LOCUS       NM_131167               1410 bp    mRNA    linear   VRT 21-NOV-2025
DEFINITION  Danio rerio homeobox D11a (hoxd11a), mRNA.
ACCESSION   NM_131167 XM_001922749
VERSION     NM_131167.1
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 1410)
  AUTHORS   Bian,C., Xun,Z., Fu,Y., Wang,Z., Wang,J. and Wu,L.
  TITLE     Maternal exposure to norfloxacin induces impairment of cardiac
            development in zebrafish offspring
  JOURNAL   Comp Biochem Physiol C Toxicol Pharmacol 297, 110263 (2025)
   PUBMED   40602649
REFERENCE   2  (bases 1 to 1410)
  AUTHORS   Ishizaka,M., Maeno,A., Nakazawa,H., Fujii,R., Oikawa,S., Tani,T.,
            Kanno,H., Koita,R. and Kawamura,A.
  TITLE     The functional roles of zebrafish HoxA- and HoxD-related clusters
            in the pectoral fin development
  JOURNAL   Sci Rep 14 (1), 23602 (2024)
   PUBMED   39384796
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1410)
  AUTHORS   Sundaramoorthi,H., Fallatah,W., Mary,J. and Jagadeeswaran,P.
  TITLE     Discovery of seven hox genes in zebrafish thrombopoiesis
  JOURNAL   Blood Cells Mol Dis 104, 102796 (2024)
   PUBMED   37717409
REFERENCE   4  (bases 1 to 1410)
  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   5  (bases 1 to 1410)
  AUTHORS   Matharu,N.K., Yadav,S., Kumar,M. and Mishra,R.K.
  TITLE     Role of vertebrate GAGA associated factor (vGAF) in early
            development of zebrafish
  JOURNAL   Cells Dev 166, 203682 (2021)
   PUBMED   33994355
REFERENCE   6  (bases 1 to 1410)
  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   7  (bases 1 to 1410)
  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   8  (bases 1 to 1410)
  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   9  (bases 1 to 1410)
  AUTHORS   Lavoie,H., Debeane,F., Trinh,Q.D., Turcotte,J.F.,
            Corbeil-Girard,L.P., Dicaire,M.J., Saint-Denis,A., Page,M.,
            Rouleau,G.A. and Brais,B.
  TITLE     Polymorphism, shared functions and convergent evolution of genes
            with sequences coding for polyalanine domains
  JOURNAL   Hum Mol Genet 12 (22), 2967-2979 (2003)
   PUBMED   14519685
REFERENCE   10 (bases 1 to 1410)
  AUTHORS   Yelon,D., Ticho,B., Halpern,M.E., Ruvinsky,I., Ho,R.K., Silver,L.M.
            and Stainier,D.Y.
  TITLE     The bHLH transcription factor hand2 plays parallel roles in
            zebrafish heart and pectoral fin development
  JOURNAL   Development 127 (12), 2573-2582 (2000)
   PUBMED   10821756
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JBMGRA010000009.1.
            
            On May 8, 2009 this sequence version replaced XM_001922749.1.
            
            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 :: BC114271.1, GFIL01012821.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505371, SAMEA3505381
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-695               JBMGRA010000009.1  1974932-1975626     c
            696-1410            JBMGRA010000009.1  1973354-1974068     c
FEATURES             Location/Qualifiers
     source          1..1410
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="9"
                     /map="9"
     gene            1..1410
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /note="homeobox D11a"
                     /db_xref="GeneID:30405"
                     /db_xref="ZFIN:ZDB-GENE-990415-117"
     exon            1..695
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /inference="alignment:Splign:2.1.0"
     CDS             98..928
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /note="hox-C11; hox-D11; homeobox protein Hox-C11;
                     homeobox gene D-11; homeo box D11a"
                     /codon_start=1
                     /product="homeobox protein Hox-D11a"
                     /protein_id="NP_571242.1"
                     /db_xref="GeneID:30405"
                     /db_xref="ZFIN:ZDB-GENE-990415-117"
                     /translation="

MTDYDDRNNCASNMYLPYYVSTPDFSSVSSFLPQTTSCQVNFPYSSNIAQVQPVREVTFRDYGLDHPSKWHYRGNYASYYSTEEIMHRDLLQSTNRAEMIFKNDSMYSHHAGTNSSCSFFTNVGRNGVLPQGFDQFFETANSEKPNPEQSKQKPDTSVPGDAACNPSTDSAEQTKQDPTDTVEEESSVSTCDEEKNSGSSATKSRKKRCPYSKYQIRELEREFFFNVYINKEKRLQLSRMLSLTDRQVKIWFQNRRMKEKKLNRDRLQYFTGNPLF"

     misc_feature    164..529
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /note="Protein of unknown function (DUF3528); Region:
                     DUF3528; pfam12045"
                     /db_xref="CDD:432284"
     misc_feature    512..718
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90470.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    710..880
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            696..1410
                     /gene="hoxd11a"
                     /gene_synonym="fk50b10; hoxc11; hoxd-11; hoxd11; sb:eu641;
                     wu:fk50b10"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

tcgcgagtcctatccgcacgcatatggtgcaatagatgggcaaagtttaacagtcaagcagacgaattttcccccctctctacggctaaagcgagcaatgacggactacgatgatcgcaacaactgtgcatctaatatgtatttaccatactacgtctctactcccgatttctcgtcggtttcgtcgtttttgcctcaaactacgtcgtgtcaagtcaatttcccctattcttcgaacatagcgcaagtccaacctgttcgcgaagtgacttttagggactatggactggatcatccgagcaaatggcattacaggggcaattacgcttcgtactattcaacggaggagataatgcaccgagatctcttgcagtccacaaacagagcggaaatgatttttaagaacgattccatgtacagccatcacgctggtactaactcctcgtgcagtttcttcaccaacgtcggccgaaacggggtacttccacaaggatttgatcagttttttgagacggcaaactccgagaagcccaaccccgagcagtccaaacaaaagccagatacgagtgtcccgggagatgctgcatgtaacccgtctacagatagcgcggagcagaccaaacaggacccgacagacaccgtggaggaggaatcctccgtttcaacctgcgatgaagaaaagaacagcggctcgagtgcgacaaagtccagaaagaagagatgcccgtattccaaataccagatccgagaacttgaacgagaattctttttcaatgtgtacataaacaaagagaaacgcctgcagttgtcaagaatgctcagtcttacagaccgacaagtgaagatttggttccagaaccgcaggatgaaagagaaaaagctgaaccgagatcgactccagtatttcactggaaacccattgttctgaaagtcatgatattggccgcttcaggagaccaaggctattctgtcatgcttgtgggacatcaaccattcgtcggacttattttcacctcagccctgtatttgtaccactatgcaaaatacttgctatatcaaacaaaaacaaaagagtcattttattcgcaactgcacttctgcacaaattacctattgcagtgtatccgcagagatggacattatcagttttcataggtaccccgacaatctcttcatactctgtgattgccattgaaatgcagttgctttgtgtttgtttgtatttatttattatgtttttttaatttcagttcttacattcaatacattcaagtaacaactcgcactgcgtaataagcaacaaacaggtttggttatatcaaatgaattcgttgaggtaaagctgtgtatgcatttattcatttgaagcatgtatatgtatcagtgtattaaataaaaatacaggacgta

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