2024-11-01 08:34:48, GGRNA.v2 : RefSeq release 226 (Sep, 2024)
LOCUS NM_182865 3807 bp mRNA linear VRT 03-APR-2024 DEFINITION Danio rerio staphylococcal nuclease and tudor domain containing 1 (snd1), transcript variant p100L, mRNA. ACCESSION NM_182865 VERSION NM_182865.3 KEYWORDS RefSeq. SOURCE Danio rerio (zebrafish) ORGANISM Danio rerio Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio. REFERENCE 1 (bases 1 to 3807) AUTHORS Wang,B., Du,X., Wang,H., Jin,C., Gao,C., Liu,J. and Zhang,Q. TITLE Comparative studies on duplicated tdrd7 paralogs in teleosts: Molecular evolution caused neo-functionalization JOURNAL Comp Biochem Physiol Part D Genomics Proteomics 30, 347-357 (2019) PUBMED 31059868 REFERENCE 2 (bases 1 to 3807) AUTHORS Dai,X., Shu,Y., Lou,Q., Tian,Q., Zhai,G., Song,J., Lu,S., Yu,H., He,J. and Yin,Z. TITLE Tdrd12 Is Essential for Germ Cell Development and Maintenance in Zebrafish JOURNAL Int J Mol Sci 18 (6), 1127 (2017) PUBMED 28590408 REMARK Publication Status: Online-Only REFERENCE 3 (bases 1 to 3807) AUTHORS Bayes,A., Collins,M.O., Reig-Viader,R., Gou,G., Goulding,D., Izquierdo,A., Choudhary,J.S., Emes,R.D. and Grant,S.G. TITLE Evolution of complexity in the zebrafish synapse proteome JOURNAL Nat Commun 8, 14613 (2017) PUBMED 28252024 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 3807) AUTHORS Pasquier,J., Cabau,C., Nguyen,T., Jouanno,E., Severac,D., Braasch,I., Journot,L., Pontarotti,P., Klopp,C., Postlethwait,J.H., Guiguen,Y. and Bobe,J. TITLE Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database JOURNAL BMC Genomics 17, 368 (2016) PUBMED 27189481 REMARK Publication Status: Online-Only REFERENCE 5 (bases 1 to 3807) AUTHORS Elkon,R., Milon,B., Morrison,L., Shah,M., Vijayakumar,S., Racherla,M., Leitch,C.C., Silipino,L., Hadi,S., Weiss-Gayet,M., Barras,E., Schmid,C.D., Ait-Lounis,A., Barnes,A., Song,Y., Eisenman,D.J., Eliyahu,E., Frolenkov,G.I., Strome,S.E., Durand,B., Zaghloul,N.A., Jones,S.M., Reith,W. and Hertzano,R. TITLE RFX transcription factors are essential for hearing in mice JOURNAL Nat Commun 6, 8549 (2015) PUBMED 26469318 REMARK Publication Status: Online-Only REFERENCE 6 (bases 1 to 3807) AUTHORS Phetrungnapha,A., Panyim,S. and Ongvarrasopone,C. TITLE A Tudor staphylococcal nuclease from Penaeus monodon: cDNA cloning and its involvement in RNA interference JOURNAL Fish Shellfish Immunol 31 (3), 373-380 (2011) PUBMED 21745576 REFERENCE 7 (bases 1 to 3807) AUTHORS Hoffmann,J.L., Thomason,R.G., Lee,D.M., Brill,J.L., Price,B.B., Carr,G.J. and Versteeg,D.J. TITLE Hepatic gene expression profiling using GeneChips in zebrafish exposed to 17alpha-methyldihydrotestosterone JOURNAL Aquat Toxicol 87 (2), 69-80 (2008) PUBMED 18339436 REFERENCE 8 (bases 1 to 3807) AUTHORS Abe,S., Wang,P.L., Takahashi,F. and Sasaki,E. TITLE Structural analysis of cDNAs coding for 4SNc-Tudor domain protein from fish and their expression in yellowtail organs JOURNAL Mar Biotechnol (NY) 7 (6), 677-686 (2005) PUBMED 16132464 REFERENCE 9 (bases 1 to 3807) AUTHORS Zhao,C.T., Shi,K.H., Su,Y., Liang,L.Y., Yan,Y., Postlethwait,J. and Meng,A.M. TITLE Two variants of zebrafish p100 are expressed during embryogenesis and regulated by Nodal signaling JOURNAL FEBS Lett 543 (1-3), 190-195 (2003) PUBMED 12753931 REMARK GeneRIF: Two alternative transcripts of p100 are expressed during embryogenesis and regulated by Nodal signaling. REFERENCE 10 (bases 1 to 3807) AUTHORS Abe,S., Sakai,M., Yagi,K., Hagino,T., Ochi,K., Shibata,K. and Davies,E. TITLE A Tudor protein with multiple SNc domains from pea seedlings: cellular localization, partial characterization, sequence analysis, and phylogenetic relationships JOURNAL J Exp Bot 54 (384), 971-983 (2003) PUBMED 12598568 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from BX897731.7, BX855622.6, CR931778.23 and BX890545.7. On Jun 13, 2014 this sequence version replaced NM_182865.2. Transcript Variant: This variant (p100L) represents the longer transcript and encodes the longer protein (isoform p100L). Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AY272050.1, GFIL01039121.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA2168446, SAMEA2168447 [ECO:0000350] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-288 BX897731.7 53106-53393 289-438 BX897731.7 56770-56919 439-559 BX897731.7 60710-60830 560-641 BX897731.7 60959-61040 642-802 BX897731.7 65530-65690 803-894 BX897731.7 70026-70117 895-1053 BX897731.7 71936-72094 1054-1160 BX897731.7 81197-81303 1161-1251 BX897731.7 82218-82308 1252-1356 BX897731.7 95334-95438 1357-1458 BX855622.6 19861-19962 1459-1562 BX855622.6 33936-34039 1563-1673 BX855622.6 38455-38565 1674-1746 BX855622.6 41870-41942 1747-1888 BX855622.6 46665-46806 1889-1998 BX855622.6 82555-82664 1999-2187 CR931778.23 33619-33807 c 2188-2329 BX890545.7 176580-176721 c 2330-2453 BX890545.7 149973-150096 c 2454-2523 BX890545.7 145998-146067 c 2524-2637 BX890545.7 142834-142947 c 2638-2841 BX890545.7 138889-139092 c 2842-2886 BX890545.7 125986-126030 c 2887-3807 BX890545.7 121112-122032 c FEATURES Location/Qualifiers source 1..3807 /organism="Danio rerio" /mol_type="mRNA" /strain="Tuebingen" /db_xref="taxon:7955" /chromosome="4" /map="4" gene 1..3807 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="staphylococcal nuclease and tudor domain containing 1" /db_xref="GeneID:324404" /db_xref="ZFIN:ZDB-GENE-030131-3124" exon 1..288 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" misc_feature 124..126 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="upstream in-frame stop codon" CDS 211..2952 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /EC_number="3.1.31.1" /note="isoform p100L is encoded by transcript variant p100L; staphylococcal nuclease domain-containing protein 1; 4SNc-Tudor domain protein; p100 co-activator; 100 kDa coactivator; staphylococcal nuclease domain containing 1" /codon_start=1 /product="staphylococcal nuclease domain-containing protein 1 isoform p100L" /protein_id="NP_878285.3" /db_xref="GeneID:324404" /db_xref="ZFIN:ZDB-GENE-030131-3124" /translation="
MASAVPAQVQSSQASAPQLQRGIVKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGALARRAIQGQPDTKDTPDEPWAFQAREFMRKKVIGKEVCFTVENKTPQGREYGMVYLGKDTSGENIAESLVAEGLAMVRREGIRGNNPEQVRLCDLEDQAKSSKKGLWSEGGGSHTIRDLKYTIENPRNFVDSLHQKPVNAIIEHVRDGCMVRALLLPDYYLVTVMLSGIKSPTFKREADGSETPEPFAAEAKFFTESRLLQRDVQIILESCPNQVILGTILHPNGNITELLLKEGFARCVDWSMAVYTQGAEKLRAAERSAKERKVRIWKDYVAPTANLDQKDRQFVAKVMQVVNADAIVVKLNSGEYKTIHLSSIRPPRLEGEEKNKDKDKRFRPLYDIPYMFEAREFLRKKLIGKKVNVTVDYIRAATNAMEMGVPAFPERTCATVTIGGINIAEALVSKGLATVIRYRQDDDQRSSHYDELLAAEARAIKNGKGLHSKKEVPIHRVADISGETQKAKQFFPFLQRAGRSEAVVEYVFSGSRLKLYMPKETCLITFLLAGIECPRGSRNMPGGMQVAEPYSEEAMLFTKELVLQREVEVEVESMDKAGNFIGWLHIEGVNLSVALVENALSKVHFTAERSSYYKTLVSAEESARQRKEKLWANYEEKPKEEVAQVTEAKERVAKYRSVYVTEITDGLHFYAQDVETGTKLENLMESMRGEIAAQPPVEGSFAPRRGEFCIAKFADGEWYRARVEKVESPAKVHVFYIDYGNREVLSSTRLAALPPAFSTRTLPPQATEYAFAYIQVPQDEDARADAVDSVVRDIHNTQCLLNVEYSGSVCPQVTLQFADTKEDVGLGLVKEGMVMVDIRKEKYLQKMVTEYLNAQESAKSARLNIWRYGDFRDDDADEFGYRR"
mat_peptide 211..2901 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /product="Staphylococcal nuclease domain-containing protein 1. /id=PRO_0000183183" /note="propagated from UniProtKB/Swiss-Prot (Q7ZT42.1)" misc_feature 262..711 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Staphylococcal nuclease homologues; Region: SNc; smart00318" /db_xref="CDD:214615" misc_feature order(301..303,355..357,373..375,382..384,520..525, 529..531) /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Catalytic site; other site" /db_xref="CDD:238102" misc_feature 790..1197 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Staphylococcal nuclease homologues; Region: SNc; smart00318" /db_xref="CDD:214615" misc_feature order(829..831,874..876,892..894,901..903,1018..1023, 1027..1029) /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Catalytic site; other site" /db_xref="CDD:238102" misc_feature 1261..1707 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175" /db_xref="CDD:238102" misc_feature order(1273..1275,1315..1317,1333..1335,1342..1344, 1522..1527,1531..1533) /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Catalytic site; other site" /db_xref="CDD:238102" misc_feature 1816..2199 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175" /db_xref="CDD:238102" misc_feature order(1831..1833,1876..1878,1894..1896,1903..1905, 2026..2031,2035..2037) /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Catalytic site; other site" /db_xref="CDD:238102" misc_feature 2326..2574 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; Region: Tudor_TDRD11; cd20433" /db_xref="CDD:410504" misc_feature order(2341..2343,2437..2439,2443..2445,2455..2457, 2506..2508,2515..2517,2521..2523) /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="peptide binding site [polypeptide binding]; other site" /db_xref="CDD:410504" misc_feature <2749..2904 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /note="Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140" /db_xref="CDD:469627" exon 289..438 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 439..559 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 560..641 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 642..802 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 803..894 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 895..1053 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1054..1160 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1161..1251 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1252..1356 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1357..1458 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1459..1562 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1563..1673 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1674..1746 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1747..1888 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1889..1998 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 1999..2187 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2188..2329 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2330..2453 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2454..2523 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2524..2637 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2638..2841 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2842..2886 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" exon 2887..3807 /gene="snd1" /gene_synonym="SN4TDR; TDRD11; wu:fc27g10" /inference="alignment:Splign:2.1.0" ORIGIN
gcgcgggtgacgctctgaccgaggaagtgcaacatttcgacgtgtacattcacgcgctgtgcttccggttaagcaaagcgtgatcagtcgtgctcagtctctcttcccttcctcggctctcagtagagacgtctcgtaggactctcccggctcctttacctctctctctcttttccctccctaacggaatactcattcatcccagcggccatggcatctgcggtaccggcacaagttcagtccagccaagcgtcagccccgcagctgcagaggggaatagtgaagatggtgttatcgggttgtgctatcattgttcgaggtcagccacgaggtggacctcctccagaacgacagatcaacctgagtaacataagagccggagctctagcccgtcgtgcaattcagggtcagccagacaccaaggacacaccagatgagccatgggctttccaggcacgagagtttatgcgcaagaaggtaatcggcaaagaagtctgcttcactgtggagaataaaactcctcaaggcagagaatatggcatggtttacctgggaaaagacacatcaggagaaaatattgccgaatccctggtggctgagggtcttgctatggttcgcagagaaggcatcagaggaaacaatcctgagcaggtcagactgtgtgatttggaggatcaagccaagtcttctaaaaagggcctgtggtctgagggtggaggctcgcacaccattcgagatctcaagtacaccatcgagaaccctcgcaacttcgtggactccctgcatcagaaaccagtcaacgctattatcgagcatgtgcgcgatggctgcatggttcgagcactacttctgcccgactactatctggtgacagtcatgctgtctggaatcaagagccctacgtttaagcgggaggcagatggcagcgagacccctgagcccttcgcagcagaggcaaagttcttcaccgagtctcgacttcttcagcgagatgtgcagatcattttggagtcctgtccaaaccaggtcattctgggaaccatcttgcatccgaacggaaacatcacggagctgctgctgaaggagggctttgctcgctgtgttgactggtccatggctgtttacactcagggtgcagagaagctcagagcagcagagcgatcagcaaaagagcgtaaagtgagaatttggaaggactatgttgctcccacagccaatctggaccagaaggacagacagtttgttgcaaaggtgatgcaggtcgtgaacgcagatgccatcgtggtgaagctgaactctggggaatataagaccatccacctgtccagcatcagacccccgaggctcgaaggcgaggagaagaacaaggacaaggacaagcgtttccgtccactctatgacattccttacatgtttgaggcacgcgaattcttgaggaagaagctcattggcaagaaggttaatgtcacagttgattacatcagagctgccaccaatgccatggaaatgggcgtcccggctttcccagagcgcacctgtgctacagtcaccattggaggaataaacatcgccgaggcactggtcagcaaaggtcttgccacagtgatcagataccgccaagatgacgatcaaagatcttctcattacgacgagctcctggcagcagaggcgagggcgatcaagaatggcaaaggacttcacagcaagaaagaagtgcccattcatagagtggcggacatttcaggggagacacagaaggcgaaacagtttttcccattcctgcagagagcgggccgctcggaggctgtggtggagtacgtgttcagtggctccagactcaagctctacatgcccaaagagacgtgtctcatcaccttcttgctcgctggaatcgagtgtccccgagggtctcgtaacatgccaggtgggatgcaggtggcagagccatacagtgaagaagctatgctgttcaccaaagaactggttcttcagagagaggtggaagtggaagtggagagcatggataaagcagggaacttcattggctggcttcacattgagggcgtgaatctgtctgtggctctggtggaaaatgccctatctaaggttcacttcactgcagagagaagctcctactacaagactctggtgtctgcagaggaaagcgcaagacagaggaaagagaagctttgggccaattatgaagagaaaccaaaagaagaggtggctcaggtcacagaggcgaaagaacgtgtggcgaaatacagatccgtctacgtcactgagatcacagatggactgcacttctatgcgcaggatgtggaaaccggtactaagctggagaacctgatggagagcatgcgaggagagattgcagcccagcctccagtggaaggatcctttgctccacgcagaggggagttctgcatcgcaaagtttgctgacggagaatggtacagagctcgtgttgagaaagtggaatctccagcaaaggttcacgtgttctacatcgactatggaaacagagaggttttatcctccacgcgtctcgcagctcttcctccagccttcagcacgcgtacacttcctccacaggctacagagtacgcgtttgcctacattcaggtcccgcaggatgaagacgctcgtgccgatgccgtggacagtgtggtgagggacatccacaacacacagtgtctgctgaatgtggagtacagcggcagcgtctgtccgcaggtcacgctccagttcgcagacactaaagaagatgtgggtctgggtctggtcaaagaaggcatggtcatggtggacatccggaaagagaagtacctccagaaaatggtgactgaatatctgaatgcccaggaatctgccaagagcgccaggctcaacatttggcgttatggagatttccgtgacgatgatgcggacgagttcggttatcgacgctaagttgttgctccaaagaccttgtggaagaccagatgcatttgcagagaacacaaaacacaaaaaatcatgaaaaaacaaactcaacaaaacatcagtatgcttttatttgttttgtttttcctatgttgaacatttgcctctctccgttgttttttttttttatatatactctgtgcatatcctctcttctgcccaaggactttcagtttctaattttttttaaagcaagtacgctacagataaatctacctgtcgctgcttctaataggaccaacgtatttaccttaattttacgttttgacatgatagccaatcacgttttttctttttttcgtcatgtaaatttttttagccaatcaccagctgtcaaaccccgtcttagcgaacctgatcagctcagtcagatgtctatgttttggggcaagacttttaaagaaatgaggggaatgatgcacagagcaaccatgagcttatcgagaaaacgcctccttaatcatgagattctatatttcaatacgtatatatatatggatattttgaagttagatcaaaactaaccaagtgaacttacttgagcgtatttccgtctctctctctctctgatgtgatctgagtgttcagtgacatttctgggcatttgtgtaggacgtgtgttttctcttttcatgtgacaaaagaagcaccttttccaggcgtctctgggcttcctgtgaggtttactctacgctcagcgtttcttcttctcccgctcttgcccgccatacagaaacagtgtttgaatttgtttcctcctgaggtagaccctgtcattgtatttaaagctgataaataaaaaaaaatgagcaaagtgaaacg
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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
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