LOCUS       NM_131169               1196 bp    mRNA    linear   VRT 01-JUN-2024
DEFINITION  Danio rerio homeobox D13a (hoxd13a), mRNA.
ACCESSION   NM_131169
VERSION     NM_131169.3
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 1196)
  AUTHORS   Cumplido,N., Arratia,G., Desvignes,T., Munoz-Sanchez,S.,
            Postlethwait,J.H. and Allende,M.L.
  TITLE     Hox genes control homocercal caudal fin development and evolution
  JOURNAL   Sci Adv 10 (3), eadj5991 (2024)
   PUBMED   38241378
REFERENCE   2  (bases 1 to 1196)
  AUTHORS   Weiss,J.M., Hunter,M.V., Cruz,N.M., Baggiolini,A., Tagore,M.,
            Ma,Y., Misale,S., Marasco,M., Simon-Vermot,T., Campbell,N.R.,
            Newell,F., Wilmott,J.S., Johansson,P.A., Thompson,J.F., Long,G.V.,
            Pearson,J.V., Mann,G.J., Scolyer,R.A., Waddell,N., Montal,E.D.,
            Huang,T.H., Jonsson,P., Donoghue,M.T.A., Harris,C.C., Taylor,B.S.,
            Xu,T., Chaligne,R., Shliaha,P.V., Hendrickson,R., Jungbluth,A.A.,
            Lezcano,C., Koche,R., Studer,L., Ariyan,C.E., Solit,D.B.,
            Wolchok,J.D., Merghoub,T., Rosen,N., Hayward,N.K. and White,R.M.
  TITLE     Anatomic position determines oncogenic specificity in melanoma
  JOURNAL   Nature 604 (7905), 354-361 (2022)
   PUBMED   35355015
REFERENCE   3  (bases 1 to 1196)
  AUTHORS   Franke,M., De la Calle-Mustienes,E., Neto,A., Almuedo-Castillo,M.,
            Irastorza-Azcarate,I., Acemel,R.D., Tena,J.J., Santos-Pereira,J.M.
            and Gomez-Skarmeta,J.L.
  TITLE     CTCF knockout in zebrafish induces alterations in regulatory
            landscapes and developmental gene expression
  JOURNAL   Nat Commun 12 (1), 5415 (2021)
   PUBMED   34518536
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1196)
  AUTHORS   Sun,L., Cao,Y., Kong,Q., Huang,X., Yu,Z., Sun,D., Ren,W., Yang,G.
            and Xu,S.
  TITLE     Over-expression of the bottlenose dolphin Hoxd13 gene in zebrafish
            provides new insights into the cetacean flipper formation
  JOURNAL   Genomics 113 (5), 2925-2933 (2021)
   PUBMED   34166750
REFERENCE   5  (bases 1 to 1196)
  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   6  (bases 1 to 1196)
  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   7  (bases 1 to 1196)
  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   8  (bases 1 to 1196)
  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   9  (bases 1 to 1196)
  AUTHORS   Fischer,S., Draper,B.W. and Neumann,C.J.
  TITLE     The zebrafish fgf24 mutant identifies an additional level of Fgf
            signaling involved in vertebrate forelimb initiation
  JOURNAL   Development 130 (15), 3515-3524 (2003)
   PUBMED   12810598
REFERENCE   10 (bases 1 to 1196)
  AUTHORS   Herault,Y., Hraba-Renevey,S., van der Hoeven,F. and Duboule,D.
  TITLE     Function of the Evx-2 gene in the morphogenesis of vertebrate limbs
  JOURNAL   EMBO J 15 (23), 6727-6738 (1996)
   PUBMED   8978698
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC091996.1.
            
            On Aug 30, 2012 this sequence version replaced NM_131169.2.
            
            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 :: BC091996.1, BC153652.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505371, SAMEA3505372
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1196              BC091996.1         5-1200
FEATURES             Location/Qualifiers
     source          1..1196
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Singapore"
                     /db_xref="taxon:7955"
                     /chromosome="9"
                     /map="9"
     gene            1..1196
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="homeobox D13a"
                     /db_xref="GeneID:30407"
                     /db_xref="ZFIN:ZDB-GENE-990415-119"
     exon            1..609
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    45..47
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="upstream in-frame stop codon"
     CDS             72..842
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="homeobox gene D-13; homeo box D13a"
                     /codon_start=1
                     /product="homeobox protein Hox-D13a"
                     /protein_id="NP_571244.2"
                     /db_xref="GeneID:30407"
                     /db_xref="ZFIN:ZDB-GENE-990415-119"
                     /translation="

MDGGGLDEEFINVYPSAFGTHSSRCTSGAPVLSAVDRPTSVCNESISPYFSFPSNIGSGSFTFGCHLENSYKVPQNAVFPPGVAKQNGQFANKPVDHGEASSWLKEFAFYQGCARSYPRIPAFIDLPVVQRAMMGDLRHETCLTMEGHQHWDWSNNCSSQLYCFQDQTRSPHIWKPSLTEEAAAASFCQRGRKKRVPYTKFQLKELEREYNTTKFITKENRRRIASSTNLSERQVTIWFQNRRVKDKKRPDVCIKC"

     misc_feature    645..815
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            610..1121
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

attttctgcgtgcatttttcttggttttgagcccataacagacatgagttaaatcccatgcactgaggaatatggacggaggaggactggatgaagagtttataaatgtttacccatctgccttcgggactcactcaagccggtgtacatcaggagcgccggtgctctccgctgttgatcgaccgacttctgtatgcaatgagtctatcagtccttacttttcttttccatccaatatcggctctggctccttcacgtttggatgccatttggaaaacagttacaaagttccacagaacgccgtgttcccgcctggtgttgcgaagcaaaacggacagttcgccaataaacccgtggaccacggtgaagcctccagctggcttaaagagttcgccttttatcaaggctgcgcgcgctcctatccgagaatccctgccttcattgatctacctgtggttcagagagcaatgatgggagatcttagacatgagacttgtttgacaatggaaggccaccaacattgggactggtcaaacaattgcagcagtcaactttattgctttcaagaccagacgcggagcccgcatatctggaaaccatcattaacagaggaagcagcagcggcttcattctgtcagcgcgggagaaagaagcgggttccttacacaaaatttcagctgaaagagctcgagcgtgaatacaacaccactaagttcattacaaaggagaacagacggcggatcgcttcttctaccaacctgtctgagagacaagtaactatatggtttcaaaaccgacgggtcaaggataagaagagacctgacgtctgcatcaaatgttaatcccattgagatctttgtagagttggtttgcataaagtaaagagtatattatagtgggatacaatgtaaattatacttagaagtaatgttaaacagttggttgtatttgtcaatcaatgaattctcccgtcaatttcctctttcccatacactcaaaatgttatactctacatttccttaaatttgagtgcataactgtgtgccatagttgtttatatcagacttttatatgcaaaaaagctataacattgatttcaaataaaatacaattaataataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaattaaaaaaaaaaaaaaaaaaaaaaaaa

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