Family Search for PF04502 (Saf4_Yju2)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF04502 hits 21 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
YJU2_DANRE / A8WHR3 Splicing factor YJU2 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_001104303 coiled-coil domain-containing protein 94 from Danio rerio
Aligns to 9:341 / 345 (96.5%), covers 100.0% of PF04502, 397.7 bits
- function: Part of the spliceosome which catalyzes two sequential transesterification reactions, first the excision of the non-coding intron from pre-mRNA and then the ligation of the coding exons to form the mature mRNA. Plays a role in stabilizing the structure of the spliceosome catalytic core and docking of the branch helix into the active site, producing 5'-exon and lariat intron-3'-intermediates (By similarity). May protect cells from TP53-dependent apoptosis upon dsDNA break damage through association with PRP19-CD5L complex (PubMed:22952453).
subunit: Component of the spliceosome. Present in the activated B complex, the catalytically activated B* complex which catalyzes the branching, the catalytic step 1 C complex catalyzing the exon ligation, and the postcatalytic P complex containing the ligated exons (mRNA) and the excised lariat intron.
disruption phenotype: Morpholino knockdown of the protein causes small head and a curled tail by day 2. Knockdown causes increased sensitivity to IR-induced apoptosis (PubMed:22952453). In double morpholino knockdown of TP53 and YJU2, TP53 deficiency rescues animals from developmental neurodegeneration observed on YJU2 mutants and radiosensitivity (PubMed:22952453). - Ccdc94 protects cells from ionizing radiation by inhibiting the expression of p53.
Sorrells, PLoS genetics 2012 - GeneRIF: Ccdc94 and the Prp19 complex protect cells from IR-induced apoptosis by repressing the expression of p53 mRNA
YJU2_HUMAN / Q9BW85 Splicing factor YJU2; Coiled-coil domain-containing protein 94 from Homo sapiens (Human) (see 2 papers)
NP_060544 splicing factor YJU2 from Homo sapiens
Aligns to 9:318 / 323 (96.0%), covers 100.0% of PF04502, 388.7 bits
- function: Part of the spliceosome which catalyzes two sequential transesterification reactions, first the excision of the non-coding intron from pre-mRNA and then the ligation of the coding exons to form the mature mRNA (PubMed:29301961). Plays a role in stabilizing the structure of the spliceosome catalytic core and docking of the branch helix into the active site, producing 5'-exon and lariat intron-3'- intermediates (By similarity). May protect cells from TP53-dependent apoptosis upon dsDNA break damage through association with PRP19-CD5L complex (PubMed:22952453).
subunit: Component of the spliceosome (PubMed:29301961). Present in the activated B complex, the catalytically activated B* complex which catalyzes the branching, the catalytic step 1 C complex catalyzing the exon ligation, and the postcatalytic P complex containing the ligated exons (mRNA) and the excised lariat intron (By similarity). Identified in the spliceosome C complex; in the complex interacts directly with PRP16 (PubMed:29301961). - Intratumoral decorin gene delivery by AAV vector inhibits brain glioblastomas and prolongs survival of animals by inducing cell differentiation.
Ma, International journal of molecular sciences 2014 - “...down 11 360 O75608 APT1 Acyl-protein thioesterase 1 24.6/6.3 26/6.5 6 28.7 down 12 266 Q9BW85 CCDC94 Coiled-coil domain-containing protein 94 37/5.8 35/5.9 4 21.4 up...”
- 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_001036597 NP_194285 No hit DDB0233566 fSAPc C19orf29 NP_067054 NP_523422 NP_171887 No hit DDB0233745 FLJ10374 CCDC94 NP_060544 NP_611092 NP_173156 NP_012828 DDB0233752 RRP6 EXOSC10 NP_001001998 NP_001097795 NP_198440 NP_014643 DDB0219931 SMC1 SMC1A NP_006297 NP_651211 NP_191027 NP_116647 DDB0219933 CAPE SMC2 NP_006435 NP_610995 NP_190330 NP_116687 DDB0233753 HUB1 UBL5 NP_077268 NP_610239 NP_199045...”
- A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing
Liu, Molecular and cellular biology 2007 - “...pombe, NP_001018234, 40%; Hs, Homo sapiens, NP_060544, 36.32%; Rn, Rattus norvegicus, XP_576700, 36.32%; Mm, Mus musculus, NP_082657, 36.32%;...”
CG8435, NP_611092 uncharacterized protein from Drosophila melanogaster
Aligns to 9:330 / 333 (96.7%), covers 100.0% of PF04502, 375.4 bits
- Whole transcriptome screening for novel genes involved in meiosis and fertility in Drosophila melanogaster
Sun, Scientific reports 2024 - “...NDJ 101, 1 NDJ CG8298 CG8298 GK3P Gk2 GL00301 514, 1 NDJ 20, 0 NDJ CG8435 CG8435 YJU2 Yju2 GL00696 STERILE 431, 0 NDJ Viable CG8435 CG8435 YJU2 Yju2 GL00696 STERILE 46, 0 NDJ CG8728 CG8728 PMPCA Pmpca HMS00561 STERILE STERILE CG8915 CG8915 YTHDC2 Ythdc2 HMS00697...”
- “...CG32344, CG4554, CG13096, CG11188, CG11660, and CG7993 ) and spliceosome complex (q<1.5e 5 in human, CG8435, CG4980, CG33228, CG11985, CG6610, CG7971, CG4849, and CG4973 ). These genes could be required for generating oocytes with enough maternal products to support embryonic development. We also found three genes...”
- Genome-wide phenotypic RNAi screen in the Drosophila wing: phenotypic description of functional classes
López-Varea, G3 (Bethesda, Md.) 2021 - “...(up), MOD, ENZ, BND, rRNA, TNLF, and SP (bottom) groups. Genotypes for CG3689, CG9218, CG11342, CG8435, CG4152, and CG1796 genes are from UAS-Dicer2/+; sal EPv -Gal4/UAS-RNAi flies. The remaining are from UAS-Dicer2/+; nub-Gal4/UAS-RNAi flies. The name of each particular gene is given in the bottom-left corner...”
- Blue light induces a neuroprotective gene expression program in Drosophila photoreceptors
Hall, BMC neuroscience 2018 - “..., DptB , jumu GO:0030431 Sleep 4.99E05 0.0397 6.02 bgm , AttA , Cyp6g1 , CG8435 , CG8329 , Iris , Amy - p , CG16926 GO:0006952 Defense response 5.33E05 0.0382 3.88 CG10433 , AttA , Lectin - galC1 , Dro , Drsl4 , cathD ,...”
- 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_194285 No hit DDB0233566 fSAPc C19orf29 NP_067054 NP_523422 NP_171887 No hit DDB0233745 FLJ10374 CCDC94 NP_060544 NP_611092 NP_173156 NP_012828 DDB0233752 RRP6 EXOSC10 NP_001001998 NP_001097795 NP_198440 NP_014643 DDB0219931 SMC1 SMC1A NP_006297 NP_651211 NP_191027 NP_116647 DDB0219933 CAPE SMC2 NP_006435 NP_610995 NP_190330 NP_116687 DDB0233753 HUB1 UBL5 NP_077268 NP_610239 NP_199045 NP_014430...”
- A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing
Liu, Molecular and cellular biology 2007 - “...of NTC (Fig. 3B, lane 2). melanogaster, NP_611092, 35.38%; At, Arabidopsis thaliana, NP_173156, 33.99%; and Ce, Caenorhabditis elegans, NP_498576, 33.33%. (B)...”
5yzgY / Q9BW85 5yzgY (see paper)
Aligns to 8:204 / 204 (96.6%), covers 57.7% of PF04502, 343.1 bits
- Ligands: rna; zinc ion (5yzgY)
NP_173156 coiled-coil protein (DUF572) from Arabidopsis thaliana
AT1G17130 cell cycle control protein-related from Arabidopsis thaliana
Aligns to 9:329 / 331 (97.0%), covers 89.8% of PF04502, 337.8 bits
- 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 - “...No hit DDB0233566 fSAPc C19orf29 NP_067054 NP_523422 NP_171887 No hit DDB0233745 FLJ10374 CCDC94 NP_060544 NP_611092 NP_173156 NP_012828 DDB0233752 RRP6 EXOSC10 NP_001001998 NP_001097795 NP_198440 NP_014643 DDB0219931 SMC1 SMC1A NP_006297 NP_651211 NP_191027 NP_116647 DDB0219933 CAPE SMC2 NP_006435 NP_610995 NP_190330 NP_116687 DDB0233753 HUB1 UBL5 NP_077268 NP_610239 NP_199045 NP_014430 DDB0233546...”
- A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing
Liu, Molecular and cellular biology 2007 - “...2). melanogaster, NP_611092, 35.38%; At, Arabidopsis thaliana, NP_173156, 33.99%; and Ce, Caenorhabditis elegans, NP_498576, 33.33%. (B) Growth curves of...”
- A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Kanno, G3 (Bethesda, Md.) 2020 - “...AT1G11650), SALK_063484C ( rbp45c ; AT4G27000), SALK_009736C, SAIL_527_G04, SALK_132471, SALK_053475 and SALK_152624 ( cwc16b ; AT1G17130), SAIL_608_B05 ( smfb ; AT2G14285). All the seeds were obtained from the Nottingham Arabidopsis Stock Center (NASC). Forward genetic screen The forward genetic screen based on an alternatively-spliced, intron-containing GFP...”
- A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana
Kanno, RNA (New York, N.Y.) 2017 - “...members, including two paralogs that are full-length and expressed: At1g25682 (identified in our screen) and At1g17130, which will be referred to hereafter as CWC16a and CWC16b, respectively. In addition, there are three unexpressed retroposed genes (retrogenes) derived from CWC16b ( Zhang et al. 2005 ), and...”
- Arabidopsis thaliana resistance to fusarium oxysporum 2 implicates tyrosine-sulfated peptide signaling in susceptibility and resistance to root infection
Shen, PLoS genetics 2013 - “...5855420 and genes AT1G17100, AT1G17110 and AT1G17120; Pac1.2includes nucleotides 5850646 to 5866025 and genes AT1G17120, AT1G17130, AT1G17140, AT1G17145 and AT1G17147; Pac1.1 includes nucleotides 5866025 to 5878981 and genes AT1G17150, AT1G17160, AT1G17170, AT1G17180 and AT1G17190; Sal1.4 includes nucleotides 5867417 to 5882030 and genes AT1G17160, AT1G17170, AT1G17180, AT1G17190...”
YJU2B_HUMAN / P13994 Probable splicing factor YJU2B; Coiled-coil domain-containing protein 130 from Homo sapiens (Human) (see paper)
Aligns to 9:395 / 396 (97.7%), covers 100.0% of PF04502, 320.1 bits
- function: May be involved in mRNA splicing.
- Serum Glycoproteomics and Identification of Potential Mechanisms Underlying Alzheimer's Disease
Kerdsaeng, Behavioural neurology 2021 - “...Q7RTX1 Taste receptor type 1 member 1 (G protein-coupled receptor 70) 93,074 N-linked (GlcNAc) asparagine P13994 Coiled-coil domain-containing protein 130 (9kDa protein) 44,802 Q5T440 Putative transferase CAF17, mitochondrial (EC 2.1.-.-) (iron-sulfur cluster assembly factor homolog) 38,155 A7E2S9 Putative ankyrin repeat domain-containing protein 30B-like 28,549 Q6QNK2 Adhesion...”
Q32PZ9 Probable splicing factor YJU2B from Rattus norvegicus
Aligns to 9:384 / 385 (97.7%), covers 100.0% of PF04502, 313.8 bits
6zymu / Q9BW85 Human c complex spliceosome - high-resolution core (see paper)
2 alignments in 8:157 / 157 (95.5%), covering up to 30.3% of PF04502, 276.0 bits
- Ligands: rna; peptide; zinc ion (6zymu)
CG15084 uncharacterized protein from Drosophila melanogaster
Aligns to 9:311 / 316 (95.9%), covers 85.3% of PF04502, 253.7 bits
AT3G43250 cell cycle control protein-related from Arabidopsis thaliana
Aligns to 9:247 / 249 (96.0%), covers 68.5% of PF04502, 231.0 bits
- Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana
Nabi, Frontiers in plant science 2020 - “...: IPR014710); BEST Arabidopsis thaliana protein match is: RmlC-like cupins superfamily protein (TAIR : AT4G10280.1) AT3G43250 0.11000 60.46000 549.63636 0.00000 9.12997 Family of unknown function (DUF572); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF572 (InterPro : IPR007590); BEST Arabidopsis thaliana protein match is: Family of unknown...”
- HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight
Zupanska, International journal of molecular sciences 2019 - “...in the cell wall and glucosinolate activation [ 90 ], along with two other genes (At3g43250, AT5G38980) reported to function in wounding and in defense response, the HSFA2 KO cells engaged the Disease resistance protein CC-NBS-LRR class gene (AT1G59124) [ 91 ] and NTA Seven transmembrane...”
- “...response to other organism GO:0098542 AT2G03760 ST1 sulphotransferase 12 1.1 1.0 AT5G38980 unknown 3.3 X At3g43250 unknown in wounding 2.6 X AT4G02460 PMS1 DNA mismatch repair protein, putative 2.2 AT2G44490 PEN2 Glycosyl hydrolase superfamily protein 1.4 X AT1G59124 Disease resistance protein (CC-NBS-LRR class) X 2.4 AT2G17430...”
- Brassica napus Infected with Leptosphaeria maculans
Ma, Genes 2019 - “...DUF family members BnaCnng76620D, BnaA09g51150D, BnaAnng22520D, and BnaC09g38570D, whose homologous genes in A. thaliana are AT3G43250 (AtDUF572), AT1G02816 (AtDUF538), AT5G01750 (AtDUF567), and AT2G20625 (AtDUF626), respectively. These genes are mainly involved in abiotic and biotic stress responses. For example, AtDUF572 and AtDUF538 are drought-inducible genes [ 55...”
- Key Components of Different Plant Defense Pathways Are Dispensable for Powdery Mildew Resistance of the Arabidopsis mlo2 mlo6 mlo12 Triple Mutant
Kuhn, Frontiers in plant science 2017 - “...mlo2 mlo6 mlo12 mutant at early stages after G. orontii inoculation. Notably, only one gene, At3g43250 ; coding for an uncharacterized protein of 249 amino acids with a domain of unknown function (DUF572) and a putative role in cell cycle regulation, exhibited higher mRNA levels also...”
- The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes
Meier, PloS one 2010 - “...Similar to syringolide-induced protein 14-1-1 15 AT3G26830 RBS,ROO 0.859 Phytoalexin deficient 3 (PAD3), camalex-biosynth. 16 AT3G43250 0.858 Cell cycle control protein 17 AT1G51890 0.858 Leucine-rich repeat PK, Serine/threonine PK 18 AT4G25030 0.857 Expressed protein 19 AT3G63380 0.856 Calcium-transporting ATPase, PM-type 20 AT1G28190 0.855 Expressed protein 21...”
TGME49_207400 hypothetical protein from Toxoplasma gondii ME49
Aligns to 9:434 / 436 (97.7%), covers 100.0% of PF04502, 226.9 bits
YJU2_SCHPO / Q9P7C5 Splicing factor YJU2; Complexed with cdc5 protein 16; Pre-mRNA-splicing factor cwf16 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
cwf16 / RF|XP_001713052.1 splicing factor (predicted) from Schizosaccharomyces pombe (see 2 papers)
SPAC9.13c splicing factor from Schizosaccharomyces pombe
Aligns to 9:269 / 270 (96.7%), covers 64.6% of PF04502, 223.6 bits
- function: Part of the spliceosome which catalyzes two sequential transesterification reactions, first the excision of the non-coding intron from pre-mRNA and then the ligation of the coding exons to form the mature mRNA. Plays a role in stabilizing the structure of the spliceosome catalytic core and docking of the branch helix into the active site, producing 5'-exon and lariat intron-3'-intermediates.
subunit: Component of the spliceosome (PubMed:11884590). Present in the activated B complex, the catalytically activated B* complex which catalyzes the branching, the catalytic step 1 C complex catalyzing the exon ligation, and the postcatalytic P complex containing the ligated exons (mRNA) and the excised lariat intron (By similarity). 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 (PubMed:11884590). - CharProtDB Source (per GeneDB): GeneDB_Spombe
- Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs
Ohi, Molecular and cellular biology 2002 - “...Yes Yes No 26 27 Cwc15p (Q03772) Cwc16p (P28320) Cwf15p (O74817) Cwf16p (Q9P7C5) 20 32 No Yes No. of hitsc Cdc5 Cef1 Prp19 Snt309 Cwc2 Cwc1 35 11 13 14 16 19 22...”
- RNA metabolism is the primary target of formamide in vivo
Hoyos-Manchado, Scientific reports 2017 - “...0,262 0,304 SPAC8C9.07 fyv7 rRNA processing protein Fyv7 (predicted) biological role inferred 0,000 0,000 CCDC59 SPAC9.13c cwf16 splicing factor Cwf16 published 0,296 0,119 CCDC94 SPAPB1E7.02c mcl1 DNA polymerase alpha accessory factor Mcl1 published 0,243 0,000 WDHD1 SPBC16H5.03c uba2 SUMO activating enzyme E1-type Uba2 (predicted) biological role...”
- Yeast Augmented Network Analysis (YANA): a new systems approach to identify therapeutic targets for human genetic diseases
Wiley, F1000Research 2014 - “...SPCC1795.01c SPBC31F10.13c 5 SPAPYUG7.04c SPCC1620.14c SPBC24C6.11 SPCC1620.14c 6 SPBC24C6.11 SPAC57A10.02 SPBC1734.08 SPAC3G6.02 7 SPBC1734.08 SPAC1556.01c SPAC9.13c SPAC1556.01c 8 SPAC23D3.09 SPAC30D11.13 SPAC23D3.09 SPAC821.05 9 SPAC17A5.11 SPCC970.07c SPAC57A10.02 SPBC6B1.04 10 SPAC16A10.05c SPAC23H4.12 SPAC16A10.05c SPCC1919.15 11 SPCP1E11.07c SPCC11E10.08 SPCC895.07 SPBC23E6.09 12 SPBC146.13c SPBC21D10.12 SPCP31B10.05 SPBC21D10.11c 13 SPAC821.09 SPCC1672.06c SPCC550.12...”
AT1G25682 cell cycle control protein-related from Arabidopsis thaliana
Aligns to 12:309 / 310 (96.1%), covers 79.9% of PF04502, 214.1 bits
- A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs, and coilin function in Arabidopsis thaliana
Kanno, G3 (Bethesda, Md.) 2023 - “...SRR13267720, SAMN17103484; SRR14917394, SAMN19865510; SRR14917406, SAMN19865511; RNAs; SRR14917408, SAMN19865501; SRR14917407, SAMN19865502; SRR14917401, SAMN19865503; cwc16a / At1g25682 / cwc16a-1 / ABRC stock number CS69846; NCBI accession numbers : small RNAs: SRR13267751, SAMN17103497; SRR13267726, SAMN17103498; cwc16a-1/dcl4 : NCBI accession numbers : small RNAs: SRR13267727, SAMN17103499; SRR13267728, SAMN17103500; dcl2...”
- A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Kanno, G3 (Bethesda, Md.) 2020 - “...bodies, which facilitate snRNP maturation 12 a negligible Kanno et al. , 2016 hgf2 CWC16a At1g25682 step I factor 3 a negligible Kanno et al. , 2017a hgf3 SMU1 At1g73720 recruited prior to B* complex formation; 1 negligible Kanno et al. , 2017a hgf4 SMFA At4g30220...”
- A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in Arabidopsis thaliana
Kanno, G3 (Bethesda, Md.) 2018 - “...which are facilitate snRNP maturation 12 * AU-AC no Kanno et al. 2016 hgf2 CWC16a At1g25682 step I factor 2 * AU-AC no Kanno et al. 2017a hgf3 SMU1 At1g73720 which may help to recognize spliceosomal targets for ubiquitination 1 AU-AC no Kanno et al. 2017a...”
- A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana
Kanno, RNA (New York, N.Y.) 2017 - “...that are either uncharacterized or not yet studied extensively in Arabidopsis : hgf2 corresponds to At1g25682, which encodes c oiled- c oil d omain- c ontaining protein Yju2/CWC16/CCDC130; hgf3 corresponds to At1g73720, which encodes WD40 repeat-containing protein SMU1 ( s uppressor of m ec-8 and u...”
- “...uncharacterized gene family that contains six members, including two paralogs that are full-length and expressed: At1g25682 (identified in our screen) and At1g17130, which will be referred to hereafter as CWC16a and CWC16b, respectively. In addition, there are three unexpressed retroposed genes (retrogenes) derived from CWC16b (...”
- A Genetic Screen for Pre-mRNA Splicing Mutants of Arabidopsis thaliana Identifies Putative U1 snRNP Components RBM25 and PRP39a
Kanno, Genetics 2017 - “...2016 , 2017 ). We previously reported four hgf mutants: hgf1 (coilin; At1g13030), hgf2 (CWC16a; At1g25682), hgf3 (SMU1; At1g73720), and hgf4 (SMFa; At4g30220) ( Kanno et al. 2016 , 2017 ), and two gfw mutants: gfw1 (RTF2; At5g58020) and gfw2 (PRP8; At1g80070) ( Sasaki et al....”
- Combining phylogenetic and syntenic analyses for understanding the evolution of TCP ECE genes in eudicots
Citerne, PloS one 2013 - “...and chromosome 5 (AT5G16030 and AT5G38660); for CYC3 three regions were identified, on chromosome 1 (AT1G25682 and AT1G13250) and chromosome 3 (AT3G25700) (Figure S4). In the asterid Solanum lycopersicum , collinearity with the rosid genomes was found to be generally extensive (with ~69% of the set...”
AT2G32050 cell cycle control protein-related from Arabidopsis thaliana
Aligns to 9:252 / 254 (96.1%), covers 70.9% of PF04502, 213.1 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...AT1G15600, AT1G15610, AT1G15620, AT1G15630, AT1G15640, AT1G17400, AT1G22980, AT1G44010, AT1G50690, AT1G54180, AT1G72490, AT2G15590, AT2G20590, AT2G24140, AT2G29880, AT2G32050, AT2G33350, AT2G33400, AT2G36540, AT2G36550, AT2G38823, AT2G45260, AT3G01015, AT3G02125, AT3G54520, AT3G54530, AT4G00390, AT4G27660, AT4G30830, AT4G30830, AT5G41380, AT5G59990, AT4G00130. The entry vectors in pDONR221 were obtained from ABRC (except for AT2G45260, whose...”
CWC16_SCHPO / O60141 Protein saf4 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
Aligns to 8:293 / 299 (95.7%), covers 65.5% of PF04502, 174.0 bits
- function: May be involved in mRNA splicing.
SPBC18H10.10c complexed with Cdc5 protein Cwf16 from Schizosaccharomyces pombe
Aligns to 3:288 / 294 (97.3%), covers 65.5% of PF04502, 173.9 bits
7b9vD C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound (see paper)
Aligns to 8:192 / 194 (95.4%), covers 47.1% of PF04502, 159.6 bits
- Ligands: rna; zinc ion (7b9vD)
YJU2_YEAST / P28320 Splicing factor YJU2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 9 papers)
NP_012828 mRNA splicing protein YJU2 from Saccharomyces cerevisiae S288C
NP_012828, YKL095W Essential protein required for pre-mRNA splicing; associates transiently with the spliceosomal NTC ('nineteen complex') and acts after Prp2p to promote the first catalytic reaction of splicing from Saccharomyces cerevisiae
Aligns to 9:273 / 278 (95.3%), covers 66.7% of PF04502, 158.2 bits
- function: Part of the spliceosome which catalyzes two sequential transesterification reactions, first the excision of the non-coding intron from pre-mRNA and then the ligation of the coding exons to form the mature mRNA (PubMed:19935684, PubMed:27445308, PubMed:27459055, PubMed:29146871). Plays a role (via N-terminus) in stabilizing the structure of the spliceosome catalytic core and docking of the branch helix into the active site, producing 5'-exon and lariat intron-3'- intermediates (PubMed:23438600, PubMed:27459055). Further stabilizes spliceosome conformation for 3'-splice site docking (via C-terminus) promoting exon ligation (PubMed:29146871).
subunit: Component of the spliceosome. Present in the activated B complex, the catalytically activated B* complex which catalyzes the branching, the catalytic step 1 C complex catalyzing the exon ligation, and the postcatalytic P complex containing the ligated exons (mRNA) and the excised lariat intron (PubMed:19935684, PubMed:27445308, PubMed:27459055, PubMed:29146871). Interacts (via C-terminus) with CLF1 (PubMed:23438600). Interacts (via N-terminus) with SYF1 (PubMed:23438600). Interacts with U2 snRNA; this interaction is direct (PubMed:23438600). Identified in the CWC complex (or CEF1-associated complex), a spliceosome sub-complex reminiscent of a late-stage spliceosome composed of the U2, U5 and U6 snRNAs and at least BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, ISY1, LEA1, MSL1, NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2, SYF1, SYF2, RSE1 and YJU2 (PubMed:11884590). - The Chaperone NASP Contributes toDe NovoDeposition of the Centromeric Histone Variant CENH3 inArabidopsisEarly Embryogenesis
Takeuchi, 2023 - H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity
Lei, Plant communications 2020 - “...core funding from the Gregor Mendel Institute and the 10.13039/501100002428 Austrian Science Fund (FWF): W1238, P28320, P26887, and P32054. References Abbott D.W. Ivanova V.S. Wang X. Bonner W.M. Ausio J. Characterization of the stability and folding of H2A.Z chromatin particles: implications for transcriptional activation J. Biol....”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...significantly overlap with the aforementioned functional domains of Slu7 protein. Protein Cwc16 (UniProt ID : P28320) . Similar to Cwc15 discussed above, Cwc16 (also known as Yju2) is a part of the CWC complex. It was shown that splicing factor Yju2 participates in spliceosome assembly, is...”
- “...283-301 Cwc23 YGL128C P52868 33.2 283 0.09 0.21 0.37 0.19 DNAJ A1 ? Yju2/ YKL095W P28320 32.3 278 0.69 0.63 0.90 0.64 7-24 CCDC130 Cwc16 76-88 147-164 162-173 186-206 214-231 212-228 236-253 245-278 261-278 Cwc24 YLR323C P53769 29.7 259 0.56 0.34 0.85 0.55 1-18 1-8 RNF113A...”
- Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs
Ohi, Molecular and cellular biology 2002 - “...11 18 Yes Yes Yes No 26 27 Cwc15p (Q03772) Cwc16p (P28320) Cwf15p (O74817) Cwf16p (Q9P7C5) 20 32 No Yes No. of hitsc Cdc5 Cef1 Prp19 Snt309 Cwc2 Cwc1 35 11 13...”
- A weak spliceosome-binding domain of Yju2 functions in the first step and bypasses Prp16 in the second step of splicing.
Chiang, Molecular and cellular biology 2013 - GeneRIF: In the absence of the C domain, Yju2-N domain is not stably associated with the spliceosome after lariat formation, and thus bypasses the need for Prp16.
- Ntc90 is required for recruiting first step factor Yju2 but not for spliceosome activation.
Chang, RNA (New York, N.Y.) 2009 - GeneRIF: Ntc90 is required for recruiting first step factor Yju2.
- Cwc25 is a novel splicing factor required after Prp2 and Yju2 to facilitate the first catalytic reaction.
Chiu, Molecular and cellular biology 2009 - GeneRIF: Cwc25 functions in the final step of the first catalytic reaction after the action of Prp2.
- A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing.
Liu, Molecular and cellular biology 2007 - GeneRIF: Yju2 acts in concert with an unidentified heat-resistant factor(s) in an ATP-independent manner to promote the first catalytic reaction of pre-mRNA splicing after Prp2-mediated structural rearrangement of the spliceosome.
- Different Toxicity Mechanisms for Citrinin and Ochratoxin A Revealed by Transcriptomic Analysis in Yeast
Vanacloig-Pedros, Toxins 2016 - “...HML YNL077W APJ1 5.6 3.33 10 6 Chaperone with a role in SUMO-mediated protein degradation YKL095W YJU2 5.6 1.29 10 3 Essential protein required for pre-mRNA splicing YJL030W MAD2 5.6 1.64 10 4 Component of the spindle-assembly checkpoint complex YHL016C DUR3 5.6 9.87 10 7 Plasma...”
- Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks
Shen, BMC bioinformatics 2015 - “...ydr235w ydr240c ydr243c ydr247w ydr515w yer029c yfl018w-a ygr013w ygr074w yhr086w yhr165c yil061c yir009w yjl188c ykl012w ykl095w ykr019c ylr147c ylr275w ylr298c ylr318w yml046w ymr001c ymr132c ymr157c yor036w yor159c yor305w yor359w ypl213w ypr057w ypr182w 1.31e-21 22 out of 35 genes, 62.9% mRNA metabolic process ybl026w ybl098w ybr055c ycr077c...”
- Genetic influences on translation in yeast
Albert, PLoS genetics 2014 - “...<2e-16 1.46 3.4E-26 0.68 1.6E-07 YKL163W ( PIR3 ) 1.19 1.6E-06 0.07 0.6 1.26 9.8E-08 YKL095W ( YJU2 ) 1.55 2.1E-06 0.60 0.03 0.95 1.9E-04 YKL012W ( PRP40 ) 1.47 9.6E-06 0.24 0.9 1.24 1.1E-04 YLL022C ( HIF1 ) 1.02 7.2E-06 0.64 6.6E-03 0.38 0.04 YLL007C...”
- A new method for the discovery of essential proteins
Zhang, PloS one 2013 - “...YIL075C 32 1.472131 essential 139 YLR200W 10 1.435959 non-essential 145 YDL087C 23 1.401966 essential 147 YKL095W 38 1.390057 essential 151 YHR081W 5 1.358778 non-essential 152 YPR088C 14 1.351337 essential 154 YOL094C 37 1.327599 essential 156 YHL030W 21 1.310346 non-essential 158 YOR259C 28 1.282556 essential 161 YBL041W...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...284-301 283-301 Cwc23 YGL128C P52868 33.2 283 0.09 0.21 0.37 0.19 DNAJ A1 ? Yju2/ YKL095W P28320 32.3 278 0.69 0.63 0.90 0.64 7-24 CCDC130 Cwc16 76-88 147-164 162-173 186-206 214-231 212-228 236-253 245-278 261-278 Cwc24 YLR323C P53769 29.7 259 0.56 0.34 0.85 0.55 1-18 1-8...”
- 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 - “...hit DDB0233566 fSAPc C19orf29 NP_067054 NP_523422 NP_171887 No hit DDB0233745 FLJ10374 CCDC94 NP_060544 NP_611092 NP_173156 NP_012828 DDB0233752 RRP6 EXOSC10 NP_001001998 NP_001097795 NP_198440 NP_014643 DDB0219931 SMC1 SMC1A NP_006297 NP_651211 NP_191027 NP_116647 DDB0219933 CAPE SMC2 NP_006435 NP_610995 NP_190330 NP_116687 DDB0233753 HUB1 UBL5 NP_077268 NP_610239 NP_199045 NP_014430 DDB0233546 Prp38...”
- A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing
Liu, Molecular and cellular biology 2007 - “...Yju2 are the following: Sc, Saccharomyces cerevisiae, NP_012828, 100%; Sp, Schizosaccharomyces pombe, NP_001018234, 40%; Hs, Homo sapiens, NP_060544, 36.32%;...”
- PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
Pitre, BMC bioinformatics 2006 - “...Protein B Protein A Protein B YAL021C YNR052C YDR394W YOR117W YJL187C YBR133C YAL032C YDR416W YDR416W YKL095W YJR068W YBR087W YAR003W YBR175W YDR477W YGL115W YJR076C YHR107C YBL007C YHR016C YDR490C YPL004C YJR093C YPR107C YBL045C YPR191W YDR490C YGR086C YJR093C YMR061W YBL056W YDR071C YEL037C YER162C YKL028W YDR311W YBR102C YLR166C YER027C YDR477W...”
- More
6j6qF / P28320 Cryo-em structure of the yeast b -B2 complex at an average resolution of 3.7 angstrom (see paper)
Aligns to 8:161 / 161 (95.7%), covers 40.5% of PF04502, 140.0 bits
- Ligands: rna; zinc ion (6j6qF)
Q5KJR4 Rap-GAP domain-containing protein from Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565)
Aligns to 2:181 / 1405 (12.8%), covers 40.2% of PF04502, 97.6 bits
Q7LE05 F20887_2 (Fragment) from Homo sapiens
Aligns to 9:41 / 41 (80.5%), covers 9.9% of PF04502, 58.1 bits
Or search for genetic data about PF04502 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory