP cooperatively accelerate carbohydrate and fatty acid consumption.
- Specific targeting of the NRF2/β-TrCP axis promotes beneficial effects in NASH.
Fernández-Ginés, Redox biology 2024 - GeneRIF: Specific targeting of the NRF2/beta-TrCP axis promotes beneficial effects in NASH.
- Exosomal GPT2 derived from triple-negative breast cancer cells promotes metastasis by activating BTRC.
Cui, Thoracic cancer 2023 - GeneRIF: Exosomal GPT2 derived from triple-negative breast cancer cells promotes metastasis by activating BTRC.
- The β-TrCP-Mediated Pathway Cooperates with the Keap1-Mediated Pathway in Nrf2 Degradation In Vivo.
Kuga, Molecular and cellular biology 2022 - GeneRIF: The beta-TrCP-Mediated Pathway Cooperates with the Keap1-Mediated Pathway in Nrf2 Degradation In Vivo.
- circHIPK3 prevents cardiac senescence by acting as a scaffold to recruit ubiquitin ligase to degrade HuR.
Ding, Theranostics 2022 - GeneRIF: circHIPK3 prevents cardiac senescence by acting as a scaffold to recruit ubiquitin ligase to degrade HuR.
- MK2 promotes Tfcp2l1 degradation via β-TrCP ubiquitin ligase to regulate mouse embryonic stem cell self-renewal.
Zhang, Cell reports 2021 (PubMed)- GeneRIF: MK2 promotes Tfcp2l1 degradation via beta-TrCP ubiquitin ligase to regulate mouse embryonic stem cell self-renewal.
- The role of SCFSkp2 and SCFβ-TrCP1/2 in the cerebellar granule cell precursors.
Yamashita, Genes to cells : devoted to molecular & cellular mechanisms 2020 (PubMed)- GeneRIF: The role of SCF(Skp2) and SCF(beta-TrCP1/2) in the cerebellar granule cell precursors.
- The ubiquitin ligase subunit β-TrCP in Sertoli cells is essential for spermatogenesis in mice.
Morohoshi, Developmental biology 2019 (PubMed)- GeneRIF: Investigated beta-TrCP function in Sertoli cells by generating mice with targeted deletion of the beta-TrCP2 gene in Sertoli cells on a background of whole-body beta-TrCP1 knockout. Loss of beta-TrCP in Sertoli cells caused infertility due to a reduction in the number of mature sperm.
- More
G3I574 F-box/WD repeat-containing protein 1A from Cricetulus griseus
24% identity, 36% coverage
COPA_YEAST / P53622 Coatomer subunit alpha; Alpha-coat protein; Alpha-COP; Retrieval from endoplasmic reticulum protein 1; Secretory protein 22; Suppressor of osmo-sensitivity 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
NP_010136 coatomer subunit alpha from Saccharomyces cerevisiae S288C
YDL145C Alpha subunit of COPI vesicle coatomer complex, which surrounds transport vesicles in the early secretory pathway from Saccharomyces cerevisiae
22% identity, 23% coverage
- function: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin- coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.
subunit: Oligomeric complex that consists of at least the alpha, beta, beta', gamma, delta, epsilon and zeta subunits. Interacts with the ESCRT-0 subunit VPS27. Interacts with KEI1 (via C-terminal region). - Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters
Valentine, Journal of proteome research 2011 - “...QIAFPQR 92.65 1 6 P16862 6 phosphofructokinase subunit beta OS Sa AVAEAIQAK 87.57 1 7 P53622 Coatomer subunit alpha OS Saccharomyces IWDISGLR 95.57 1 6 P12398 Heat shock protein SSC1 mitochondrial OS IIENAEGSR 93.23 3 7 P08524 Farnesyl pyrophosphate synthase OS Sacch IGTDIQDNK 96.31 4 9...”
- COPI mediates recycling of an exocytic SNARE by recognition of a ubiquitin sorting signal.
Xu, eLife 2017 - GeneRIF: These results indicate that ubiquitination, a modification well known to target membrane proteins to the lysosome or vacuole for degradation, can also function as recycling signal to sort a SNARE into COPI vesicles in a non-degradative pathway.
- COPI selectively drives maturation of the early Golgi.
Papanikou, eLife 2015 - GeneRIF: These findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins.
- Crystal structure of alpha-COP in complex with epsilon-COP provides insight into the architecture of the COPI vesicular coat.
Hsia, Proceedings of the National Academy of Sciences of the United States of America 2010 - GeneRIF: analysis of the structure of alpha-COP in complex with epsilon-COP provides insight into the architecture of the COPI vesicular coat
- Mutations in a highly conserved region of the Arf1p activator GEA2 block anterograde Golgi transport but not COPI recruitment to membranes.
Park, Molecular biology of the cell 2005 - GeneRIF: COPI in these mutants is released from Golgi membranes by brefeldin A, a drug that binds directly to guanine nucleotide exchange factor for ADP-ribosylation factor ribosylation factors and blocks Arf1 activation
- Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
Sen, Genome research 2015 - “...ribosome density observed for the corresponding native genes ( YPR159W , YNL101W , YIL090W , YDL145C , YML035C , and YBL102W ) (Supplemental Table S2). One possible explanation for this discrepancy is that Ded1 function is relatively less impaired in ded1-cs cells at the 23C temperature...”
- A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells
Alver, G3 (Bethesda, Md.) 2013 - “...YGR291c COF1 a YLL050c MGA2 YIR033w RFC2 a YJR068w SSD1 YDR293c YKR035C YKR035C COP1 a YDL145c MMR1 YLR190w RFC4 a , b YOL094c STT4 a YLR305c YLR125W YLR125w COT1 YOR316c MMS21 a YEL019c RIC1 YLR039C STU1 a YBL034c YOR008C a YOR008c CSM3 b YMR048w MOB2 a...”
- High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome
Yu, BMC genomics 2012 - “...- - - - - - 5.09 - - - - - - - Mg YDL145C COP1 A - - - - - - 4.41 - - - - - - - Mg YDR188W CCT6 A - - - - - - 5.20 - - -...”
- A comparative analysis of DNA barcode microarray feature size
Ammar, BMC genomics 2009 - “...others knockout sensitive [ 21 - 23 ], overexpressor resistant [ 21 ] to tunicamycin YDL145C COP1 ER to Golgi vesicle-mediated transport and others involved in ER to Golgi vesicle-mediated transport [ 25 ] YGR196C FYV8 unknown knockout sensitive to tunicamycin [ 21 ] YER083C GET2...”
- Endoplasmic reticulum-associated secretory proteins Sec20p, Sec39p, and Dsl1p are involved in peroxisome biogenesis
Perry, Eukaryotic cell 2009 - “...SEC65 YBL050w YBR080c YDR498c YNL287w YDR238c YGL137w YLR078c YDL145c YLR440c YMR013c YLR378c YOR254c YML105c a SED2 ANU3 PIT1 ANU4 BOS1 COPI, RET1, SOO1 PTL1...”
- Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway
Jørgensen, BMC genomics 2009 - “...GEA2 (YEL022w) guanine nucleotide exchange factor on ARF 1.3 6.810 -4 1.310 -2 An16g02460 COP1 (YDL145c) COPI complex, SU 1.4 3.510 -5 1.710 -3 An07g06030 SEC21 (YNL287w) COPI complex, SU 1.4 2.910 -5 1.510 -3 An08g06330 SEC28 (YIL076w) COPI complex, SU 1.5 3.210 -5 1.610 -3...”
MHCKD_DICDI / Q54SF9 Myosin heavy chain kinase D; MHCK-D; EC 2.7.11.7 from Dictyostelium discoideum (Social amoeba) (see paper)
26% identity, 25% coverage
- function: Phosphorylates threonine (By similarity). Not critical for regulating the assembly and disassembly of myosin II filament.
catalytic activity: L-threonyl-[myosin heavy-chain] + ATP = O-phospho-L-threonyl- [myosin heavy-chain] + ADP + H(+) (RHEA:11424)
Tery_0059 serine/threonine protein kinase with WD40 repeats from Trichodesmium erythraeum IMS101
27% identity, 33% coverage
- Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria
Zhang, BMC genomics 2007 - “...CwatDRAFT_2895 cbSTKI-other CwatDRAFT_6269 cbSTKI CwatDRAFT_3022 cbSTKI CwatDRAFT_6420 cbSTKI CwatDRAFT_3184 cbSTKI-TM CwatDRAFT_6607 cbSTKI Trichodesmium erythraeum IMS101 Tery_0059 cbSTKII WD40 (7) Tery_2348 cbSTKI-other Tery_0088 cbSTKII FHA Tery_2556 cbSTKIII GAF, HiskA Tery_0184 cbSTKII WD40 (7) Tery_2609 cbSTKII RDD Tery_0247 cbSTKII DUF323 Tery_2829 cbSTKII DUF323 Tery_0460 cbSTKII DUF323 Tery_2831 cbSTKII...”
G6FXC6 WD40 repeat-containing protein from Fischerella thermalis JSC-11
25% identity, 22% coverage
O76734 General transcriptional corepressor tupA from Dictyostelium discoideum
29% identity, 31% coverage
Tery_2471 peptidase C14, caspase catalytic subunit p20 from Trichodesmium erythraeum IMS101
24% identity, 22% coverage
- The tale of caspase homologues and their evolutionary outlook: deciphering programmed cell death in cyanobacteria
Bhattacharjee, Journal of experimental botany 2020 - “...the transmembrane domain, probably indicating energy-dependent activity of OCAs. Nevertheless, three putative cytoplasmic OCAs consisting Tery_2471, AMI_G0162, and Ava_2184 also have an AAA_16 domain providing NTPase and chaperone activities. The prevalence of abhydrolase, a domain having serine protease-like activity due to the catalytic triad of Ser,...”
- “...a single strain, such as Ava_2184, Ava_3246, and Ava_3079 from A. variabilis ATCC 2943 or Tery_2471, Tery_1841, and Tery_2760 from T. erythraeum IMS101, is apparently explained by multiple independent HGT events during the course of evolution. However, the tree displayed two distinct OCA clusters denoting YN...”
KTN83_ARATH / F4KB17 Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.3 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G08390 hypothetical protein from Arabidopsis thaliana
25% identity, 25% coverage
- function: May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity). Microtubule severing may promote rapid reorganization of cellular microtubule arrays (By similarity). Confers precision to microtubule (MT) severing by specific targeting of KTN1 to MT cleavage sites such as crossover or branching nucleation sites (PubMed:28978669). Together with other KTN80s, regulates cell elongation by modulating MT organization (PubMed:28978669).
subunit: Component of KTN80-KTN1 complexes composed of a hexamer of KTN1-KTN80 heterodimers that sense microtubule (MT) geometry to confer precise MT severing (PubMed:28978669). Interacts directly with AAA1/KTN1 and KTN80.1, and weakly with KTN80.4 (PubMed:28978669).
disruption phenotype: The double mutant ktn80.3 ktn80.4 exhibits normal growth, but the quadruple mutant ktn80.1 ktn80.2 ktn80.3 ktn80.4 has a severe dwarf phenotype, with small and round dark-green rosette leaves as well as wide and short petioles, probably due to cell elongation defects, and associated with a complex cortical microtubule (MT) network with stable entanglements (PubMed:28978669). Plants missing KTN80s have a disruption of KTN1 recruitment at MT crossover or branching nucleation sites, leading to an abolishment of MT severing (PubMed:28978669). - KTN80 confers precision to microtubule severing by specific targeting of katanin complexes in plant cells
Wang, The EMBO journal 2017 - “...four loci encoding katanin p80 subunits, At1G11160, At1G61210, At5G08390, and At5G23430, which we designated the encoded katanin subunits KTN80.1, 2, 3, and 4,...”
- “...KTN80-encoding genes KTN80.1 (At1g11160), KTN80.2 (At1g61210), KTN80.3 (At5g08390), and KTN80.4 (At5g23430), we first generated the ktn80.12 double mutants and...”
- Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination
Srivastava, PloS one 2015 - “...other plants encompass more than 200 putative WD40 domain containing proteins [ 57 ]. Arabidopsis At5g08390 and At5g23430 displayed protein similarity with corresponding S . cerevisiae SPT8. However, in plant genome, a large number of plant proteins comprising either Bromo-domain or WD40 domain, exhibited a substantial...”
- Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein
Mahfouz, Plant molecular biology 2012 - “...twofold across all dHax3.SRDX lines. The repressed genes that contain the binding box (ATX1, AT2G07280, AT5G08390, AAP6, AT2G41230, ATTAP1, AT5G45580, LTI78) are shown in blue boxes and their relative distance from the transcriptional start is shown at left and the nucleotides that bind to the NS...”
- Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce
Porth, PloS one 2012 - “...WS0097_H22 0.092 1.7E30 AT4G25500 ATRSP35 (Arabidopsis thaliana arginine/serine-rich splicing factor 35) transcriptional/posttranscriptional WS00910_O08 0.096 7.00E048 AT5G08390 similar to transducin family protein/WD-40 repeat family protein [Arabidopsis thaliana] transcriptional/posttranscriptional WS00815_A12 0.099 7.20E120 AT1G20110 zinc finger (FYVE type) family protein transcriptional/posttranscriptional WS01031_K02 0.102 1.80E139 AT3G26935 zinc finger (DHHC type)...”
- Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes
Jung, BMC genomics 2006 - “...flavonoid 3'-monooxygenase PP_LEa0007M11f FxT-G3F AT5G07340 calnexin PP_LEa0006I23f AT5G08470 peroxisome biogenesis protein (PEX1) PP_LEa0001O24f gp126 3 AT5G08390 transducin family protein PP_LEa0010I06f TxE-G1 AT5G07990 flavonoid 3'-monooxygenase PP_LEa0007M11f AT5G07340 calnexin PP_LEa0006I23f gp128 4 AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f TxE-G2 AT5G46870 RNA recognition motif (RRM)-containing protein PP_LEa0027L14f AT5G47810...”
Q177S9 Beta'-coat protein (Fragment) from Aedes aegypti
24% identity, 27% coverage
8ro1T / G5EEL2 8ro1T (see paper)
27% identity, 21% coverage
CNAG_02153 glucose repression regulatory protein TUP1 from Cryptococcus neoformans var. grubii H99
24% identity, 35% coverage
- The Role of Testosterone and Gibberellic Acid in the Melanization of Cryptococcus neoformans
Tucker, Frontiers in microbiology 2020 - “...melanization in C. neoformans ( Lee et al., 2007 ; Eisenman et al., 2011 ) CNAG_02153 TUP1 3.25 CNAG_03465 LAC1 592.34 Gene responsible for the synthesis of melanin in C. neoformans ( Eisenman et al., 2007 ) 1 Fold changes reflect the differences between testosterone versus...”
- Comparative Ecology of Capsular Exophiala Species Causing Disseminated Infection in Humans
Song, Frontiers in microbiology 2017 - “...Pascon et al., 2004 PV08_04416T0 HMPREF1120_05363T0 CNAG_02029 WSP1 Hypo Shen et al., 2011 PV08_03067T0 N/A CNAG_02153 TUP1 Hyper Lee et al., 2009 PV08_11209T0 HMPREF1120_04775T0 CNAG_02215 HAP3 Hypo Jung et al., 2010 PV08_04195T0 N/A CNAG_02236 PPG1 Hypo Gerik et al., 2005 PV08_01602T0 HMPREF1120_01040T0 CNAG_02702 GEF1 Hypo Zhu...”
NP_001185277 Transducin/WD40 repeat-like superfamily protein from Arabidopsis thaliana
24% identity, 21% coverage
KTN82_ARATH / F4HTH8 Katanin p80 WD40 repeat-containing subunit B1 homolog KTN80.2; DDB1 binding WD40 hypersensitive to ABA 3; DWD hypersensitive to ABA 3 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
24% identity, 20% coverage
- function: May participate in a complex which severs microtubules in an ATP-dependent manner (By similarity). Microtubule severing may promote rapid reorganization of cellular microtubule arrays (By similarity). Confers precision to microtubule (MT) severing by specific targeting of KTN1 to MT cleavage sites such as crossover or branching nucleation sites (PubMed:28978669). Together with other KTN80s, regulates cell elongation by modulating MT organization (PubMed:28978669). Negative regulator of abscisic acid (ABA) responses (PubMed:21421380). May function as a substrate receptor for cullin-RING ubiquitin ligase 4 complexes (CRL4), a family of E3 ligases involved in protein degradation (PubMed:21421380).
subunit: Component of KTN80-KTN1 complexes composed of a hexamer of KTN1-KTN80 heterodimers that sense microtubule (MT) geometry to confer precise MT severing (PubMed:28978669). Interacts directly with AAA1/KTN1 (PubMed:28978669). Interacts with subunits of the CUL4-based E3 ligase complex DDB1A and DDB1B (PubMed:21421380).
disruption phenotype: Hyper-induction of abscisic acid (ABA)-inducible transcription factors (e.g. ABI5 and MYC2) and their downstream genes in response to ABA (PubMed:21421380). Increased sensitivity to ABA and salt stress leading to reduced root length and increased dehydration tolerance (PubMed:21421380). The double mutant ktn80.1 ktn80.2 exhibits normal growth, but the quadruple mutant ktn80.1 ktn80.2 ktn80.3 ktn80.4 has a severe dwarf phenotype, with small and round dark-green rosette leaves as well as wide and short petioles, probably due to cell elongation defects, and associated with a complex cortical microtubule (MT) network with stable entanglements (PubMed:28978669). Plants missing KTN80s have a disruption of KTN1 recruitment at MT crossover or branching nucleation sites, leading to an abolishment of MT severing (PubMed:28978669).
AT1G61210 WD-40 repeat family protein / katanin p80 subunit, putative from Arabidopsis thaliana
24% identity, 21% coverage
- Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae
Liu, Plant communications 2024 - “...AT4G27730 AT4G24740 AT4G27540 B3 AT1G27290 AT1G30755 AT1G27320 AT1G30755 B4 AT1G30757 AT1G32750 AT1G30760 AT1G32750 CBK2 D2 AT1G61210 AT1G56210 AT1G61210 AT1G56230 D1 AT1G64670 AT1G61215 AT1G64670 AT1G61240 E1 AT1G64960 AT1G67270 AT1G65020 AT1G67260 E2 AT1G67280 AT1G71100 AT1G67530 AT1G71100 E3 AT1G71110 AT1G78310 AT1G71110 AT1G78310 E4 AT1G78320 AT1G79720 AT1G78380 AT1G79720 E5 AT1G79730...”
- ABA Mediates Plant Development and Abiotic Stress via Alternative Splicing
Yang, International journal of molecular sciences 2022 - “...interacted with U2AF35 to mediate the splicing of HAB1 (AT1G72770, ABA signal regulator) and DWA3 (AT1G61210, ABA signal regulator), affecting salt and drought stress [ 79 ]. LUC7 is a subunit of U1 snRNP in plants that respond to both ABA and abiotic stresses. LUC7 interacts...”
- KTN80 confers precision to microtubule severing by specific targeting of katanin complexes in plant cells
Wang, The EMBO journal 2017 - “...has four loci encoding katanin p80 subunits, At1G11160, At1G61210, At5G08390, and At5G23430, which we designated the encoded katanin subunits KTN80.1, 2, 3, and...”
- “...the four KTN80-encoding genes KTN80.1 (At1g11160), KTN80.2 (At1g61210), KTN80.3 (At5g08390), and KTN80.4 (At5g23430), we first generated the ktn80.12 double...”
- Composition, roles, and regulation of cullin-based ubiquitin e3 ligases
Choi, The arabidopsis book 2014 - “...et al., 2010). A third member of the DWA family, DWA3 (At1g61210), is also able to interact with DDB1b and CUL4 (Lee et al., 2011). Although it was suggested to...”
- “...ABA signaling, salt tolerance Lee et al 2010 DWA3 AT1G61210 ABA signaling Lee et al 2011 FY At5g13480 Flowering, autonomous promotion pathway Lee et al 2008...”
XP_001657383 coatomer subunit beta' isoform X2 from Aedes aegypti
23% identity, 27% coverage
KTNB1_MOUSE / Q8BG40 Katanin p80 WD40 repeat-containing subunit B1; Katanin p80 subunit B1; p80 katanin from Mus musculus (Mouse) (see 3 papers)
Q8BG40 microtubule-severing ATPase (subunit 1/2) (EC 5.6.1.1) from Mus musculus (see paper)
XP_006531475 katanin p80 WD40 repeat-containing subunit B1 isoform X1 from Mus musculus
26% identity, 29% coverage
- function: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation. Microtubule release from the mitotic spindle poles may allow depolymerization of the microtubule end proximal to the spindle pole, leading to poleward microtubule flux and poleward motion of chromosome. The function in regulating microtubule dynamics at spindle poles seems to depend on the association of the katanin KATNA1:KATNB1 complex with ASPM which recruits it to microtubules. Reversely KATNA1:KATNB1 can enhance ASPM blocking activity on microtubule minus-end growth. Microtubule release within the cell body of neurons may be required for their transport into neuronal processes by microtubule-dependent motor proteins. This transport is required for axonal growth.
subunit: Interacts with KATNA1. This interaction enhances the microtubule binding and severing activity of KATNA1 and also targets this activity to the centrosome (PubMed:16203747). This interaction is weakly competed by KATNBL1 which has a lower affinity for it (By similarity). Interacts with ASPM; the katanin complex formation KATNA1:KATNB1 is required for the association of ASPM (PubMed:28436967). Interacts with dynein, microtubules, NDEL1 and PAFAH1B1 (PubMed:16203747). Interacts with KATNAL1; this interaction is weakly competed by KATNBL1 which has a lower affinity for it (By similarity). Interacts with CAMSAP2 and CAMSAP3; leading to regulate the length of CAMSAP-decorated microtubule stretches (By similarity).
disruption phenotype: Homozygous loss of the gene is embryonic lethal. Mutant animals have dramatically reduced body size, reduced limb bud outgrowth, microphthalmia to anophthalmia and forebrain abnormalities ranging from microcephaly to holoprosencephaly. Brains of mutant mice have reduced cycling and proliferating radial neuroepithelial progenitor cells compared to wild-type, with a more profound loss of cells that depend upon asymmetrical cell divisions. These cells also show evidence of increased apoptosis. - KATNB1 is a master regulator of multiple katanin enzymes in male meiosis and haploid germ cell development.
Dunleavy, Development (Cambridge, England) 2021 (PubMed)- GeneRIF: KATNB1 is a master regulator of multiple katanin enzymes in male meiosis and haploid germ cell development.
- Crystal Structure of a Heterotetrameric Katanin p60:p80 Complex.
Faltova, Structure (London, England : 1993) 2019 (PubMed)- GeneRIF: Study uncovered an unexpected role of the p60-MIT and p80-CTD domains of katanin in the oligomerization and regulation of the protein. p80-CTD mediates the assembly of p60-MIT:p80-CTD heterodimers into heterotetramers that have an impact on katanin MT end and lattice binding as well as on the severing activity of the enzyme. The heterotetrameric structure of the p60-MIT:p80-CTD K555A/R591A mutant revealed a domain swap.
- Mutations in the Katnb1 gene cause left-right asymmetry and heart defects.
Furtado, Developmental dynamics : an official publication of the American Association of Anatomists 2017 (PubMed)- GeneRIF: Katnb1 is ubiquitously expressed during embryonic development, although a stronger expression is seen in the crown cells of the gastrulation organizer, the murine node. Furthermore, null and hypomorphic Katnb1 gene mutations show a novel correlation between Katnb1 dysregulation and the development of impaired left-right signaling, including cardiac malformations.
- Structural basis of katanin p60:p80 complex formation.
Rezabkova, Scientific reports 2017 - GeneRIF: This study structurally and functionally characterized the interaction between the two katanin subunits that is mediated by the p60-MIT domain and the p80 C-terminal domain (p80-CTD). p60-MIT and p80-CTD form a tight heterodimeric complex, whose high-resolution structure was determined by X-ray crystallography.
- An essential role for katanin p80 and microtubule severing in male gamete production.
O'Donnell, PLoS genetics 2012 - GeneRIF: Collectively these data demonstrate that katanin p80 serves an essential and evolutionarily conserved role in several aspects of male germ cell development
- The Cul3/Klhdc5 E3 ligase regulates p60/katanin and is required for normal mitosis in mammalian cells.
Cummings, The Journal of biological chemistry 2009 - GeneRIF: Cul3-deficient cells or Ctb9/KLHDC5-deficient cells show an increase in p60/katanin levels, indicating that Cul3/Ctb9/KLHDC5 is required for efficient p60/katanin removal
XP_570974 general transcriptional repressor, putative from Cryptococcus neoformans var. neoformans JEC21
XP_570974 general transcriptional repressor from Cryptococcus neoformans var. neoformans JEC21
24% identity, 35% coverage
- TUP1 disruption reveals biological differences between MATa and MATalpha strains of Cryptococcus neoformans.
Lee, Molecular microbiology 2005 (PubMed)- GeneRIF: Disruption of the TUP1 gene, which encodes a global repressor, reveals non-mating-related biological differences between MAT-alpha and MATa strains. [TUP1]
- The general transcriptional repressor Tup1 is required for dimorphism and virulence in a fungal plant pathogen
Elías-Villalobos, PLoS pathogens 2011 - “...the following accession numbers: S. cerevisiae Tup1p, NP_010007; C. albicans Tup1, AAB63195; C. neoformans Tup1, XP_570974; P. marneffei TupA, AAL99251; N. crassa Rco-1, AAB37245; A. nidulans TupA ACD46267; S. pombe Tup11, NP_592873; S. pombe Tup12, NP_592910. Supporting Information Figure S1 Sequence alignment of Tup1 proteins from...”
KTNB1_HUMAN / Q9BVA0 Katanin p80 WD40 repeat-containing subunit B1; Katanin p80 subunit B1; p80 katanin from Homo sapiens (Human) (see 8 papers)
NP_005877 katanin p80 WD40 repeat-containing subunit B1 from Homo sapiens
26% identity, 29% coverage
- function: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation. Microtubule release from the mitotic spindle poles may allow depolymerization of the microtubule end proximal to the spindle pole, leading to poleward microtubule flux and poleward motion of chromosome. Microtubule release within the cell body of neurons may be required for their transport into neuronal processes by microtubule-dependent motor proteins. This transport is required for axonal growth.
subunit: Interacts with PAFAH1B1 (By similarity). Interacts with KATNA1 (PubMed:10751153, PubMed:26929214). This interaction enhances the microtubule binding and severing activity of KATNA1 and also targets this activity to the centrosome (PubMed:10751153). This interaction is weakly competed by KATNBL1 which has a lower affinity for it (PubMed:26929214). Interacts with ASPM; the katanin complex formation KATNA1:KATNB1 is required for the association of ASPM (By similarity). Interacts with dynein, microtubules and NDEL1 (PubMed:16203747). Interacts with KATNAL1; this interaction is weakly competed by KATNBL1 which has a lower affinity for it (PubMed:26929214). Interacts with CAMSAP2 and CAMSAP3; leading to regulate the length of CAMSAP-decorated microtubule stretches (PubMed:24486153). - Models, Regulations, and Functions of Microtubule Severing by Katanin
Ghosh, ISRN molecular biology 2012 - “...p60491 p80655 p60-PRK04195 (209265), AAA (241382), Vps4_C (456489), p80-WD40 (7257), Con80 (492652) p60: AAC25114 p80: NP_005877 Spastin Homo sapiens 584 MIT (116195), AAA (313476) AAI50261 Fidgetin Homo sapiens 759 AAA (519654), Vps4_C (707756) NP_060556 Lipotransin Mus musculus 491 PRK04195 (211265) AAA (241382) Vps4_C (456489) AAD42087 Katanin-like...”
- “...B motif NCBI accession number Homo sapiens 491 655 241382 249256 304309 p60: AAC25114 p80: NP_005877 Xenopus laevis 486 351 238 379 246253 301306 p60: AAD53310 p80: AAC25113 Arabidopsis thaliana 523 836 271414 279286 334339 p60: AEE36390 p80: AED93167 Drosophila melanogaster 571 823 325462 333340 388393...”
- Pathogenic variants in autism gene KATNAL2 cause hydrocephalus and disrupt neuronal connectivity by impairing ciliary microtubule dynamics.
DeSpenza, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...p80 WD40 repeat-containing subunit B1 (KTNB1_HUMAN) was obtained from the Alphafold database with accession number Q9BVA0. The downloaded structure accounted for residues 1 to 655.The pathogenic variants were constructed, and the free energy of change calculated (G) in silico using the ICM mutagenesis program ( https://www.molsoft.com...”
- A novel nanobody as therapeutics target for EGFR-positive colorectal cancer therapy: exploring the effects of the nanobody on SW480 cells using proteomics approach
Lamtha, Proteome science 2022 - “...Ratio: R9VH36/Con p -value: R9VH36/Con Q8IVF2 Protein AHNAK2 0 100 1.78E 16 100 1.51E 16 Q9BVA0 Katanin p80 WD40 repeat-containing subunit B1 0.001 100 1.78E 16 100 1.51E 16 P02042 Hemoglobin subunit delta 0 0.728 3.01E 02 25.327 1.51E 16 Q5VZ66 Janus kinase and microtubule-interacting protein...”
- The Mammalian Family of Katanin Microtubule-Severing Enzymes
Lynn, Frontiers in cell and developmental biology 2021 - “...subunitsA1 (UniProt ID: O75449), AL1 (UniProt ID: Q9BW62), AL2 (UniProt ID: Q8IYT4), B1 (UniProt ID: Q9BVA0), and BL1 [UniProt ID: Q9H079 (human)]and their corresponding domains are displayed. For each human katanin subunit, the relative percent identity to full-length (FL) and to each domain therein is indicated...”
- Proteomic Analysis of the Mammalian Katanin Family of Microtubule-severing Enzymes Defines Katanin p80 subunit B-like 1 (KATNBL1) as a Regulator of Mammalian Katanin Microtubule-severing
Cheung, Molecular & cellular proteomics : MCP 2016 (no snippet) - Oxidative stress induced carbonylation in human plasma
Madian, Journal of proteomics 2011 - “...Biotinylated methyl glyoxal adduct Extracellular 62,5 1.31 6.6 Q9BVA0 |KTNB1_HUMAN Katanin p80 WD40-containing subunit B1 HUMAN 6 0.3 0.2 2.7E02 ND Cytoplasm...”
Q4VFZ4 Katanin p80 WD40 repeat-containing subunit B1 from Rattus norvegicus
26% identity, 29% coverage
- Exogenous L-lactate administration in rat hippocampus increases expression of key regulators of mitochondrial biogenesis and antioxidant defense
Akter, Frontiers in molecular neuroscience 2023 - “...Nudcd3 2.2524 0.0109 Up NudC domain-containing 3 G3V963 Tmem132a 2.1615 0.0091 Up RCG47487, isoform CRA_b Q4VFZ4 Katnb1 1.8478 0.0406 Up Katanin p80 WD40 repeat-containing subunit B1 Q9WVI4 Gucy1a2 1.8243 0.0031 Up Guanylate cyclase soluble subunit alpha-2 M0R608 Rtn1 1.8214 0.0184 Up Reticulon A0A0G2JTK4 Ppp6r1 1.7173 0.0127...”
- Peptidomic Analysis of Rat Plasma: Proteolysis in Hemorrhagic Shock.
Aletti, Shock (Augusta, Ga.) 2016 - “...P23764 Gpx3 chymotrypsin-like YVGRPLVSQYNV 13.72 Q9WUW3 Cfi elastase-like FDWISYYVGRPLVSQYNV Q9WUW3 Cfi FRLLGNMIV P02091 Hbb MATPVVTKTAWKLQEIV Q4VFZ4 Katnb1 FAIEEYSAPFSSDSEQGNA 6.87 Q63041 A1m elastase-like/MMPs YPSKPDNPGEDAPAEDMA 4.16 P07808 Npy elastase-like/MMPs FLSRLMSPEEKPAPAA 1.92 P04638 Apoa2 elastase-like/MMPs AAGTLYTYPENWRAFKALIA Q68FR6 Eef1g elastase-like/MMPs AEVVFTANDSGHRHYTIA P02767 Ttr elastase-like/MMPs AGQAFRKFLPLFDRVLVERSA P26772 Hspe1 elastase-like/MMPs ASDPILYRPVA P11980...”
- “...alpha-trypsin inhibitor, heavy chain 4 Q5EBC0 Itih4 x x Katanin p80 WD40 repeat-containing subunit B1 Q4VFZ4 Katnb1 x x Potassium channel subfamily T member 1 F1LSG1 Kcnt1 x x Kinesin-like protein B1WC01 Kif20a x x Keratin, type II cytoskeletal 6A Q4FZU2 Krt6a x x Lymphocyte cytosolic...”
XP_017456690 katanin p80 WD40 repeat-containing subunit B1 isoform X2 from Rattus norvegicus
26% identity, 29% coverage
KTNB1_XENLA / Q4V7Y7 Katanin p80 WD40 repeat-containing subunit B1; Katanin p80 subunit B1; p80 katanin from Xenopus laevis (African clawed frog) (see paper)
30% identity, 21% coverage
- function: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation.
subunit: Interacts with katna1. This interaction enhances the microtubule binding and severing activity of katna1 and also targets this activity to the centrosome.
CDC4_YEAST / P07834 Cell division control protein 4; E3 ubiquitin ligase complex SCF subunit CDC4; F-box protein CDC4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 15 papers)
NP_116585 SCF ubiquitin ligase complex subunit CDC4 from Saccharomyces cerevisiae S288C
YFL009W Cdc4p from Saccharomyces cerevisiae
25% identity, 30% coverage
- function: Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes and binds to phosphorylated target proteins. Directs ubiquitination of the phosphorylated CDK inhibitor SIC1. Involved in the degradation of CDC6 together with CDC34/UBC3 and CDC53, and in restricting the degradation of FAR1 to the nucleus. Is essential for initiation of DNA replication and separation of the spindle pole bodies to form the poles of the mitotic spindle. It also plays a role in bud development, fusion of zygotic nuclei after conjugation and various aspects of sporulation. Required for HTA1-HTB1 locus transcription activation. Required for G1/S and G2/M transition.
subunit: Interacts with DCD53 and SKP1. Component of the SCF(CDC4) complex containing CDC53, SKP1, RBX1 and CDC4. CDC34. Interacts with CDC6 and CIC1. Interacts with SIC1; the interaction involves a SIC1 double phosphorylated motif (degron). Homodimerizes; the dimerization increases SIC1 ubiquitination in vitro. - Redundant targeting of Isr1 by two CDKs in mitotic cells.
Alme, Current genetics 2021 - GeneRIF: Redundant targeting of Isr1 by two CDKs in mitotic cells.
- Cdc4 phospho-degrons allow differential regulation of Ame1CENP-U protein stability across the cell cycle.
Böhm, eLife 2021 - GeneRIF: Cdc4 phospho-degrons allow differential regulation of Ame1(CENP-U) protein stability across the cell cycle.
- Skp, Cullin, F-box (SCF)-Met30 and SCF-Cdc4-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A for Chromosomal Stability in Budding Yeast.
Au, PLoS genetics 2020 - GeneRIF: Study revealed that two essential Skp, Cullin, F-box (SCF) ubiquitin ligases defined by the F-box proteins Met30 and Cdc4 cooperatively regulate Cse4 (S. cerevisiae homolog of human centromere protein-A (CENP-A)) proteolysis under normal physiological conditions. Results suggest SCF-Met30/Cdc4-mediated proteolysis of Cse4 is one of the major mechanisms that prevents stable maintenance of Cse4 at non-centromeric regions.
- An allosteric conduit facilitates dynamic multisite substrate recognition by the SCFCdc4 ubiquitin ligase.
Csizmok, Nature communications 2017 - GeneRIF: An allosteric conduit facilitates dynamic multisite substrate recognition by the SCF ubiquitin ligase.
- The anaphase-promoting complex works together with the SCF complex for proteolysis of the S-phase cyclin Clb6 during the transition from G1 to S phase.
Wu, Fungal genetics and biology : FG & B 2016 (PubMed)- GeneRIF: Our observations suggest that both APC(Cdh1) and SCF(Cdc4)-dependent proteolysis of Clb6 at the G1/S border are crucial for multiple cell cycle regulated events including proper expression of Clb2, the G1/S and G2/M cell cycle transitions and for proper completion of cell division at mitotic exit.
- Regulation of the histone deacetylase Hst3 by cyclin-dependent kinases and the ubiquitin ligase SCFCdc4.
Delgoshaie, The Journal of biological chemistry 2014 - GeneRIF: an intricate coordination between Hst3 synthesis, genome-wide H3K56 deacetylation by Hst3, and cell cycle-regulated degradation of Hst3 by cyclin-dependent kinases and SCF(Cdc4).
- Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase.
Tang, Proceedings of the National Academy of Sciences of the United States of America 2012 - GeneRIF: Individually weak dispersed Sic1 phospho sites engage Cdc4 in a dynamic equilibrium. The multisite nature of this interaction confers cooperative dependence on kinase activity for Sic1 recognition
- F-box protein specificity for g1 cyclins is dictated by subcellular localization.
Landry, PLoS genetics 2012 - GeneRIF: we show that Cln3 is redundantly targeted by two F-box proteins with key cell cycle-regulatory roles, Cdc4 and Grr1
- More
- Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes
Stefanini, International journal of environmental research and public health 2022 - “...( RDS1 -YCR106W), a protein required for the progression of the cell cycle ( CDC4 -YFL009W), and a protein controlling telomere length ( RIF2 -YLR453C). Furthermore, two additional genes (YPR195C and YPR197C) with unknown functions, located in the same region of chromosome XVI where the ARR...”
- Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network
Shen, PloS one 2017 - “...ydr404c GO:0003899 0.722 2.17e-45 5 ypr110c ypr190c yor116c yfl023w yer162c yel048c ypr187w ynl113w yjr132w yjl076w yfl009w ydl116w ypr010c yor341w yor340c yor210w yor207c yol021c ynl248c ynl186w ynl151c yjr063w yjl011c yhr143w-a ydr156w ydl150w ydl042c ybr154c ydr045c ynr003c ykl144c GO:0003899 0.667 4.12e-40 24 ynl113w ypr190c ypr187w ypr010c yor116c ynr003c...”
- “...ynr003c ykl144c GO:0003899 0.704 1.25e-39 10 ypr110c ypr190c yor116c yfl023w yel048c ypr187w ynl113w yjr132w yjl076w yfl009w yor340c yor210w yor207c yol021c ynl248c ynl186w ynl151c ykr025w yjr063w yjl011c yhr143w-a ydr156w ydl150w ybr154c ydr045c ynr003c ydl042c ykl144c GO:0003899 0.667 8.83e-39 18 yor210w ypr187w ypr190c ypr110c yor340c yor151c yor116c ynl113w...”
- An efficient method for protein function annotation based on multilayer protein networks
Zhao, Human genomics 2016 - “...GO:0000055, GO:0000082, GO:0000086, GO:0000122, and GO:0000209, which were derived from YBR234C, YJL112W, YKL021C, YDR267C, YDR364C, YFL009W, YLR055C, and YIL046W, respectively. All of these proteins have at least one domain with YGL100W. So, we can draw a conclusion that we cannot predict functions for the protein YGL100W...”
- Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism
Wildenhain, Scientific data 2016 - “...degradation Null mutant is inviable, temperature sensitive mutant arrests at G1/S with multiple buds S000002461 YFL009W CDC4 + F-box protein required for G1/S and G2/M transition, associates with Skp1p and Cdc53p to form a complex, SCFCdc4, which acts as ubiquitin-protein ligase directing ubiquitination of the phosphorylated...”
- A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis
Ziv, Molecular & cellular proteomics : MCP 2011 - “...cytosol + YMR275C BUL1 3.9 Ubiquitin-binding component of the Rsp5p E3-ubiquitin ligase complex + + YFL009W CDC4 3.9 F-box protein required for G1/S and G2/M transition YDR320C SWA2 3.9 Auxilin-like protein involved in vesicular transport + YOL038W PRE6 3.9 20S proteasome alpha-type subunit YEL037C RAD23 3.9...”
- Systematic analysis of essential genes reveals important regulators of G protein signaling
Cappell, Molecular cell 2010 - “...PIK1 f Phosphatidylinositol-4- kinase; may control cytokinesis through actin cytoskeleton Yes 88.3% 4.9% 5.82 0.05 YFL009W CDC4 F-Box protein; component of the SCF ubiquitin ligase Yes 46.1% 3.1% 5.40 0.03 YDR054C CDC34 E2 ubiquitin conjugating enzyme; component of the SCF ubiquitin ligase Yes 6.2% 0.2% 5.98...”
- Markov logic networks in the analysis of genetic data
Sakhanenko, Journal of computational biology : a journal of computational molecular cell biology 2010 - “...S YFL037W, TUB2 M YFL033C, RIM15 M YFL029C, CAK1 M YFL009W, CDC4 M YFL005W, SEC4 S YBR180W, DTR1 S YBR186W, PCH2 M YKR029C, SET3 M YKR031C, SPO14 S YCR033W,...”
- Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling
Li, PloS one 2008 - “...HUL5 YGL141W UFD4 YKL010C RSP5 YER125W F BOX COS111 YBR203W SAF1 YBR280C MFB1 YDR219C CDC4 YFL009W MET30 YIL046W YJL149W RCY1 YJL204C GRR1 YJR090C HRT3 YLR097C YLR224W YLR352W MDM30 YLR368W UFO1 YML088W SKP2 YNL311C DIA2 YOR080W ELA1 YNL230C AMN1 YBR158W CTF13/CBF3 YMR094W RAD7 YJR052W YDR306C YMR258C BTB...”
- More
C0P165 Transcriptional repressor Tup1 N-terminal domain-containing protein from Ajellomyces capsulatus (strain G186AR / H82 / ATCC MYA-2454 / RMSCC 2432)
28% identity, 31% coverage
AFUA_5G13140 WD repeat-containing protein from Aspergillus fumigatus Af293
26% identity, 35% coverage
- Conservation of nucleosome positions in duplicated and orthologous gene pairs
Nishida, TheScientificWorldJournal 2012 - “...AFUA_8G01340 0.536753536 YGL119W AFUA_6G04380 0.528264148 YDR054C AFUA_5G09200 0.520282879 YNR036C AFUA_5G10750 0.51817226 YJL050W AFUA_4G07160 0.517374235 YKR036C AFUA_5G13140 0.515007541 YML041C AFUA_2G05030 0.514819597 YML080W AFUA_1G16550 0.512494533 YJL093C AFUA_1G14250 0.5107227 YDR238C AFUA_1G10970 0.509749906 YJL197W AFUA_2G14130 0.501902821 YER173W AFUA_8G02820 0.501581347 YJR160C AFUA_8G01340 0.499250408 YOL058W AFUA_2G04310 0.497155736 YGR006W AFUA_1G16990 0.496383573 YPR161C AFUA_5G05510...”
WDR5A_ARATH / Q9M2Z2 COMPASS-like H3K4 histone methylase component WDR5A; AtWDR5A from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
NP_190535 Transducin/WD40 repeat-like superfamily protein from Arabidopsis thaliana
AT3G49660 transducin family protein / WD-40 repeat family protein from Arabidopsis thaliana
25% identity, 32% coverage
- function: Forms multiple COMPASS-like complexes involved in histone methylation by interacting with different histone H3 'Lys-4' methyltransferases such as ATX1, SDG14 or SDG16 (PubMed:21423667). Binds to target loci chromatin, increasing H3K4 trimethylation and causing activation of the gene (PubMed:19567704). Up-regulates FLC and MAF4 expression to delay flowering (PubMed:19567704). Present at the promoters and at the transcription start sites (TSS) regions of WRKY70 and LTP7; this occupancy is ATX1-dependent (PubMed:23284292). Involved in the transition from transcription initiation to transcription elongation (PubMed:23284292).
subunit: Part of a complex composed of TRO, RBL and WDR5A (PubMed:21423667). This complex is formed during both vegetative and reproductive development (PubMed:21423667). Interacts with SDG14, SDG16, RBL, but not with TRO (PubMed:21423667). Interacts with ATX1 and K4-methylated H3 tails (PubMed:19567704).
disruption phenotype: Eearly flowering (PubMed:23284292). Decreased TATA-binding protein (TBP) levels lower Ser5P Pol II levels near the transcription start sites (TSSs) of target genes and of Pol II at the genes 3'-ends thus affecting the transition from transcription initiation to transcription elongation (PubMed:23284292). Significantly reduced trimethylated 'Lys-4' of histone H3 (H3K4me3) levels at the 5'- ends of WRKY70 and LTP7 genes leading to reduced transcript accumulation (PubMed:23284292). - WDR5a functions in cadmium-inhibited root meristem growth by regulating nitric oxide accumulation in Arabidopsis.
Zhang, Planta 2020 (PubMed)- GeneRIF: WDR5a functions in cadmium-inhibited root meristem growth by regulating nitric oxide accumulation in Arabidopsis.
- WD40-REPEAT 5a represses root meristem growth by suppressing auxin synthesis through changes of nitric oxide accumulation in Arabidopsis.
Liu, The Plant journal : for cell and molecular biology 2018 (PubMed)- GeneRIF: WDR5a role in controlling root meristem size in Arabidopsis.WDR5a affects auxin levels in roots by modulating the accumulation of nitric oxide.
- Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA.
Zhao, Nature communications 2018 - GeneRIF: MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3
- WD40-REPEAT 5a functions in drought stress tolerance by regulating nitric oxide accumulation in Arabidopsis.
Liu, Plant, cell & environment 2017 (PubMed)- GeneRIF: WDR5a functions as a novel factor to modulate nitric oxide synthase-like activity for changes of nitric oxide accumulation and stomatal closure in drought stress tolerance.
- Transcription factor interaction with COMPASS-like complex regulates histone H3K4 trimethylation for specific gene expression in plants.
Song, Proceedings of the National Academy of Sciences of the United States of America 2015 - GeneRIF: bZIP28 and bZIP60 interact with Ash2 and WDR5a, both of which are core COMPASS-like components.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_200424 No hit DDB0233537 fSAP57 SMU1 NP_060695 NP_650766 NP_177513 NP_014082 DDB0233739 fSAP35 THOC6 NP_077315 NP_648557 NP_190535 No hit DDB0233741 MGC4238 WDR83 NP_115708 NP_609782 NP_193325 No hit Cap binding proteins DDB0233457 CBP80 NCBP1 NP_002477 NP_726938 NP_565356 NP_013844 DDB0233456 CBP20 NCBP2 NP_031388 NP_524396 NP_199233 NP_015147 Polyadenylation machinery DDB0233359...”
- Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis.
Jiang, The Plant cell 2009 - GeneRIF: WDR5a directly interacts with an H3K4 methyltransferase, ARABIDOPSIS TRITHORAX1.
- The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings
Koskimäki, Tree physiology 2022 - “...it shares similarity with WD-repeat protein-like of P. pinaster (DR092239) that corresponds to Arabidopsis ATWDR5a (AT3G49660), which is associated with auxin signaling and root growth ( Liu etal. 2018 ). The second one, 2507324313 , has similarity with Caenorhabditis elegans miR-790 stem-loop and mature miRNA structures,...”
- Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction
Fang, Frontiers in plant science 2021 - “...PHD-BAH JMJ14 At4g20400 KDM5/JARID1-JMJs ATX5 SDG29 At5g53430 SHL At4g39100 JMJ15 At2g34880 ATXR3 SDG2 At4g15180 WDR5a At3g49660 WD40 repeats JMJ16 At1g08620 ATXR7 SDG25 At5g42400 MRG1/2 At4g37280/At1g02740 Chromo domain JMJ17 At1g63490 ASHR3 SDG4 At4g30860 Class II ASH1-SDG EML1 At3g12140 Tudor domain JMJ18 At1g30810 ASHH1 SDG26 At1g76710 MSH6 At4g02070...”
- Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility
Lanaud, Journal of experimental botany 2017 - “...Tc01_g007270 is homologous to the COMPASS-like H3K4 histone methylase component WDR5a from A. thaliana ( At3g49660 ). It is a transducin WD-40 repeat-containing protein acting as a site of proteinprotein interactions and plays central roles in biological processes ( Stirnimann et al. , 2010 ). It...”
- WD40-Repeat Proteins in Plant Cell Wall Formation: Current Evidence and Research Prospects
Guerriero, Frontiers in plant science 2015 - “...wall AT1G65580 FRA3 III Cell wall AT3G50590 TWD40-1 III Cell wall AT5G45760 WDR53 III Unknown AT3G49660 WDR5 I Histone methylation AT5G27030 TPR3 II Chromatin regulation AT3G21060 RBL II Histone methylation AT3G49180 RID3 III Pre-rRNA processing AT1G03060 SPIRRIG, SPI III Membrane; RNA processing Biotechnological Prospects: WDR Proteins...”
- The complexity of vesicle transport factors in plants examined by orthology search
Paul, PloS one 2014 - “...Khan et al, 2013 [44] A. thaliana protein localization Plants with plastid-localized orthologue COP-II Sec13 At3g49660 Plastid Plastid Plastid * 8 of 14 Sec13 At2g43770 - Plastid Cyto * - Sec31 At1g68690 - - Plastid * 12 of 14 Sec31 At5g38560 Plastid Plastid PM a -...”
- “...29 (co-)orthologues for Sec13 and Sec31 in plants, respectively. Previously, two of the Sec13 (At2g43770, At3g49660) have been assigned as chloroplast proteins [141] , [177] , while we predict an additional chloroplast-localized protein (At1g68690; Table 8 ). However, contradicting to the previously described chloroplast localization for...”
- New putative chloroplast vesicle transport components and cargo proteins revealed using a bioinformatics approach: an Arabidopsis model
Khan, PloS one 2013 - “...117.7 3/5 Sec24b (At4g32640) * 306 (29/49) 4e90 82 1 116.3 3/5 Sec13 (33.0) Sec13a (At3g49660) * 68.2 (28/43) 8e15 78 1 34.8 3/5 Sec13b (At2g43770) 76.3 (26/41) 2e17 94 1 37.9 5/5 Sec31 (138.7) Sec31a (At5g38560) * N.I N.I N.I 5 72.4 1/5 Sec31b (At2g45000)...”
- “...the TAIR proteome (At3g01340 and At2g30050), and the best matches from the TAIR chloroplast proteome (At3g49660 and At2g43770). (RTF) Click here for additional data file. Figure S3 A multiple sequence alignment including three putative chloroplast cargo receptor proteins (At1g72150, At4g09160, and At1g22530), and two other proteins...”
- ATX1-generated H3K4me3 is required for efficient elongation of transcription, not initiation, at ATX1-regulated genes
Ding, PLoS genetics 2012 - “...1. Genes used in this study have the following IDs: ATX1 ( At2g31650 ), WDR5a (At3g49660), AtASH2 (At1g51450), AtRbBp5 (At3g21060), TBP(At3g13445) , W RKY70 ( AT3G56400 ), LTP7 ( AT2G15050 ). Yeast two-hybrid assay The AH190 strain was transformed with one of the following bait constructs:...”
- Computing gene expression data with a knowledge-based gene clustering approach
Rosa, International journal of biochemistry and molecular biology 2010 (secret)
LIS1_EMENI / Q00664 Nuclear distribution protein nudF; Lissencephaly-1 homolog; LIS-1; Nuclear migration protein nudF from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see 6 papers)
nudF / GB|AAA91301.1 nuclear distribution protein nudF from Emericella nidulans (see 5 papers)
XP_663801 dynein regulator nudF from Aspergillus nidulans FGSC A4
26% identity, 31% coverage
- function: Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for nuclear migration during vegetative growth as well as development. Required for retrograde early endosome (EE) transport from the hyphal tip. Required for localization of dynein to the mitotic spindle poles. Recruits additional proteins to the dynein complex at SPBs.
subunit: Interacts with dynein (By similarity). Self-associates. Interacts with bnfA, nudC and nudE. - CharProtDB Description: protein involved in nuclear migration; mutants are defective in asexual and sexual sporulation; similar to human LIS-1 (Miller-Dieker lissencephaly-1); interacts directly with NudC; localizes to spindle-pole bodies; Source:AspGD
- The nuclear migration protein NUDF/LIS1 forms a complex with NUDC and BNFA at spindle pole bodies.
Helmstaedt, Eukaryotic cell 2008 - GeneRIF: These results show that the conserved NUDF and NUDC proteins play a concerted role at spindle pole bodies (SPBs) at different stages of the cell cycle and that NUDF recruits additional proteins specifically to the dynein complex at SPBs.
TUP11_SCHPO / Q09715 Transcriptional repressor tup11 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 3 papers)
tup11 transcriptional corepressor Tup11 from Schizosaccharomyces pombe (see 5 papers)
NP_592873 transcriptional corepressor Tup11 from Schizosaccharomyces pombe
NP_592873, SPAC18B11.10 transcriptional corepressor Tup11 from Schizosaccharomyces pombe
25% identity, 37% coverage
- function: Transcriptional repressor
subunit: Interacts with fep1. Binds to histones H3 and H4. - CharProtDB Source (per GeneDB): GeneDB_Spombe
- Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast
Fagerström-Billai, Molecular and cellular biology 2005 - “...(CAC81004); Dictostelium discodeum, Tup1 (AAC29438); S. pombe, Tup11 (Q09715); and S. pombe, Tup12 (Q9UUG8). Full-length protein sequences were used in Fig. 1A...”
- Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast.
Sprague, The EMBO journal 2000 (no snippet) - The LAMMER kinase homolog, Lkh1, regulates Tup transcriptional repressors through phosphorylation in Schizosaccharomyces pombe.
Kang, The Journal of biological chemistry 2010 - GeneRIF: The LAMMER kinase homolog, Lkh1, regulates Tup11,12 transcriptional repressors through phosphorylation in Schizosaccharomyces pombe.
- WD40 domain divergence is important for functional differences between the fission yeast Tup11 and Tup12 co-repressor proteins.
Ferreira, PloS one 2010 - GeneRIF: Tup11 and Tup12 proteins in fission yeasts thus provide an excellent model system for studying the functional divergence of WD40 repeat domains
- Individual subunits of the Ssn6-Tup11/12 corepressor are selectively required for repression of different target genes.
Fagerström-Billai, Molecular and cellular biology 2007 - GeneRIF: Ssn6, Tup11, and Tup12 are preferentially found at genomic locations at which histones are deacetylated, primarily by the Clr6 class I histone deacetylases.
- Reciprocal nuclear shuttling of two antagonizing Zn finger proteins modulates Tup family corepressor function to repress chromatin remodeling.
Hirota, Eukaryotic cell 2006 - GeneRIF: Tup11 and Tup12 persist in the nucleus and bind to the fbp1+ promoter under both derepressed and repressed conditions
- Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast.
Fagerström-Billai, Molecular and cellular biology 2005 - GeneRIF: The transcriptional corepressors Tup11 and Tup12 have retained the ability to interact with the Ssn6 protein and with each other, but they also have some distinct functions. Tup12 has evolved a specialized role in stress response regulation. [Tup11]
- The general transcriptional repressor Tup1 is required for dimorphism and virulence in a fungal plant pathogen
Elías-Villalobos, PLoS pathogens 2011 - “...P. marneffei TupA, AAL99251; N. crassa Rco-1, AAB37245; A. nidulans TupA ACD46267; S. pombe Tup11, NP_592873; S. pombe Tup12, NP_592910. Supporting Information Figure S1 Sequence alignment of Tup1 proteins from different organisms. Different conserved domains are indicated. The U. maydis Tup1, S. cerevisiae Tup1p, C. albicans...”
- Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast
Fagerström-Billai, Molecular and cellular biology 2005 - “...medium. The tup11 and tup12 open reading frame (SPAC18B11.10 and SPAC620.14c, respectively) and the ssn6 open reading frame (SPAC23E6.09) were tagged by a...”
- Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism
Borkovich, Microbiology and molecular biology reviews : MMBR 2004 - “...NP_595227; 8.00e-46 Penicillium marneffei; 1.00e-167 S. pombe NP_592873; 1.00e-117 06411.1 03593.1 No hits below 1e-05 Podospora anserina CAC16792; 0.00 03070.1...”
- Transcriptional regulators of the Schizosaccharomyces pombe fbp1 gene include two redundant Tup1p-like corepressors and the CCAAT binding factor activation complex
Janoo, Genetics 2001 - “...of the tup11 and tup12 genes: The tup11 ORF (SPAC18B11.10, accession no. Z50728) was disrupted using a PCR-based approach as described by Bahler et al. (1998)....”
- Conservation of histone binding and transcriptional repressor functions in a Schizosaccharomyces pombe Tup1p homolog
Mukai, Molecular and cellular biology 1999 - “...identified by the S. pombe genome project. This sequence, SPAC18B11.10, is located on chromosome I and is termed tup11. Since the S. pombe tup11 sequence also...”
Npun_R6612 WD-40 repeat-containing protein from Nostoc punctiforme
26% identity, 23% coverage
- New β-Propellers Are Continuously Amplified From Single Blades in all Major Lineages of the β-Propeller Superfamily
Pereira, Frontiers in molecular biosciences 2022 - “...diversification. The most symmetric -propeller known to date is that of the WRAP domain in Npun_R6612 from the cyanobacterium Nostoc punctiforme PCC73102, with only 10 point mutations across 14 predicted blades ( Chaudhuri et al., 2008 ; Dunin-Horkawicz et al., 2014 ). The near identity of...”
- “...sequences collected are of the WD40 superfamily, to which WRAP belongs. The WRAP domain in Npun_R6612 of Nostoc punctiforme PCC 73102 was the -propeller with the highest internal sequence symmetry we had found up to that point and contains no synonymous substitutions at the DNA level...”
- Structural diversity of oligomeric β-propellers with different numbers of identical blades
Afanasieva, eLife 2019 - “...to another highly symmetric -propeller of the WD40 family, found in the C-terminal part of Npun_R6612 from the multicellular cyanobacterium Nostoc punctiforme PCC 73102 and referred to henceforth as WRAP (WD40-family Recently Amplified Propeller; ACC84870.1). WRAP, which we identified during a systematic bioinformatic survey of -propellers...”
- “...other single-blade constructs, obtained no folding. 10.7554/eLife.49853.005 Figure 2. The recently amplified WRAP propeller in Npun_R6612 of Nostoc punctiforme PCC73102. ( A ) Multiple sequence alignment of the 14 blades of WRAP. Non-identical repeats are colored in red and the non-repeating -strand 4 of the velcro...”
- Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study
Hu, Scientific reports 2017 - “...repeats can be regarded as forming two typical WD40 domains. For example, B2J0I0_NOSP7 (Gene symbol: Npun_R6612 , PDB ID: 2YMU, Zeth, et al . unpublished), containing 14 repeats, forms two WD40 domains (Supplementary Fig. S1c ). Accordingly, the number of repeats of a WD40 protein can...”
CNA06710 ubiquitin-protein ligase from Cryptococcus neoformans var. neoformans JEC21
23% identity, 30% coverage
PRP46_SCHPO / O13615 Pre-mRNA-splicing factor prp5; Complexed with cdc5 protein 1; Pre-mRNA-processing protein 5 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 3 papers)
prp5 / GI|13810226 WD repeat protein Prp5 from Schizosaccharomyces pombe (see 3 papers)
SPBP22H7.07 WD repeat protein Prp5 from Schizosaccharomyces pombe
29% identity, 31% coverage
- function: Required for both cell cycle progression at G2/M and pre-mRNA splicing. Interacts genetically with the PRP4 kinase.
subunit: Belongs to the 40S cdc5-associated complex (or cwf complex), a spliceosome sub-complex reminiscent of a late-stage spliceosome composed of the U2, U5 and U6 snRNAs and at least brr2, cdc5, cwf2/prp3, cwf3/syf1, cwf4/syf3, cwf5/ecm2, spp42/cwf6, cwf7/spf27, cwf8, cwf9, cwf10, cwf11, cwf12, prp45/cwf13, cwf14, cwf15, cwf16, cwf17, cwf18, cwf19, cwf20, cwf21, cwf22, cwf23, cwf24, cwf25, cwf26, cyp7/cwf27, cwf28, cwf29/ist3, lea1, msl1, prp5/cwf1, prp10, prp12/sap130, prp17, prp22, sap61, sap62, sap114, sap145, slu7, smb1, smd1, smd3, smf1, smg1 and syf2. - CharProtDB Source (per GeneDB): GeneDB_Spombe
- Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex
Weigt, Epigenetics & chromatin 2021 - “...(predicted) SPBC119.13c Prp31 U4/U6 U5 tri-snRNP complex subunit Prp31 SPBC16H5.10c Prp43 ATP-dependent RNA helicase Prp43 SPBP22H7.07 Prp5 WD repeat protein Prp5 SPAC227.12 Rna4 U4/U6 U5 tri-snRNP complex subunit Prp4 family, Rna4 SPAC19G12.07c Rsd1 RNA-binding protein Rsd1 (predicted) SPAC22A12.09c Sap114 U2 snRNP subunit Sap114 SPBC29A3.07c Sap14 U2...”
- A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast
Bayne, Genome biology 2014 - “...prp17 31.7 63.1 SPAC10F6.02c prp22 31.7 131.5 SPCC188.11 cwf13 28.7 62.7 SPBC13E7.01 cwf22 25.0 102.7 SPBP22H7.07 prp5 23.0 52.4 SPAC3A12.11c cwf2 19.3 44.3 SPCC550.02c cwf5 17.3 39.6 SPBC1289.11 spf38 16.3 37.4 SPAC29A4.08c prp19 15.0 54.2 SPBC3E7.13c syf2 14.7 28.0 SPBC337.06c cwf15 14.7 30.4 SPBC32F12.05c cwf12 13.7...”
- Poly(A) tail-mediated gene regulation by opposing roles of Nab2 and Pab2 nuclear poly(A)-binding proteins in pre-mRNA decay
Grenier, Molecular and cellular biology 2013 - “...SPBC1289.11 SPAC27D7.07c SPBC16H5.10c SPAC26A3.08 SPBC19C2.14 SPBP22H7.07 SPBC1861.08c SPAC22A12.09c SPBC3E7.14 SPAC22F8.10c SPBC4B4.09 SPBC337.06c 54.2 274.6...”
B2RQS1 Striatin, calmodulin binding protein 3 from Mus musculus
NP_001165569 striatin-3 isoform 2 from Mus musculus
25% identity, 37% coverage
- Modulation of calcium signaling depends on the oligosaccharide of GM1 in Neuro2a mouse neuroblastoma cells.
Lunghi, Glycoconjugate journal 2020 - “...V member 1 Trpv1 Q9WTR1 Transient receptor potential cation channel subfamily V member 2 Trpv2 B2RQS1 Striatin-3 Strn3 V9GXI9 Striatin-4 Strn4 P48455 Serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform Ppp3cc P63328 Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform Ppp3ca A0A087WQ44 Snf2-related CREBBP activator protein Srcap Q9QVP9...”
- Molecular modeling and molecular dynamics simulations based structural analysis of the SG2NA protein variants.
Soni, BMC research notes 2014 - “...protein variants (35kDa, 78kDa, and 87kDa) were retrieved from UNIPROT (IDs: B3STQ1 [ 4 ], B2RQS1 [ 15 ] and Q9ERG2 [ 2 ] respectively). These SG2NA sequences were used to screen similar sequences with known 3D structures against Protein Data Bank (PDB) using NCBIs BLAST...”
- “...properties of three SG2NA isoforms Sequence variant 35kDa 78kDa 87kDa Accession number (from Uniprot) B3STQ1 B2RQS1 Q9ERG2 Molecular formula C 1480 H 2325 N 429 O 454 S 6 C 3426 H 5339 N 947 O 1081 S 20 C 3825 H 5995 N 1069 O...”
- Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia.
Zhang, Blood 2023 (PubMed)- GeneRIF: Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia.
- Ectopic expression of 35 kDa and knocking down of 78 kDa SG2NAs induce cytoskeletal reorganization, alter membrane sialylation, and modulate the markers of EMT.
Gupta, Molecular and cellular biochemistry 2021 (PubMed)- GeneRIF: Ectopic expression of 35 kDa and knocking down of 78 kDa SG2NAs induce cytoskeletal reorganization, alter membrane sialylation, and modulate the markers of EMT.
- SG2NA is a regulator of endoplasmic reticulum (ER) homeostasis as its depletion leads to ER stress.
Jain, Cell stress & chaperones 2017 - GeneRIF: Cell cycle analysis suggested that while loss of SG2NA reduces the level of cyclin D1 and retains a population of cells in the G1 phase, concurrent ER stress facilitates their exit from G1 and traverse through subsequent phases with concomitant cell death. Thus, SG2NA is a component of intrinsic regulatory pathways that maintains ER homeostasis
- GSK3β and ERK regulate the expression of 78 kDa SG2NA and ectopic modulation of its level affects phases of cell cycle.
Pandey, Scientific reports 2017 - GeneRIF: In cells depleted from striatin, calmodulin binding protein 3 (SG2NA) by shRNA, the levels of glycogen synthase kinase 3 beta (pGSK3beta) and pERK are reduced, suggesting that these kinases and SG2NA regulate each other's expression.
- Tissue specific expression of SG2NA is regulated by differential splicing, RNA editing and differential polyadenylation.
Jain, Gene 2015 (PubMed)- GeneRIF: Results suggest a highly versatile and dynamic mode of regulation of SG2NA with potential implications in tissue development.
- SG2NA enhances cancer cell survival by stabilizing DJ-1 and thus activating Akt.
Tanti, Biochemical and biophysical research communications 2015 (PubMed)- GeneRIF: results demonstrate that XBP1 mRNA splicing plays an important role in maintaining the function of bone marrow-derived macrophages and provide new insight into the study and treatment of atherosclerosis
- SG2NA recruits DJ-1 and Akt into the mitochondria and membrane to protect cells from oxidative damage.
Tanti, Free radical biology & medicine 2014 (PubMed)- GeneRIF: SG2NA associates with the antioxidant protein DJ-1 and the survival kinase Akt resulting in resistance to apoptosis induced by oxidative stress.
- WD-40 repeat protein SG2NA has multiple splice variants with tissue restricted and growth responsive properties.
Sanghamitra, Gene 2008 (PubMed)- GeneRIF: Taken together, splicing variation of SG2NA might have some critical roles in differentiation and maturation in metazoan cells.
TTHERM_00497660 katanin con80 domain protein from Tetrahymena thermophila SB210
28% identity, 25% coverage
- Microtubule-severing enzymes
Roll-Mecak, Current opinion in cell biology 2010 - “...thaliana T. thermophila T. brucei P80 katanin canonical KATNB1 CG13956 F47G4.4 AT5G08390 AT5G23430 AT1G11160 AT1G61210 TTHERM_00497660 Tb09.211.1500 WD40less C15orf29 MEI-2 F47G4.5 P60 katanin canonical KATNA1 KATNAL1 CG10229 MEI-1 AT1G80350 TTHERM_00322760 Tb11.01.0200 Tb10.70.6880 lisH KATNAL2 CG10793 TTHERM_00414230 Tb11.02.1370 orphan CG1193 spastin SPAST CG5977 SPAS-1 AT2G45500 TTHERM_01128570 Tb927.3.1440...”
P58405 Striatin-3 from Rattus norvegicus
NP_001025068 striatin-3 from Rattus norvegicus
25% identity, 35% coverage
- iTRAQ-based proteomics analysis on insomnia rats treated with Mongolian medical warm acupuncture
Xu, Bioscience reports 2020 - “...D3ZIC4 Protein phosphatase 1 regulatory subunit 0.797201943 0.006803938 Q3KR51 HMP19 protein, isoform CRA_a 0.813904866 0.009560059 P58405 Striatin-3 0.811684263 0.015950492 Q4KLX9 Protein Ccdc163 0.716197358 0.016416855 D3ZWP8 Protein Lrrc58 0.756999583 0.017218939 Q5UAJ6 Cytochrome c oxidase subunit 2 0.735583341 0.021848769 A0A0G2K7Z3 Acyl-coenzyme A thioesterase 1 0.824303275 0.024433777 P15205 Microtubule-associated...”
- Preliminary quantitative profile of differential protein expression between rat L6 myoblasts and myotubes by stable isotope labeling with amino acids in cell culture.
Cui, Proteomics 2009 - “...2 protein IPI00231216.1 1.55NA 1 Q9QY17 124461 Striatin, calmodulin binding protein 3 IPI00476338.2 2.370.19 4 P58405 114520 Translocon-associated protein gamma subunit IPI00196589.2 1.67NA 1 Q08013 81784 A-kinase anchor protein 11 IPI00210194.1 1.84NA 1 Q62924 498549 Protein Synthesis 3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor IPI00202658.1 2.05NA 1 P29266 63938...”
- In the Rat Midbrain, SG2NA and DJ-1 have Common Interactome, Including Mitochondrial Electron Transporters that are Comodulated Under Oxidative Stress.
Bisoyi, Cellular and molecular neurobiology 2023 (PubMed)- GeneRIF: In the Rat Midbrain, SG2NA and DJ-1 have Common Interactome, Including Mitochondrial Electron Transporters that are Comodulated Under Oxidative Stress.
- Striatin-3 gamma inhibits estrogen receptor activity by recruiting a protein phosphatase.
Tan, Journal of molecular endocrinology 2008 (PubMed)- GeneRIF: A rat STRN3 gamma-protein phosphatase 2A complex is recruited to agonist-activated estrogen receptor alpha, thereby leading to its dephosphorylation and inhibiting transcription.
7ajtUA / P25635 structure of the 90S-exosome super-complex (state Pre-A1-exosome) (see paper)
24% identity, 39% coverage
6lqsB1 / P25635 structure of 90S small subunit preribosomes in transition states (State D) (see paper)
24% identity, 40% coverage
XP_001684560 activated protein kinase c receptor (LACK) from Leishmania major strain Friedlin
Q4Q7Y7 Activated protein kinase c receptor from Leishmania major
XP_001684561 activated protein kinase c receptor (LACK) from Leishmania major strain Friedlin
31% identity, 19% coverage
Q76LS6 LACK from Leishmania donovani
P62884 Small ribosomal subunit protein RACK1 from Leishmania infantum
LDBPK_282970 activated protein kinase c receptor (LACK) from Leishmania donovani
31% identity, 19% coverage
STRN3_MOUSE / Q9ERG2 Striatin-3; Cell cycle autoantigen SG2NA; S/G2 antigen from Mus musculus (Mouse) (see paper)
25% identity, 35% coverage
- function: Calmodulin-binding scaffolding protein which is the center of the striatin-interacting phosphatase and kinase (STRIPAK) complexes. STRIPAK complexes have critical roles in protein (de)phosphorylation and are regulators of multiple signaling pathways including Hippo, MAPK, nuclear receptor and cytoskeleton remodeling. Different types of STRIPAK complexes are involved in a variety of biological processes such as cell growth, differentiation, apoptosis, metabolism and immune regulation.
subunit: Tetramerizes. Part of the core of STRIPAK complexes composed of PP2A catalytic and scaffolding subunits, the striatins (PP2A regulatory subunits), the striatin-associated proteins MOB4, STRIP1 and STRIP2, PDCD10 and members of the STE20 kinases, such as STK24 and STK26. The STRIPAK complex can be extended by adapter proteins such as SLMAP:SIKE1 or CTTNBP2NL. Interacts with CDC42BPB. - PKA-independent vasopressin signaling in renal collecting duct.
Datta, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2020 - “...Mitotic interactor and substrate of PLK1 G L QR S LS*SDC I LS 0.59 2.67 Q9ERG2 Strn3 S202 Striatin-3 RSQRVRS*LLGLSN 0.58 2.95 Q3UHI0 Ccser2 S222 Serine-rich coiled-coil domain-containing protein 2 K M VR S QS*FSHSIQ 0.58 2.66 P19001 Krt19 S59 Keratin, type I cytoskeletal 19 VTSSSGS*YGGVRG...”
- Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition
Mahadevan, eLife 2017 - “...0.98 X X SNRPA Q62189 4.0 0.96 X STOML2 Q99JB2 4.0 0.96 X X STRN3 Q9ERG2 4.0 0.96 X YWHAQ P68254 4.0 0.78 X X INA P46660 3.6 1 X X ATP6V1F Q9D1K2 3.5 0.95 X X DCTN2 Q99KJ8 3.5 1 X X X CD47 Q61735...”
- Integrated analysis of proteome and transcriptome changes in the mucopolysaccharidosis type VII mouse hippocampus
Parente, Molecular genetics and metabolism 2016 - “...predicted gene 12350 Q9D8S9 Bola1 bolA-like 1 (E. coli) Q9D8T7 Slirp RIKEN cDNA 1810035L17 gene Q9ERG2 Strn3 striatin, calmodulin binding protein 3 Q9ERU9 Ranbp2 RAN binding protein 2 Q9JKL4 Ndufaf3 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3 Q9JL26 Fmnl1 formin-like 1 Q9QWY8 Asap1 similar...”
- Molecular modeling and molecular dynamics simulations based structural analysis of the SG2NA protein variants.
Soni, BMC research notes 2014 - “...87kDa) were retrieved from UNIPROT (IDs: B3STQ1 [ 4 ], B2RQS1 [ 15 ] and Q9ERG2 [ 2 ] respectively). These SG2NA sequences were used to screen similar sequences with known 3D structures against Protein Data Bank (PDB) using NCBIs BLAST program [ 16 ]. Primary...”
- “...of three SG2NA isoforms Sequence variant 35kDa 78kDa 87kDa Accession number (from Uniprot) B3STQ1 B2RQS1 Q9ERG2 Molecular formula C 1480 H 2325 N 429 O 454 S 6 C 3426 H 5339 N 947 O 1081 S 20 C 3825 H 5995 N 1069 O 1216...”
- Spatio-temporal analysis of molecular determinants of neuronal degeneration in the aging mouse cerebellum
de, Molecular & cellular proteomics : MCP 2013 - “...proteins P28651 CARP Q3TGF2 Fam107b Q99K30 EPS8-LP2 Q9ERG2 P62748 Striatin-3 Hpcal1 Q61704 Q9ERQ8 Q8BKX1 ITI-HC3 CA-VII BAI-ap2 Q1RLL3 Q9CRD4 Q80ZW2 Q3UVC0...”
XP_416167 apoptotic protease-activating factor 1 isoform X1 from Gallus gallus
27% identity, 19% coverage
TTHERM_01345820 coatomer alpha subunit, putative from Tetrahymena thermophila SB210
22% identity, 22% coverage
- Mismatch Repair Protein Msh6Tt Is Necessary for Nuclear Division and Gametogenesis in Tetrahymena thermophila
Wang, International journal of molecular sciences 2023 - “...protein with proton transmembrane transporter activity; TTHERM_00295120, a vacuolar protein sorting-associated protein 35 containing protein; TTHERM_01345820, a protein that is involved in intracellular protein translocation; TTHERM_00101160, a nucleoporin; endoplasmic reticulum membrane proteins TTHERM_00043890 and TTHERM_00772030 with transglycosylase activity; and TTHERM_00418280, a metalloendopeptidase, is involved in proteolysis....”
- Microarray analyses of gene expression during the Tetrahymena thermophila life cycle
Miao, PloS one 2009 - “...in order of their locations on the scaffold with TTHERM_01345750 located at one end and TTHERM_01345820 at the other end. Stages are as described in Materials and Methods . The physiological significance of the fragmentation of the small number of micronuclear chromosomes to give numerous, smaller...”
Q9BIJ5 LACK protective antigen from Leishmania donovani
31% identity, 19% coverage
5t2a7 / Q9BIJ5 5t2a7 (see paper)
31% identity, 19% coverage
D2XMQ7 Beta-TCRP E3 ligase from Saccoglossus kowalevskii
23% identity, 33% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory