LOCUS       NM_131165               1540 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Danio rerio homeobox C11a (hoxc11a), mRNA.
ACCESSION   NM_131165
VERSION     NM_131165.2
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 1540)
  AUTHORS   Xue,S., Ly,T.T.N., Vijayakar,R.S., Chen,J., Ng,J., Mathuru,A.S.,
            Magdinier,F. and Reversade,B.
  TITLE     HOX epimutations driven by maternal SMCHD1/LRIF1 haploinsufficiency
            trigger homeotic transformations in genetically wildtype offspring
  JOURNAL   Nat Commun 13 (1), 3583 (2022)
   PUBMED   35739109
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1540)
  AUTHORS   Banu,S., Gaur,N., Nair,S., Ravikrishnan,T., Khan,S., Mani,S.,
            Bharathi,S., Mandal,K., Kuram,N.A., Vuppaladadium,S., Ravi,R.,
            Murthy,C.L.N., Quoseena,M., Babu,N.S. and Idris,M.M.
  TITLE     Understanding the complexity of epimorphic regeneration in
            zebrafish caudal fin tissue: A transcriptomic and proteomic
            approach
  JOURNAL   Genomics 114 (2), 110300 (2022)
   PUBMED   35134499
REFERENCE   3  (bases 1 to 1540)
  AUTHORS   Yamada,K., Maeno,A., Araki,S., Kikuchi,M., Suzuki,M., Ishizaka,M.,
            Satoh,K., Akama,K., Kawabe,Y., Suzuki,K., Kobayashi,D., Hamano,N.
            and Kawamura,A.
  TITLE     An atlas of seven zebrafish hox cluster mutants provides insights
            into sub/neofunctionalization of vertebrate Hox clusters
  JOURNAL   Development 148 (11) (2021)
   PUBMED   34096572
REFERENCE   4  (bases 1 to 1540)
  AUTHORS   Malmstrom,M., Britz,R., Matschiner,M., Torresen,O.K., Hadiaty,R.K.,
            Yaakob,N., Tan,H.H., Jakobsen,K.S., Salzburger,W. and Ruber,L.
  TITLE     The Most Developmentally Truncated Fishes Show Extensive Hox Gene
            Loss and Miniaturized Genomes
  JOURNAL   Genome Biol Evol 10 (4), 1088-1103 (2018)
   PUBMED   29684203
REFERENCE   5  (bases 1 to 1540)
  AUTHORS   Jimenez,L., Wang,J., Morrison,M.A., Whatcott,C., Soh,K.K.,
            Warner,S., Bearss,D., Jette,C.A. and Stewart,R.A.
  TITLE     Phenotypic chemical screening using a zebrafish neural crest EMT
            reporter identifies retinoic acid as an inhibitor of epithelial
            morphogenesis
  JOURNAL   Dis Model Mech 9 (4), 389-400 (2016)
   PUBMED   26794130
REFERENCE   6  (bases 1 to 1540)
  AUTHORS   Zou,S.M., Jiang,X.Y., He,Z.Z., Yuan,J., Yuan,X.N. and Li,S.F.
  TITLE     Hox gene clusters in blunt snout bream, Megalobrama amblycephala
            and comparison with those of zebrafish, fugu and medaka genomes
  JOURNAL   Gene 400 (1-2), 60-70 (2007)
   PUBMED   17618068
REFERENCE   7  (bases 1 to 1540)
  AUTHORS   Kurosawa,G., Takamatsu,N., Takahashi,M., Sumitomo,M., Sanaka,E.,
            Yamada,K., Nishii,K., Matsuda,M., Asakawa,S., Ishiguro,H.,
            Miura,K., Kurosawa,Y., Shimizu,N., Kohara,Y. and Hori,H.
  TITLE     Organization and structure of hox gene loci in medaka genome and
            comparison with those of pufferfish and zebrafish genomes
  JOURNAL   Gene 370, 75-82 (2006)
   PUBMED   16472944
  REMARK    Erratum:[Gene. 2006 Jul;376(2):298-9]
REFERENCE   8  (bases 1 to 1540)
  AUTHORS   Corredor-Adamez,M., Welten,M.C., Spaink,H.P., Jeffery,J.E.,
            Schoon,R.T., de Bakker,M.A., Bagowski,C.P., Meijer,A.H.,
            Verbeek,F.J. and Richardson,M.K.
  TITLE     Genomic annotation and transcriptome analysis of the zebrafish
            (Danio rerio) hox complex with description of a novel member, hox b
            13a
  JOURNAL   Evol Dev 7 (5), 362-375 (2005)
   PUBMED   16174031
REFERENCE   9  (bases 1 to 1540)
  AUTHORS   Santini,S. and Bernardi,G.
  TITLE     Organization and base composition of tilapia Hox genes:
            implications for the evolution of Hox clusters in fish
  JOURNAL   Gene 346, 51-61 (2005)
   PUBMED   15716008
REFERENCE   10 (bases 1 to 1540)
  AUTHORS   Kudoh,T., Tsang,M., Hukriede,N.A., Chen,X., Dedekian,M.,
            Clarke,C.J., Kiang,A., Schultz,S., Epstein,J.A., Toyama,R. and
            Dawid,I.B.
  TITLE     A gene expression screen in zebrafish embryogenesis
  JOURNAL   Genome Res 11 (12), 1979-1987 (2001)
   PUBMED   11731487
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC091858.1.
            
            On Aug 31, 2012 this sequence version replaced NM_131165.1.
            
            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 :: BC091858.1, BC164748.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505371
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1540              BC091858.1         5-1544
FEATURES             Location/Qualifiers
     source          1..1540
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Singapore"
                     /db_xref="taxon:7955"
                     /chromosome="23"
                     /map="23"
     gene            1..1540
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /note="homeobox C11a"
                     /db_xref="GeneID:30403"
                     /db_xref="ZFIN:ZDB-GENE-990415-111"
     exon            1..717
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /inference="alignment:Splign:2.1.0"
     CDS             30..950
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /note="homeobox gene C-11; homeo box C11a"
                     /codon_start=1
                     /product="homeobox protein Hox-C11a"
                     /protein_id="NP_571240.1"
                     /db_xref="GeneID:30403"
                     /db_xref="ZFIN:ZDB-GENE-990415-111"
                     /translation="

MFNSVNLGNFCSQTRKDRTSEFGDRTGCASNIYLPSCTYYVPEFSAVSSFLPQGPSRQITYPYSTNLSQVQPVRDVSYGLDPSSKWHHRSNYASCYSGEDLVHRDCLPPSTMTEMLMKNESVYSHHHQHHPNSSHPSTGFYTGVGKNNVLPQGFDRFFETAYCSTDNQSEHCLQKSEMNKLETSSQQPTAVSAAREPEKDPEDEEEHTNSGSCTSAATKDGNASKSSHSSTPRTRKKRCPYSKFQIRELEREFFFNVYINKEKRLQLSRMLNLTDRQVKIWFQNRRMKEKKLSRDRLQYFSGNPLL"

     misc_feature    153..530
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /note="Protein of unknown function (DUF3528); Region:
                     DUF3528; pfam12045"
                     /db_xref="CDD:432284"
     misc_feature    558..743
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /note="propagated from UniProtKB/Swiss-Prot (Q58EL0.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    732..902
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            718..1512
                     /gene="hoxc11a"
                     /gene_synonym="hoxc11; id:ibd3176; zgc:110834"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atatctgtagtacggactacaggagaaagatgtttaactctgttaatctgggcaacttctgctcccagacgcgtaaagaccggacgtccgagtttggggacaggacgggctgtgcctccaacatctacctccccagctgcacttactacgttcctgaattttccgccgtctcttcgttccttccacaggggccctcgcgacaaatcacatacccatattccacaaatctatctcaagtgcaaccggtacgagatgtttcctatggtttggacccgtccagcaagtggcaccacagatccaactatgcatcttgctactcaggagaagacctggtgcatagagactgtcttccgccatccaccatgacagaaatgctcatgaaaaacgagagtgtgtacagccaccaccaccagcatcatccgaactctagccacccttccaccgggttctacaccggcgtggggaaaaacaacgtgctccctcaaggttttgaccgtttctttgaaaccgcttattgtagtacggacaatcagtcagaacattgtttacaaaagagcgagatgaacaaattagagacttcgtcccagcaacccacagctgtttccgcagcacgagagccggaaaaggacccagaggatgaggaggaacacacaaattcgggctcgtgcacttcagcggctactaaggacgggaacgcaagcaagagcagccattcgagtaccccgcgcacaagaaagaagagatgtccatactccaaatttcagattcgtgaactggagcgagaatttttctttaacgtttacatcaacaaggagaaaaggctacagctatccagaatgttaaaccttactgacagacaagtcaaaatatggtttcaaaatcgtagaatgaaagaaaagaaattaagcagagatcgcctgcagtatttctctggaaatccgttgctgtaattgttgaaatggcgttgcctgttatttaatatttttgcaaacaaactctattaaatatgtcaaatatgcccttcagtctaattaaataattagatatgtttttgtctaggccagcaacagtactgaagaagcctaagacagttggaggctaacaggattgtaatggctgagggtggggacagacaatacaaatttgcttaatgtcaaactgatatttcaagtttaaagttcacaaaccaaaacgtaatcttcacaaacttaaggtttctatttgtttgtgacccgtcttttaagtgaaaataattaaaatattcactttgaataaggcgacaaaatagcctactataatatattataaaattgtacccttatcattttatgcttgtatatatgtacattaaaacacactctcgactctggtttaaatctggagatgtcatacttttttatgttttcaccatttagaactgtgacttgtacaatctgtaataatgtattccttgtacagagattatgcattgtgcattcgtgaatgtaaatataatgttattttgagtatccttaaaaaaaaaaaaaaaaaaaaaaaaaaa

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