LOCUS       NM_001293681            2340 bp    mRNA    linear   VRT 26-FEB-2023
DEFINITION  Danio rerio staphylococcal nuclease and tudor domain containing 1
            (snd1), transcript variant p100S, mRNA.
ACCESSION   NM_001293681
VERSION     NM_001293681.1
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 2340)
  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 2340)
  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 2340)
  AUTHORS   Bayes A, Collins MO, Reig-Viader R, Gou G, Goulding D, Izquierdo A,
            Choudhary JS, Emes RD and Grant SG.
  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 2340)
  AUTHORS   Pasquier J, Cabau C, Nguyen T, Jouanno E, Severac D, Braasch I,
            Journot L, Pontarotti P, Klopp C, Postlethwait JH, 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 2340)
  AUTHORS   Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M,
            Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD,
            Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov
            GI, Strome SE, Durand B, Zaghloul NA, Jones SM, 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 2340)
  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 2340)
  AUTHORS   Hoffmann JL, Thomason RG, Lee DM, Brill JL, Price BB, Carr GJ and
            Versteeg DJ.
  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 2340)
  AUTHORS   Abe S, Wang PL, 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 2340)
  AUTHORS   Zhao CT, Shi KH, Su Y, Liang LY, Yan Y, Postlethwait J and Meng AM.
  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 2340)
  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 and BX855622.6.
            
            Transcript Variant: This variant (p100S) lacks multiple 3' exons
            and extends beyond a splice site used in variant p100L. The
            resulting protein (isoform p100S) is shorter and has a distinct
            C-terminus compared to 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 :: AF422806.1 [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
            1747-2340           BX855622.6         46665-47258
FEATURES             Location/Qualifiers
     source          1..2340
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="4"
                     /map="4"
     gene            1..2340
                     /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..1935
                     /gene="snd1"
                     /gene_synonym="SN4TDR; TDRD11; wu:fc27g10"
                     /EC_number="3.1.31.1"
                     /note="isoform p100S is encoded by transcript variant
                     p100S; 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 p100S"
                     /protein_id="NP_001280610.1"
                     /db_xref="GeneID:324404"
                     /db_xref="ZFIN:ZDB-GENE-030131-3124"
                     /translation="

MASAVPAQVQSSQASAPQLQRGIVKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGALARRAIQGQPDTKDTPDEPWAFQAREFMRKKVIGKEVCFTVENKTPQGREYGMVYLGKDTSGENIAESLVAEGLAMVRREGIRGNNPEQVRLCDLEDQAKSSKKGLWSEGGGSHTIRDLKYTIENPRNFVDSLHQKPVNAIIEHVRDGCMVRALLLPDYYLVTVMLSGIKSPTFKREADGSETPEPFAAEAKFFTESRLLQRDVQIILESCPNQVILGTILHPNGNITELLLKEGFARCVDWSMAVYTQGAEKLRAAERSAKERKVRIWKDYVAPTANLDQKDRQFVAKVMQVVNADAIVVKLNSGEYKTIHLSSIRPPRLEGEEKNKDKDKRFRPLYDIPYMFEAREFLRKKLIGKKVNVTVDYIRAATNAMEMGVPAFPERTCATVTIGGINIAEALVSKGLATVIRYRQDDDQRSSHYDELLAAEARAIKNGKGLHSKKEVPIHRVADISGETQKAKQFFPFLQRAGRSEAVVEYVFSGSRLKLYMPKETCLITFLLAGKCQPASACQLYHHL"

     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    790..1197
                     /gene="snd1"
                     /gene_synonym="SN4TDR; TDRD11; wu:fc27g10"
                     /note="Staphylococcal nuclease homologues; Region: SNc;
                     smart00318"
                     /db_xref="CDD:214615"
     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"
     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..2340
                     /gene="snd1"
                     /gene_synonym="SN4TDR; TDRD11; wu:fc27g10"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcgcgggtgacgctctgaccgaggaagtgcaacatttcgacgtgtacattcacgcgctgtgcttccggttaagcaaagcgtgatcagtcgtgctcagtctctcttcccttcctcggctctcagtagagacgtctcgtaggactctcccggctcctttacctctctctctcttttccctccctaacggaatactcattcatcccagcggccatggcatctgcggtaccggcacaagttcagtccagccaagcgtcagccccgcagctgcagaggggaatagtgaagatggtgttatcgggttgtgctatcattgttcgaggtcagccacgaggtggacctcctccagaacgacagatcaacctgagtaacataagagccggagctctagcccgtcgtgcaattcagggtcagccagacaccaaggacacaccagatgagccatgggctttccaggcacgagagtttatgcgcaagaaggtaatcggcaaagaagtctgcttcactgtggagaataaaactcctcaaggcagagaatatggcatggtttacctgggaaaagacacatcaggagaaaatattgccgaatccctggtggctgagggtcttgctatggttcgcagagaaggcatcagaggaaacaatcctgagcaggtcagactgtgtgatttggaggatcaagccaagtcttctaaaaagggcctgtggtctgagggtggaggctcgcacaccattcgagatctcaagtacaccatcgagaaccctcgcaacttcgtggactccctgcatcagaaaccagtcaacgctattatcgagcatgtgcgcgatggctgcatggttcgagcactacttctgcccgactactatctggtgacagtcatgctgtctggaatcaagagccctacgtttaagcgggaggcagatggcagcgagacccctgagcccttcgcagcagaggcaaagttcttcaccgagtctcgacttcttcagcgagatgtgcagatcattttggagtcctgtccaaaccaggtcattctgggaaccatcttgcatccgaacggaaacatcacggagctgctgctgaaggagggctttgctcgctgtgttgactggtccatggctgtttacactcagggtgcagagaagctcagagcagcagagcgatcagcaaaagagcgtaaagtgagaatttggaaggactatgttgctcccacagccaatctggaccagaaggacagacagtttgttgcaaaggtgatgcaggtcgtgaacgcagatgccatcgtggtgaagctgaactctggggaatataagaccatccacctgtccagcatcagacccccgaggctcgaaggcgaggagaagaacaaggacaaggacaagcgtttccgtccactctatgacattccttacatgtttgaggcacgcgaattcttgaggaagaagctcattggcaagaaggttaatgtcacagttgattacatcagagctgccaccaatgccatggaaatgggcgtcccggctttcccagagcgcacctgtgctacagtcaccattggaggaataaacatcgccgaggcactggtcagcaaaggtcttgccacagtgatcagataccgccaagatgacgatcaaagatcttctcattacgacgagctcctggcagcagaggcgagggcgatcaagaatggcaaaggacttcacagcaagaaagaagtgcccattcatagagtggcggacatttcaggggagacacagaaggcgaaacagtttttcccattcctgcagagagcgggccgctcggaggctgtggtggagtacgtgttcagtggctccagactcaagctctacatgcccaaagagacgtgtctcatcaccttcttgctcgctggtaagtgtcagccggcctcggcctgtcaactataccaccatctgtgaccacataaccaccacaatgtggcagctgaccgctgttgcgccaccgctctaatgctttttgttcacttgggctagaaaatgaaaatccagtcatgttttcatccatatgctgttgtgtgttttctctttggttgaacaatagagaagtttaagctgctctcatcatatattgaaaatgagaatctctaaaaagcacaaaagtcctcactatattctatataacttgcgatataaataaaattctcttacatttcctgcgttgataaggttggagtttgcatgtacgaccaggaactagaacatatggctttactataagactaaaaaagtaagtgtacggcaggaccatatgtttgatgaggtgttatgaaaaggagcggaataaaacatgattatgcaacactg

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