PaperBLAST

PaperBLAST Hits for NP_001273965.1 uncharacterized protein KIAA1958 isoform a (Homo sapiens) (744 a.a., MEDCLHTSSE...)

Show query sequence

>NP_001273965.1 uncharacterized protein KIAA1958 isoform a (Homo sapiens)
MEDCLHTSSENLSKLVSWAHSHGTICSLIPNLKHLLSEGSHGNLTAMWGCSAGHAYHWPL
TATCRAGSQERVCFQDNRSFNSDSPSIIGVPSETQTSPVERYPGRPVKAKLDCNRTRDSC
DFSYCSEPSELDETVEEYEDENTLFDMVCESSVTDEDSDFEPQTQRPQSIARKRPGVVPS
SLHSSSQTQMVDECSNDVIIKKIKQEIPEDYYIVANAELTGGVDGPALSLTQMAKPKPQT
HAGPSCVGSAKLIPHVTSAISTELDPHGMSASPSVISRPIVQKTARVSLASPNRGPPGTH
GTNQQVAMQMPVSTSHPNKQISIPLSALQLPGQDEQVASEEFLSHLPSQVSSCEVALSPS
VNTEPEVSSSQQQPPVAPAITTEATAQCIPDQDERAAELSREQNEKTIRSTQTALRNFPY
STKLNKFPVFNINDDLNDLCTSAVSPNTTKATRYALNVWRYWCMTNGLKDHTDITKIPAV
KLNELLENFYVTVKKSDGSDFLATSLHAIRRGLDRILKNAGVGFSITSSTFSSSTKKLKE
KLWVLSKAGMSGARSRNIVYFSLSDEEEMWQAGCLGDDSPITLLSTVVKYNSQYLNMRTL
QEHADLMYGDIELLKDPQNQPYFARTDSVKRESRSGSTRVCHGKIYHEHSRGHKQCPYCL
LYKYMYIHRPPTQMEAKSPFYLTARKEATDMGSVWYEEQRMGLRSLRGIVPNLAKKVKLE
NCENFTFVSFTQVSRRLGSHSCCQ

Running BLASTp...

Found 18 similar proteins in the literature:

NP_001273965 uncharacterized protein KIAA1958 isoform a from Homo sapiens
100% identity, 100% coverage

• Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  Rose, Molecular medicine (Cambridge, Mass.)
  • GeneRIF: Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)

Q8N8K9 Uncharacterized protein KIAA1958 from Homo sapiens
96% identity, 100% coverage

• Using plasma proteomics to investigate viral infections of the central nervous system including patients with HIV-associated neurocognitive disorders.
  Ahmed, Journal of neurovirology 2022
  • “...1.73 2.22 AZGP1 P25311 0.019 0.44 1.72 0.66 NECTIN1 Q15223 0.0202 0.46 1.7 0.68 KIAA1958 Q8N8K9 0.0207 5.92 1.68 2.43 IGHV3-15 A0A0B4J1V0 0.021 3.96 1.68 1.99 IGHV3-21 A0A0B4J1V1 0.0215 2.08 1.67 -1.44 C1QB P02746 0.0232 0.65 1.63 0.81 ICAM1 P05362 0.0254 0.99 1.6 1 KIAA2026 Q5HYC2...”

NP_001120376 uncharacterized protein LOC100145450 from Xenopus tropicalis
24% identity, 44% coverage

• Crypton transposons: identification of new diverse families and ancient domestication events
  Kojima, Mobile DNA 2011
  • “...3 Molecular fossils of Cryptons in chordates Species Accession numbers Danio rerio BX530066* Xenopus tropicalis NP_001120376, AAMC01135377*, AAMC01082917* Callorhinchus milii AAVX01521991*, AAVX01068049*, AAVX01132927* Ciona intestinalis XP_002124034, XP_002125964 Ciona savignyi AACT01002283*, AACT01041791* Halocynthia roretzi BAB40645 Oikopleura dioica CBY34656 Branchiostoma floridae XP_00260067, XP_002595788, XP_002613958, XP_002613959, XP_002587732, XP_002607491 *Nucleotide...”

XP_002125964 uncharacterized protein LOC100186276 from Ciona intestinalis
23% identity, 30% coverage

• Crypton transposons: identification of new diverse families and ancient domestication events
  Kojima, Mobile DNA 2011
  • “...rerio BX530066* Xenopus tropicalis NP_001120376, AAMC01135377*, AAMC01082917* Callorhinchus milii AAVX01521991*, AAVX01068049*, AAVX01132927* Ciona intestinalis XP_002124034, XP_002125964 Ciona savignyi AACT01002283*, AACT01041791* Halocynthia roretzi BAB40645 Oikopleura dioica CBY34656 Branchiostoma floridae XP_00260067, XP_002595788, XP_002613958, XP_002613959, XP_002587732, XP_002607491 *Nucleotide sequences including Crypton fragments. However, two similar sequences (ABQF01015803 from the...”
  • “...A representative of DUF3504 from Halocynthia roretzi (BAB40645) has orthologs in other tunicates: Ciona intestinalis (XP_002125964), Ciona savignyi (AACT01002283 and AACT10141791) and Oikopleura dioica (CBY34656). They could also represent a domestication event of Crypton . Another representative (YP_025778) is coded in the mitochondrion of the green...”

NP_001263010 without children, isoform E from Drosophila melanogaster
23% identity, 15% coverage

• The zinc-finger proteins WOC and ROW play distinct functions within the HP1c transcription complex.
  Di, Biochimica et biophysica acta. Gene regulatory mechanisms 2020 (PubMed)
  • GeneRIF: The results suggest that WOC and ROW play distinct functions within the HP1c complex, supporting a model in which WOC interacts with Dsk2 and recruits it to the complex, while ROW mediates binding of the complex to chromatin.
• Without children is required for Stat-mediated zfh1 transcription and for germline stem cell differentiation.
  Maimon, Development (Cambridge, England) 2014
  • GeneRIF: Without children is required for Stat-mediated zfh1 transcription and for germline stem cell differentiation.
• Drosophila HP1c is regulated by an auto-regulatory feedback loop through its binding partner Woc.
  Abel, PloS one 2009
  • GeneRIF: interaction between HP1c and Woc constitutes a transcriptional feedback loop that operates to balance the concentration of HP1c within the cell
• Drosophila HP1c isoform interacts with the zinc-finger proteins WOC and Relative-of-WOC to regulate gene expression.
  Font-Burgada, Genes & development 2008
  • GeneRIF: HP1c, WOC, and ROW regulate a common gene expression program that, in part, is executed in the context of the nervous system.
• Woc gene mutation causes 20E-dependent alpha-tubulin detyrosination in Drosophila melanogaster.
  Jin, Archives of insect biochemistry and physiology 2005 (PubMed)
  • GeneRIF: Woc gene mutation causes 20E-dependent alpha-tubulin detyrosination in Drosophila melanogaster.
• The putative Drosophila transcription factor woc is required to prevent telomeric fusions.
  Raffa, Molecular cell 2005 (PubMed)
  • GeneRIF: Data show that mutations in the woc gene cause frequent telomeric fusions in Drosophila brain cells.

XP_036017934 zinc finger MYM-type protein 3 isoform X4 from Mus musculus
23% identity, 11% coverage

• Gene knockout of Zmym3 in mice arrests spermatogenesis at meiotic metaphase with defects in spindle assembly checkpoint.
  Hu, Cell death & disease 2017
  • GeneRIF: Zmym3 KO also resulted in up-regulated expression of meiotic genes in spermatogonia. These results show that ZMYM3 has an essential role in metaphase to anaphase transition during mouse spermatogenesis by regulating the expression of diverse families of genes.

ZMYM3_MOUSE / Q9JLM4 Zinc finger MYM-type protein 3; DXHXS6673E protein; Zinc finger protein 261 from Mus musculus (Mouse) (see paper)
22% identity, 12% coverage

• function: Plays a role in the regulation of cell morphology and cytoskeletal organization.
  subunit: May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I.
• Microarray-based analysis of fish egg quality after natural or controlled ovulation.
  Bonnet, BMC genomics 2007
  • “...Zinc finger protein 16 (Zinc finger protein KOX9) 311 Omy.6191 tcbk0009.g.08 BX875276 tcbk0009c.g.08_5.1.s.om.8 ZNF261 MOUSE (Q9JLM4) Zinc finger protein 261 (DXHXS6673E protein) 254 Omy.2759 Genes subsequently studied by real time PCR are bolded. For each gene, clone name, GenBank accession number, official human symbol and corresponding...”

ZMYM3_HUMAN / Q14202 Zinc finger MYM-type protein 3; Zinc finger protein 261 from Homo sapiens (Human) (see 5 papers)
22% identity, 12% coverage

• function: Plays a role in the regulation of cell morphology and cytoskeletal organization.
  subunit: May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I.
• Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype
  Hiatt, American journal of human genetics 2023 (secret)
• High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells.
  Chiu, PloS one 2014
  • “...protein KIF20A 0.34 2 1.7210 29 Mitotic kinesin required for chromosome passenger complex-mediated cytokinesis. ZMYM3 Q14202 Zinc finger MYM-type protein 3 0.35 2 3.0810 6 Plays a role in the regulation of cell morphology and cytoskeletal organization. CENPF P49454 Centromere protein F 0.35 2 1.167810 2...”
• Heme-binding-mediated negative regulation of the tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) by IDO2.
  Lee, Experimental & molecular medicine 2014
  • “...1.988 O75503 CLN5 ceroid-lipofuscinosis neuronal protein 5 1.919 P61970 NUTF2 Nuclear transport factor 2 1.908 Q14202 ZMYM3 Isoform 1 of zinc finger MYM-type protein 3 1.904 P00918 CA2 Carbonic anhydrase 2 1.904 P05387 RPLP2 60S acidic ribosomal protein P2 1.904 P49643 PRIM2 Isoform 1 of DNA...”

XP_047298589 zinc finger MYM-type protein 3 isoform X2 from Homo sapiens
22% identity, 12% coverage

• Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype.
  Hiatt, American journal of human genetics 2023
  • GeneRIF: Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype.
• Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition.
  Afshar, Scientific reports 2020
  • GeneRIF: Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition.
• Aicardi-Goutières Syndrome associated mutations of RNase H2B impair its interaction with ZMYM3 and the CoREST histone-modifying complex.
  Shapson-Coe, PloS one 2019
  • GeneRIF: AGS mutations in this cluster impair the interaction of RNase H2 with several members of the CoREST chromatin-silencing complex that include the histone deacetylase HDAC2 and the demethylase KDM1A, the transcriptional regulators RCOR1 and GTFII-I as well as ZMYM3, an MYM-type zinc finger protein.
• Disease-only alleles at the extreme ends of the human ZMYM3 exceptionally long 5' UTR short tandem repeat in bipolar disorder: A pilot study.
  Alizadeh, Journal of affective disorders 2019 (PubMed)
  • GeneRIF: The ZMYM3 "exceptionally long" 5' UTR STR findings may alter our perspective of disease pathogenesis in psychiatric disorders, and set an example in which the low frequency alleles at the extreme short and long ends of the human STRs are, at least in part, a result of natural selection against these alleles and their unambiguous link to major human disorders.
• Skewing of the genetic architecture at the ZMYM3 human-specific 5' UTR short tandem repeat in schizophrenia.
  Alizadeh, Molecular genetics and genomics : MGG 2018 (PubMed)
  • GeneRIF: Data found skewing of the genetic architecture at the ZMYM3 short tandem repeats (STR) in schizophrenia. Further, results found a bell-shaped distribution of alleles and selection against alleles at the extreme ends of this STR.

XP_026564670 zinc finger MYM-type protein 2 isoform X1 from Pseudonaja textilis
22% identity, 12% coverage

• Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles
  Manuwar, Toxins 2020
  • “...domain-containing protein 6 XP_026572863 1 Pseudonaja textilis 118 Zinc finger MYM-type protein 2 isoform X1 XP_026564670 1 Pseudonaja textilis 119 Zinc finger BED domain-containing protein 1 XP_026522663 1 Notechis scutatus 120 NHS Family NHS-like protein 1 isoform X1 XP_026561348 1 Pseudonaja textilis 121 Protein family not...”

ZMYM2_HUMAN / Q9UBW7 Zinc finger MYM-type protein 2; Fused in myeloproliferative disorders protein; Rearranged in atypical myeloproliferative disorder protein; Zinc finger protein 198 from Homo sapiens (Human) (see 3 papers)
19% identity, 19% coverage

• function: Involved in the negative regulation of transcription.
  subunit: Can form homodimers (PubMed:32891193). May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Interacts with FOXP1 and FOXP2 (PubMed:32891193).
• Proteomics identifies differentially expressed proteins in glioblastoma U87 cells treated with hederagenin.
  Zhang, Proteome science 2023
  • “...Methyltransferase-like protein 7B UP 1.204628949 0.02206929 O60291 MGRN1 E3 ubiquitin-protein ligase MGRN1 DOWN 0.833180568 0.00804476 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 DOWN 0.823154057 0.03109416 Q9NUE0 ZDHHC18 Palmitoyltransferase ZDHHC18 DOWN 0.823154057 0.03070765 Q9BSL1 UBAC1 Ubiquitin-associated domain-containing protein 1 DOWN 0.822600243 0.02781847 P54252 ATXN3 Ataxin-3 DOWN 0.822546338...”
• Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets.
  Qiu, Clinical proteomics 2023
  • “...Q9Y3R5 DOP1B Protein dopey-2 DOP2_HUMAN 7.047271208 132.2635031 0.009017667 0.067617556 390.7667237 51,684.17579 455.894511 53,527.82245 145.6301596 43,456.97949 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 ZMYM2_HUMAN 6.288898031 78.18923194 0.004630235 0.050678673 529.169983 41,375.39454 4620.847708 40,939.30145 9149.269534 26,504.5089 P12532 CKMT1A Creatine kinase U-type, mitochondrial KCRU_HUMAN 5.738345477 53.38436902 0.001805234 0.030247698 16,038.71924 856,216.9063...”
• Screening and identification of endometrial proteins as novel potential biomarkers for repeated implantation failure.
  Wang, PeerJ 2021
  • “...NSL complex subunit 2 1.54 P02647 APOA1 Apolipoprotein A-I 1.53 P48509 CD151 CD151 antigen 1.53 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1.52 Q96LD8 SENP8 Sentrin-specific protease 8 1.52 P35237 SPB6 Serpin B6 1.52 Q5HYK9 ZN667 Zinc finger protein 667 1.51 Q99735 MGST2 Microsomal glutathione S-transferase...”
• Proteomic analysis of ubiquitin-like posttranslational modifications induced by the adenovirus E4-ORF3 protein
  Sohn, Journal of virology 2015
  • “...Small ubiquitin-related modifier 2 Chromatin target of PRMT1 protein Q9UBW7 P61956 Q9Y3Y2 ZMYM2 SUMO2 CHTOP 1 1 1 3.8 3.8 3.4 RNF168 RING finger protein 168...”
• Quantitative gingival crevicular fluid proteome in health and periodontal disease using stable isotope chemistries and mass spectrometry
  Carneiro, Journal of clinical periodontology 2014
  • “...V-type proton ATPase 116 kDa subunit a isoform 2 Q8NFY9 Kelch repeat/BTB domain-containing protein 8 Q9UBW7 Zinc finger MYM-type protein 2 A4D0S4 Laminin subunit beta-4 Q5VU65 Nuclear pore membrane glycoprotein 210-like Q9NS15 Latent-transforming growth factor -binding protein 3 Q9H7F0 Cation-transporting ATPase 13A3 O00562 Membrane-associated phosphatidylinositol transfer...”
• Proteomics approaches for identification of tumor relevant protein targets in pulmonary squamous cell carcinoma by 2D-DIGE-MS.
  Lihong, PloS one 2014
  • “...FGB 64/5.9 56577/9.3 48 0.02 2.14 P08670 Vimentin 142 VIM 60/4.4 53676/4.9 49 0.045 2.93 Q9UBW7 Zinc finger MYM-type protein 2 67 ZMYM2 60/6.7 158403/5.9 Q14532 Keratin, type I cuticular 59 KRT32 51769/4.7 50 0.03 2.22 P50454 Serpin H1 57 SERPINH1 60/8 46525/9.3 51 0.0066 2.01...”
• A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics
  Van, International journal of biological sciences 2010
  • “...RIP140 to act as a repressor for its target Oct4 150 - O95551 TTRAP Unknown Q9UBW7 ZNF198 K963 SUMOylation of ZNF198 is important for PML body formation 151 + Q9Y4E5 ZNF451 NDSM ZNF451 exerts its effects via SUMOylation and trafficking of transcription regulators between promyelocytic leukemia...”

XP_011243522 zinc finger MYM-type protein 2 isoform X1 from Mus musculus
20% identity, 18% coverage

• ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development.
  Graham-Paquin, Nucleic acids research 2023
  • GeneRIF: ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development.
• Constitutive Notch pathway activation in murine ZMYM2-FGFR1-induced T-cell lymphomas associated with atypical myeloproliferative disease.
  Ren, Blood 2011
  • GeneRIF: The study demonstrates frequent, constitutive activation of Notch1 and its downstream target genes in T-cell lymphomas that arose in a murine model of Zmym2-Fgfr1 stem cell leukemia-lymphoma syndrome.

ZMYM2_MOUSE / Q9CU65 Zinc finger MYM-type protein 2; Zinc finger protein 198 from Mus musculus (Mouse) (see paper)
20% identity, 19% coverage

• function: Involved in the negative regulation of transcription.
  subunit: Can form homodimers (By similarity). May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Interacts with FOXP1 and FOXP2 (By similarity).

F1MNA8 Zinc finger MYM-type containing 2 from Bos taurus
22% identity, 12% coverage

• Comparison of nanotube-protein corona composition in cell culture media
  Shannahan, Small (Weinheim an der Bergstrasse, Germany) 2013
  • “...6,296,211 F1MI56 ANKRD17 Ankyrin repeat domain-containing protein 17 6,637,200 E1BC55 LOC533883 Uncharacterized protein KIAA1671 6,824,667 F1MNA8 ZMYM2 Zinc finger MYM-type protein 2 7,565,700 F1MGK5 PTPRZ1 Receptor-type tyrosine-protein phosphatase zeta 7,929,133 F1MYC9 SPTBN1 Spectrin beta chain, brain 1 8,029,370 E1BM04 TBKBP1 TANK-binding kinase 1-binding protein 1 8,685,600...”

ZMYM4_HUMAN / Q5VZL5 Zinc finger MYM-type protein 4; Zinc finger protein 262 from Homo sapiens (Human) (see 2 papers)
24% identity, 10% coverage

• function: Plays a role in the regulation of cell morphology and cytoskeletal organization.
• Proteome Analysis of Aflibercept Intervention in Experimental Central Retinal Vein Occlusion
  Cehofski, Molecules (Basel, Switzerland) 2022
  • “...light chain roadblock-type 1 DYNLRB1 0.027 0.85 P36955 Pigment epithelium-derived factor (PEDF) SERPINF1 0.020 0.84 Q5VZL5 Zinc finger MYM-type protein 4 ZMYM4 0.030 0.83 P83916 Chromobox protein homolog 1 CBX1 0.046 0.82 P62272;P62269 40S ribosomal protein S18 RPS18 0.030 0.76 Q9Y2R9 28S ribosomal protein S7, mitochondrial...”
• Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease.
  Lygirou, Journal of translational medicine 2018
  • “...Q5T481 RNA-binding protein 20 4 4.84 9.84E04 4 4.61 2.35E01 [ 47 , 82 ] Q5VZL5 Zinc finger MYM-type protein 4 2 0.36 5.30E03 2 0.38 2.62E01 O15553 Pyrin 2 11.75 1.72E03 2 2.65 2.74E01 [ 49 51 , 83 ] Q96PV0 Ras/Rap GTPase-activating protein SynGAP...”
• Proteomic identification of cyclophilin A as a potential biomarker and therapeutic target in oral submucous fibrosis.
  Yuan, Oncotarget 2016
  • “...Fibrinogen beta chain FGB 55,928/4.14 2 87 P02679 Fibrinogen gamma chain FGG 51,512/5.24 5 112 Q5VZL5 Zinc finger MYM-type protein 4 ZMYM4 172,788/6.46 3 85 Q9UJY1 Heat shock protein beta-8 HSPB8 21,604/ 3 69 P02766 Transthyretin TTR 15,887/5.35 5 188 P06732 muscle creatine kinase M CKM...”
• Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum
  Gao, Cancer biology & medicine 2015
  • “...6 OS=Homo sapiens GN=UBXN6 PE=1 SV=1 - [UBXN6_HUMAN] 4.08 1 1 1 441 49.7 6.89 Q5VZL5 Zinc finger MYM-type protein 4 OS=Homo sapiens GN=ZMYM4 PE=1 SV=1 - [ZMYM4_HUMAN] 0.52 1 1 1 1,548 172.7 6.84 Q6ZQV5 Zinc finger protein 788 OS=Homo sapiens GN=ZNF788 PE=2 SV=2 -...”
• Splicing factor 2-associated protein p32 participates in ribosome biogenesis by regulating the binding of Nop52 and fibrillarin to preribosome particles
  Yoshikawa, Molecular & cellular proteomics : MCP 2011
  • “...112 113 Unknown Q96JP5 Q9H5H4 Q14966 Q8NAF0 Q5VZL5 Q8N9Z2 Q9Y4P3 Q9UJZ1 Q9P2N5 Q5T8P6 Q9NWS8 ZFP91_HUMAN ZN768_HUMAN ZN638_HUMAN ZN579_HUMAN ZMYM4_HUMAN...”

ZN276_HUMAN / Q8N554 Zinc finger protein 276; Zfp-276; Zinc finger protein 477 from Homo sapiens (Human) (see paper)
29% identity, 13% coverage

• function: May be involved in transcriptional regulation
• Proteomic profile of follicular fluid from patients with polycystic ovary syndrome (PCOS) submitted to in vitro fertilization (IVF) compared to oocyte donors
  Domingues, JBRA assisted reproduction 2019
  • “...2 tight junction(PC00070);transcription cofactor(PC00214) sequence-specific DNA binding transcription factor activity(GO:0005488);transcription cofactor activity(GO:0003676) plasma membrane(GO:0016020) 1 Q8N554 Zinc finger protein 276 NA NA NA 1 Q8N8Z8 Zinc finger protein 441 NA NA NA 1 Q8NA56 Tetratricopeptide repeat protein 29 guanyl-nucleotide exchange factor(PC00095);transmembrane receptor regulatory/adaptor protein(PC00022) guanyl-nucleotide exchange...”

ZN276_MOUSE / Q8CE64 Zinc finger protein 276; Zfp-276 from Mus musculus (Mouse) (see paper)
NP_065243 zinc finger protein 276 from Mus musculus
35% identity, 9% coverage

• function: May be involved in transcriptional regulation
• Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program.
  Aberle, Nucleic acids research 2022
  • GeneRIF: Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program.

QRIC1_HUMAN / Q2TAL8 Transcriptional regulator QRICH1; Glutamine-rich protein 1 from Homo sapiens (Human) (see 4 papers)
NP_001307513 transcriptional regulator QRICH1 from Homo sapiens
22% identity, 34% coverage

• function: Transcriptional regulator that acts as a mediator of the integrated stress response (ISR) through transcriptional control of protein homeostasis under conditions of ER stress (PubMed:33384352). Controls the outcome of the unfolded protein response (UPR) which is an ER-stress response pathway (PubMed:33384352). ER stress induces QRICH1 translation by a ribosome translation re-initiation mechanism in response to EIF2S1/eIF-2-alpha phosphorylation, and stress-induced QRICH1 regulates a transcriptional program associated with protein translation, protein secretion-mediated proteotoxicity and cell death during the terminal UPR (PubMed:33384352). May cooperate with ATF4 transcription factor signaling to regulate ER homeostasis which is critical for cell viability (PubMed:33384352). Up-regulates CASP3/caspase-3 activity in epithelial cells under ER stress. Central regulator of proteotoxicity associated with ER stress-mediated inflammatory diseases in the intestines and liver (PubMed:33384352). Involved in chondrocyte hypertrophy, a process required for normal longitudinal bone growth (PubMed:30281152).
• Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets.
  Gubina, Biomolecules 2020
  • “...3 ( PSMC3 ) PRS6A P17980 DILDPALL Stab glutamine rich 1 ( QRICH1 ) QRIC1 Q2TAL8 LTVDSAHL Stab RNA binding motif protein 22 ( RBM22 ) RBM22 Q9NW64 SNSDGTRP Stab RNA binding motif protein 39 ( RBM39 ) RBM39 Q14498 ERTDASSA Stab replication factor C subunit...”
• TCTEX1D4 interactome in human testis: unraveling the function of dynein light chain in spermatozoa
  Freitas, Omics : a journal of integrative biology 2014
  • “...KYVFF RKVNW RVAW - 2 1 1 1 2 Q96GD0 22cen-q12.3 - Q2TAL8 3p21.31 All isoforms (2) Q96S59 6p23 - Q9BQ04 11q13 - Q96T21 9q22.2 - - - RMIHF - LNVAW 1 Q9HCE7 7q22.1...”
• QRICH1 suppresses pediatric T-cell acute lymphoblastic leukemia by inhibiting GRP78.
  Zhao, Cell death & disease 2024
  • GeneRIF: QRICH1 suppresses pediatric T-cell acute lymphoblastic leukemia by inhibiting GRP78.
• QRICH1 variants in Ververi-Brady syndrome-delineation of the genotypic and phenotypic spectrum.
  Föhrenbach, Clinical genetics 2021 (PubMed)
  • GeneRIF: QRICH1 variants in Ververi-Brady syndrome-delineation of the genotypic and phenotypic spectrum.
• QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis.
  You, Science (New York, N.Y.) 2021
  • GeneRIF: QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis.
• A case of Ververi-Brady syndrome due to QRICH1 loss of function and the literature review.
  Baruch, American journal of medical genetics. Part A 2021 (PubMed)
  • GeneRIF: A case of Ververi-Brady syndrome due to QRICH1 loss of function and the literature review.
• QRICH1 mutations cause a chondrodysplasia with developmental delay.
  Lui, Clinical genetics 2019
  • GeneRIF: Our findings indicate that QRICH1 mutations cause not only developmental delay but also a chondrodysplasia characterized by diminished linear growth and abnormal growth plate morphology due to impaired growth plate chondrocyte hypertrophic differentiation.
• Phenotypic spectrum associated with de novo mutations in QRICH1 gene.
  Ververi, Clinical genetics 2018 (PubMed)
  • GeneRIF: Despite their small number, the patients had a relatively consistent pattern of clinical features suggesting the presence of a QRICH1-associated phenotype. LoF mutations in QRICH1 are suggested as a novel cause of developmental delay.

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How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.