LOCUS       NM_001045334            3735 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Danio rerio selenoprotein S (selenos), mRNA.
ACCESSION   NM_001045334
VERSION     NM_001045334.3
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 3735)
  AUTHORS   Ichino,N., Serres,M.R., Urban,R.M., Urban,M.D., Treichel,A.J.,
            Schaefbauer,K.J., Tallant,L.E., Varshney,G.K., Skuster,K.J.,
            McNulty,M.S., Daby,C.L., Wang,Y., Liao,H.K., El-Rass,S., Ding,Y.,
            Liu,W., Anderson,J.L., Wishman,M.D., Sabharwal,A., Schimmenti,L.A.,
            Sivasubbu,S., Balciunas,D., Hammerschmidt,M., Farber,S.A.,
            Wen,X.Y., Xu,X., McGrail,M., Essner,J.J., Burgess,S.M., Clark,K.J.
            and Ekker,S.C.
  TITLE     Building the vertebrate codex using the gene breaking protein trap
            library
  JOURNAL   Elife 9, e54572 (2020)
   PUBMED   32779569
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3735)
  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   3  (bases 1 to 3735)
  AUTHORS   Gladyshev,V.N., Arner,E.S., Berry,M.J., Brigelius-Flohe,R.,
            Bruford,E.A., Burk,R.F., Carlson,B.A., Castellano,S., Chavatte,L.,
            Conrad,M., Copeland,P.R., Diamond,A.M., Driscoll,D.M., Ferreiro,A.,
            Flohe,L., Green,F.R., Guigo,R., Handy,D.E., Hatfield,D.L.,
            Hesketh,J., Hoffmann,P.R., Holmgren,A., Hondal,R.J., Howard,M.T.,
            Huang,K., Kim,H.Y., Kim,I.Y., Kohrle,J., Krol,A., Kryukov,G.V.,
            Lee,B.J., Lee,B.C., Lei,X.G., Liu,Q., Lescure,A., Lobanov,A.V.,
            Loscalzo,J., Maiorino,M., Mariotti,M., Sandeep Prabhu,K.,
            Rayman,M.P., Rozovsky,S., Salinas,G., Schmidt,E.E., Schomburg,L.,
            Schweizer,U., Simonovic,M., Sunde,R.A., Tsuji,P.A., Tweedie,S.,
            Ursini,F., Whanger,P.D. and Zhang,Y.
  TITLE     Selenoprotein Gene Nomenclature
  JOURNAL   J Biol Chem 291 (46), 24036-24040 (2016)
   PUBMED   27645994
REFERENCE   4  (bases 1 to 3735)
  AUTHORS   Garcia-Reyero,N., Escalon,L., Prats,E., Faria,M., Soares,A.M. and
            Raldua,D.
  TITLE     Targeted Gene Expression in Zebrafish Exposed to Chlorpyrifos-Oxon
            Confirms Phenotype-Specific Mechanisms Leading to Adverse Outcomes
  JOURNAL   Bull Environ Contam Toxicol 96 (6), 707-713 (2016)
   PUBMED   27086301
REFERENCE   5  (bases 1 to 3735)
  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 3735)
  AUTHORS   Mariotti,M., Ridge,P.G., Zhang,Y., Lobanov,A.V., Pringle,T.H.,
            Guigo,R., Hatfield,D.L. and Gladyshev,V.N.
  TITLE     Composition and evolution of the vertebrate and mammalian
            selenoproteomes
  JOURNAL   PLoS One 7 (3), e33066 (2012)
   PUBMED   22479358
REFERENCE   7  (bases 1 to 3735)
  AUTHORS   Canestro,C., Catchen,J.M., Rodriguez-Mari,A., Yokoi,H. and
            Postlethwait,J.H.
  TITLE     Consequences of lineage-specific gene loss on functional evolution
            of surviving paralogs: ALDH1A and retinoic acid signaling in
            vertebrate genomes
  JOURNAL   PLoS Genet 5 (5), e1000496 (2009)
   PUBMED   19478994
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CU856378.10.
            
            On Jan 23, 2017 this sequence version replaced NM_001045334.2.
            
            Summary: This gene encodes a transmembrane protein that is
            localized in the endoplasmic reticulum (ER). It is involved in the
            degradation process of misfolded proteins in the ER, and may also
            have a role in inflammation control in higher eukaryotes. This
            protein is a selenoprotein, containing the rare amino acid
            selenocysteine (Sec). Sec is encoded by the UGA codon, which
            normally signals translation termination. The 3' UTRs of
            selenoprotein mRNAs in vertebrates contain a conserved stem-loop
            structure, designated the Sec insertion sequence (SECIS) element,
            that is necessary for the recognition of UGA as a Sec codon, rather
            than as a stop signal. [provided by RefSeq, Aug 2017].
            
            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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: EG574131.1, BC118685.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2168446, SAMEA2168447
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            protein contains selenocysteine :: inferred from conservation
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-231               CU856378.10        27231-27461         c
            232-366             CU856378.10        23268-23402         c
            367-473             CU856378.10        23003-23109         c
            474-563             CU856378.10        17990-18079         c
            564-636             CU856378.10        17849-17921         c
            637-3735            CU856378.10        13445-16543         c
FEATURES             Location/Qualifiers
     source          1..3735
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="7"
                     /map="7"
     gene            1..3735
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="selenoprotein S"
                     /db_xref="GeneID:735249"
                     /db_xref="ZFIN:ZDB-GENE-060804-1"
     exon            1..231
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    144..146
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="upstream in-frame stop codon"
     CDS             150..722
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="UGA stop codon recoded as selenocysteine;
                     VCP-interacting membrane protein; VCP-interacting membrane
                     selenoprotein"
                     /codon_start=1
                     /transl_except=(pos:714..716,aa:Sec)
                     /product="selenoprotein S"
                     /protein_id="NP_001038799.2"
                     /db_xref="GeneID:735249"
                     /db_xref="ZFIN:ZDB-GENE-060804-1"
                     /translation="

MEAEDGARVRNEDVPPQNQDLSFLQPSVTAFMSEYGWYLLFGCVGVYLLIQHLRKSRSSTQTRSSSGSAEAHDVGSVVRRQEALEASRRRMQEEQDARAAEFREKQRMLEEEKRRQKIEMWDSMQEGKSYKGSAKVAQQNTEEAASSSSLRPKTEKKPLRSSGYSPLSGDAGGSCSWRPGRRGPSAGGUG"

     misc_feature    150..713
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="Selenoprotein S (SelS); Region: Selenoprotein_S;
                     pfam06936"
                     /db_xref="CDD:462043"
     misc_feature    150..209
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="propagated from UniProtKB/Swiss-Prot (Q0VFV6.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    237..299
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="propagated from UniProtKB/Swiss-Prot (Q0VFV6.2);
                     transmembrane region"
     misc_feature    327..719
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="propagated from UniProtKB/Swiss-Prot (Q0VFV6.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    714..716
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="Selenocysteine; other site"
     exon            232..366
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /inference="alignment:Splign:2.1.0"
     exon            367..473
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /inference="alignment:Splign:2.1.0"
     exon            474..563
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /inference="alignment:Splign:2.1.0"
     exon            564..636
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /inference="alignment:Splign:2.1.0"
     exon            637..3735
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1404..1481
                     /regulatory_class="recoding_stimulatory_region"
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
                     /note="SECIS_element"
                     /function="essential for recoding UGA to specify
                     selenocysteine"
     regulatory      3585..3590
                     /regulatory_class="polyA_signal_sequence"
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
     polyA_site      3606
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
     regulatory      3717..3722
                     /regulatory_class="polyA_signal_sequence"
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
     polyA_site      3735
                     /gene="selenos"
                     /gene_synonym="sels; vimp; wu:fc16a03; zgc:136970"
ORIGIN      

cgctgattggctgtctcacggctgcggaagtgagtcagtgtggcgttgcaggttagctcgcgtacagcaacaagaagagaataaacatgtgttagttattatatattttcaaaacaatatcgtaaaacagctcaaaggtgctgtgaaggatggaggcggaggacggagcgcgtgtccggaatgaagatgttcctccgcagaaccaggatctaagtttccttcaaccgtctgtcactgcgttcatgtcggagtatggctggtatctgctgttcggatgtgttggagtgtatctgctcatccagcatctccgcaagagcagatcctccacacaaacacgcagctcgtctggctcagccgaggctcacgatgtggggtcagtggtgaggcgtcaggaggctctggaggcgtcccgcaggagaatgcaggaggagcaggacgccagagcagctgagttcagggagaaacagcgcatgctggaggaggagaagaggaggcagaagatcgagatgtgggacagcatgcaggaaggaaagagttacaaagggagcgctaaagttgcacaacagaacacagaagaggcggcttcatccagctcgctgagaccaaagacagagaagaaacccctgcgcagcagtggctacagtcctctgtcaggagacgctggaggctcgtgctcctggaggcccggccgcagaggcccgtctgctggaggatgaggataaacgcccgtcagactcgtctctgacgctcccacaggaacacacacatctatatctgaatgaagctgtcagcctcatcactgcacaataactcccataatacacacaatacagaatcattgcatttccaatcatgcatactgttacttttagtcacactttacaataaggtttcataactgaagtatttacttacttataatgaacaatactagtacagcatttgttaatcatagttcaacattacctaatgcattattcaaatcctaaatcatcatcgttaacactatgagctagcattaaatggctttattttcatgaactaacattaacagagctaaatactgtaatatattgtttatgtaagtaaatattaactaatatgtcctattgtaaaccatattaacctatttatttatattactcaacaaatatatgtattcttaaatgaatatactgtagtgcgcagcttaaaacaaacatattcagttaaattaaaggttaaattacacaataatgcttaaaatagacaattatatacttcttttatgcataataatcacatttgcgatcaaaatgacgtcaatatccacatttgtttttcttttctgccttgtaaatgatttttaaacaagtgtttttcactttctttatgattattatgatggttattatgccagtgtatgattgacggcttcagatgacgcctcctcaccaaaggtattatttactcccgaggcggctgatgagtttcagtaatgaaacgtgttcctctttttttatttcgttgttgcttttgcacttaaatgctgtgctaaatacaaatctagagggatttaaagggggcagatcactcaaaaatgaaagtttccttgtttacttactcacctacagaacatgcaagatcgtaggcactttctttcttcttcagcagaacattaaagaagcgtttaagctgaatctgacgtgattcatataatgaaaataaatggtgagcagtttttttttacattaataataaacgcatatcaatgagtccaagtcagtagtcatggcacactgaggtttctagaagtaaaatgattggtctgtgtaagacattaaacatgatgcacaatattattaccttaaatccacagcctgctcaatgtagtccaattgtaacttcaattacaaatacggaagaaagcatgctaggatggaggaaatcaaaagagaaatatattcatcatcaaaggtgcctagaccaggggtcaccaaccctgttcctggagagctgccttcctgcagaattcagtcccaaccctgatcaaacacacctgaaccaattaatagtacctaaagcagcacttgataattacaaacaggtgtgtttggtcagggttgcaactgaaatgtgcaggaaggtagatctccaggaacagggttggtgacccctggcctagactacatttacataagaatagagatgcactgatttattggttaaattgtgtttttggatgggtttttttcccgaaaaagaaaaaaatgagcgaaataatgcaccaataacaggactttttaagcgttcacagctaggtaaagtaactcaatcactgtcaattaaaattttaccttcatataatgaactatcataattaattgtcatggtttaagtgacagatgcatttaaaaagtcttactttatttaacaagtactaaattgttacggcattttcatttcattttttatttcaagtgcatccagaattttaggtttcctccctgaattttcatttcagcgcatccctgcaatcttgatttccatttttgtgaattgtgtcacacaagaaatatctgttaatgaacagtttctgtattttgtgattcacaggtgtgtgtttttgtgttgatttacagttgtgaactgcattatgagaccttaatctctgctctgttgaattttgatgatgattttttttttaaagttgaaaattttaagttctattgacattttagtagtttgaaataatatttagagaaataagattgtaaaatagcagaaaatgtactggcggtttattatgaggcttttgttgtgtaatatacaacaccaatccagacaatatatcactttaaactatgaaaaatgttcactttttccaacttttcagtgttataagttattggaagatcaagagcccataatgcgattcaaaagcagaaataaattaggtaaaatacaaacatgaatcacaaaaaacagaaaactgctcatttatgaatatttttagagtgcatattagtttacagttatggctccatttacacaagttccctaaagaaagtcactttcaggccatttaaacagttctcagcgcatatgcgactggagtctgaatgtagtcctgtcacttcaagtgagcgacctataatcttggctatgcagtttgttgattaaagtgggtttaaagagtgggaataaagctaataacattgtaaataatgctcaatttcttcaacaaactgattatttcacttcacctgacctcagtgtgtcattaggagccacaactattgatctggacttaatctaaaaaacctgtcaccattcactgccattatataaaccaccaaggacccctgattcagctcaaatcttctactgacatcttggatgaggtgagagccagtaaattaactgggtaatttcatttttgtgtgagctattccttgaatacaaacgcaaagtgctatatttctattgtttgtggtgtttgtattctgttgtgaaagtaggagttactgatgtgtctttagtgttgcgcgatctgttttctgaagcttttcttcagaaatattcctgctttggagattctttcaattaaaaagcatatttgcccaatgtttgtatgtgttctttatcaggacaacgaattttaaagggacagttcacccaaaaatttaaatgtagaagcctcaagtgcttctaaacctttcttctgttaaacacaaaataaaatgttttgaagaa

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