LOCUS       NM_131169               1196 bp    mRNA    linear   VRT 05-AUG-2023
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   Weiss JM, Hunter MV, Cruz NM, Baggiolini A, Tagore M, Ma Y, Misale
            S, Marasco M, Simon-Vermot T, Campbell NR, Newell F, Wilmott JS,
            Johansson PA, Thompson JF, Long GV, Pearson JV, Mann GJ, Scolyer
            RA, Waddell N, Montal ED, Huang TH, Jonsson P, Donoghue MTA, Harris
            CC, Taylor BS, Xu T, Chaligne R, Shliaha PV, Hendrickson R,
            Jungbluth AA, Lezcano C, Koche R, Studer L, Ariyan CE, Solit DB,
            Wolchok JD, Merghoub T, Rosen N, Hayward NK and White RM.
  TITLE     Anatomic position determines oncogenic specificity in melanoma
  JOURNAL   Nature 604 (7905), 354-361 (2022)
   PUBMED   35355015
REFERENCE   2  (bases 1 to 1196)
  AUTHORS   Franke M, De la Calle-Mustienes E, Neto A, Almuedo-Castillo M,
            Irastorza-Azcarate I, Acemel RD, Tena JJ, Santos-Pereira JM and
            Gomez-Skarmeta JL.
  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   3  (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   4  (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   5  (bases 1 to 1196)
  AUTHORS   Matharu NK, Yadav S, Kumar M and Mishra RK.
  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 1196)
  AUTHORS   Corredor-Adamez M, Welten MC, Spaink HP, Jeffery JE, Schoon RT, de
            Bakker MA, Bagowski CP, Meijer AH, Verbeek FJ and Richardson MK.
  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 QD, Turcotte JF, Corbeil-Girard LP,
            Dicaire MJ, Saint-Denis A, Page M, Rouleau GA 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 BW and Neumann CJ.
  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    order(645..659,663..665,714..716,732..734,771..773,
                     777..782,789..794,798..806,810..815)
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    651..812
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(651..653,660..662,780..782,789..794,801..803)
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            610..1121
                     /gene="hoxd13a"
                     /gene_synonym="hoxd-13; hoxd13; zgc:110511"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

attttctgcgtgcatttttcttggttttgagcccataacagacatgagttaaatcccatgcactgaggaatatggacggaggaggactggatgaagagtttataaatgtttacccatctgccttcgggactcactcaagccggtgtacatcaggagcgccggtgctctccgctgttgatcgaccgacttctgtatgcaatgagtctatcagtccttacttttcttttccatccaatatcggctctggctccttcacgtttggatgccatttggaaaacagttacaaagttccacagaacgccgtgttcccgcctggtgttgcgaagcaaaacggacagttcgccaataaacccgtggaccacggtgaagcctccagctggcttaaagagttcgccttttatcaaggctgcgcgcgctcctatccgagaatccctgccttcattgatctacctgtggttcagagagcaatgatgggagatcttagacatgagacttgtttgacaatggaaggccaccaacattgggactggtcaaacaattgcagcagtcaactttattgctttcaagaccagacgcggagcccgcatatctggaaaccatcattaacagaggaagcagcagcggcttcattctgtcagcgcgggagaaagaagcgggttccttacacaaaatttcagctgaaagagctcgagcgtgaatacaacaccactaagttcattacaaaggagaacagacggcggatcgcttcttctaccaacctgtctgagagacaagtaactatatggtttcaaaaccgacgggtcaaggataagaagagacctgacgtctgcatcaaatgttaatcccattgagatctttgtagagttggtttgcataaagtaaagagtatattatagtgggatacaatgtaaattatacttagaagtaatgttaaacagttggttgtatttgtcaatcaatgaattctcccgtcaatttcctctttcccatacactcaaaatgttatactctacatttccttaaatttgagtgcataactgtgtgccatagttgtttatatcagacttttatatgcaaaaaagctataacattgatttcaaataaaatacaattaataataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaattaaaaaaaaaaaaaaaaaaaaaaaaa

//