LOCUS       NM_001085494            1703 bp    mRNA    linear   VRT 01-JUN-2024
DEFINITION  Danio rerio homeobox A13a (hoxa13a), mRNA.
ACCESSION   NM_001085494 XM_693696
VERSION     NM_001085494.1
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 1703)
  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 1703)
  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 1703)
  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 1703)
  AUTHORS   Hawkins,M.B., Henke,K. and Harris,M.P.
  TITLE     Latent developmental potential to form limb-like skeletal
            structures in zebrafish
  JOURNAL   Cell 184 (4), 899-911 (2021)
   PUBMED   33545089
REFERENCE   5  (bases 1 to 1703)
  AUTHORS   Smeeton,J., Natarajan,N., Naveen Kumar,A., Miyashita,T., Baddam,P.,
            Fabian,P., Graf,D. and Crump,J.G.
  TITLE     Zebrafish model for spondylo-megaepiphyseal-metaphyseal dysplasia
            reveals post-embryonic roles of Nkx3.2 in the skeleton
  JOURNAL   Development 148 (2) (2021)
   PUBMED   33462117
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1703)
  AUTHORS   Chiu,C.H., Dewar,K., Wagner,G.P., Takahashi,K., Ruddle,F.,
            Ledje,C., Bartsch,P., Scemama,J.L., Stellwag,E., Fried,C.,
            Prohaska,S.J., Stadler,P.F. and Amemiya,C.T.
  TITLE     Bichir HoxA cluster sequence reveals surprising trends in
            ray-finned fish genomic evolution
  JOURNAL   Genome Res 14 (1), 11-17 (2004)
   PUBMED   14707166
REFERENCE   7  (bases 1 to 1703)
  AUTHORS   Amores,A., Suzuki,T., Yan,Y.L., Pomeroy,J., Singer,A., Amemiya,C.
            and Postlethwait,J.H.
  TITLE     Developmental roles of pufferfish Hox clusters and genome evolution
            in ray-fin fish
  JOURNAL   Genome Res 14 (1), 1-10 (2004)
   PUBMED   14707165
REFERENCE   8  (bases 1 to 1703)
  AUTHORS   Santini,S., Boore,J.L. and Meyer,A.
  TITLE     Evolutionary conservation of regulatory elements in vertebrate Hox
            gene clusters
  JOURNAL   Genome Res 13 (6A), 1111-1122 (2003)
   PUBMED   12799348
  REMARK    Erratum:[Genome Res. 2003 Aug;13(8):1973]
REFERENCE   9  (bases 1 to 1703)
  AUTHORS   Chiu,C.H., Amemiya,C., Dewar,K., Kim,C.B., Ruddle,F.H. and
            Wagner,G.P.
  TITLE     Molecular evolution of the HoxA cluster in the three major
            gnathostome lineages
  JOURNAL   Proc Natl Acad Sci U S A 99 (8), 5492-5497 (2002)
   PUBMED   11943847
REFERENCE   10 (bases 1 to 1703)
  AUTHORS   Amores,A., Force,A., Yan,Y.L., Joly,L., Amemiya,C., Fritz,A.,
            Ho,R.K., Langeland,J., Prince,V., Wang,Y.L., Westerfield,M.,
            Ekker,M. and Postlethwait,J.H.
  TITLE     Zebrafish hox clusters and vertebrate genome evolution
  JOURNAL   Science 282 (5394), 1711-1714 (1998)
   PUBMED   9831563
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC133882.1.
            
            On May 23, 2007 this sequence version replaced XM_693696.2.
            
            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 :: BC133882.1, EH504711.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505378, SAMEA3505380
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1703
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="19"
                     /map="19"
     gene            1..1703
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /note="homeobox A13a"
                     /db_xref="GeneID:570239"
                     /db_xref="ZFIN:ZDB-GENE-990415-5"
     exon            1..781
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    52..54
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /note="upstream in-frame stop codon"
     CDS             97..1029
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /note="homeobox gene A-13; homeo box A13a"
                     /codon_start=1
                     /product="homeobox protein Hox-A13a"
                     /protein_id="NP_001078963.1"
                     /db_xref="GeneID:570239"
                     /db_xref="ZFIN:ZDB-GENE-990415-5"
                     /translation="

MTTSLLLRPRWIDPVMFLYDNGGGLDDTSKNMEGFTGGNFSPSPCRNLMSHPASLAPSATYPSSEVAAAAAGDSGKQCSPCSAVQGSASASISYGYFGGGGYYPCRMSHHHGSGGGVKTCAQSPASGSPYGEKYMDTSASTGEDYTSSRAKEFALYSSYASSPYQPVPSYLDVPVVQAISGPSEPRHESLLPMESYQPWAITTSGWNGQVYCTKEQQQTGNVWKSSIPESVSHGGADGSSFRRGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISAQTNLSERQVTIWFQNRRVKEKKVVNKLKSSS"

     misc_feature    181..540
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /note="Hox protein A13 N terminal; Region: HoxA13_N;
                     pfam12284"
                     /db_xref="CDD:463521"
     misc_feature    829..999
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            782..1663
                     /gene="hoxa13a"
                     /gene_synonym="hoxa13"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

tctggatgtacgagggtgcgtcagagtcaactgtctccccttttcagtgtctaagcttcacaaaaaagagccacacgtctcaatgtccgacgggctatgacaacgtcactacttctccgcccgcgctggattgacccggtcatgtttctctatgataacggtggcggtttagacgacaccagcaaaaatatggaagggttcacaggaggtaacttctcgccaagcccgtgcaggaatttgatgtctcaccctgcctctcttgcgcccagtgctacttatccgtccagcgaagtggctgctgctgcagcgggtgattctggaaagcaatgcagcccctgctcagccgttcaaggttcagccagcgcctcaatttcctatggatatttcggaggcggtggatactatccttgccgaatgtcccaccaccatgggagtggtggaggtgtaaagacatgcgcccagtcccctgcctctggttcaccttacggagaaaaatacatggacacatcagcttctacaggcgaagattataccagctcacgcgccaaggagtttgccttgtactcaagctacgcctcaagtccatatcaaccagttccgagctatctggatgttccagtagtccaggcaataagcgggccttcggagccccgacatgagtctttactgccgatggagagttaccaaccgtgggcaatcacaaccagtggatggaacggacaggtctactgcaccaaagagcagcaacaaacgggaaacgtgtggaagtcgtcaataccagagtcagtatcccatggaggggcagacggcagctccttccgccgcggaaggaagaaacgtgttccatataccaaggtgcagctgaaggagcttgaacgggagtatgccactaacaagtttatcaccaaggacaaacgcagacggatatccgctcagaccaacctatctgaacgacaggtcactatctggttccaaaaccgacgggtaaaggagaaaaaagttgtcaacaaattaaaaagtagcagttagctttgctctgtgtaaatgtaagggaactatttttttaacaatgatgcccccaaatacacacagagagagagagagagaaagagagagagctatgaaagtatagacgtttaacgaatatgtgtttccttggactactgcttttgaagtggccactttggatcgcacagggttgatggtgacgcggtgcgtcatttctgcacttcagtgcatggccatattcccaactcagggcaaaaacggccaaaggatgagttgtttgatgagatttagtcactgctcaacaaaatatctcataaagaataatacattggatgtgtaaatgttgaaaccgtaattctttacggtgtggtacgatttttctttcaccactcccatggtcgattagaatcaaaattatgctttgcttgaaattcaagttcatgagatttcgtggaatatttgatgtggagcctgcagtttatcagtcacgtgtacatatcagtgacatgtacaatctttggctatatttgtgcaaaacaggccgtgaatactataaaatggctgttcctgtaaaagagtgttttattttatttttatttttttcgttgtatagtgtttgcaaaatccctcttaataaactctaattgaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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