LOCUS       NM_131166               1644 bp    mRNA    linear   VRT 13-MAY-2023
DEFINITION  Danio rerio homeobox D10a (hoxd10a), mRNA.
ACCESSION   NM_131166
VERSION     NM_131166.2
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 1644)
  AUTHORS   Xue S, Ly TTN, Vijayakar RS, Chen J, Ng J, Mathuru AS, 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 1644)
  AUTHORS   Banu S, Gaur N, Nair S, Ravikrishnan T, Khan S, Mani S, Bharathi S,
            Mandal K, Kuram NA, Vuppaladadium S, Ravi R, Murthy CLN, Quoseena
            M, Babu NS and Idris MM.
  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 1644)
  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 1644)
  AUTHORS   Malmstrom M, Britz R, Matschiner M, Torresen OK, Hadiaty RK, Yaakob
            N, Tan HH, Jakobsen KS, 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 1644)
  AUTHORS   Payumo AY, McQuade LE, Walker WJ, Yamazoe S and Chen JK.
  TITLE     Tbx16 regulates hox gene activation in mesodermal progenitor cells
  JOURNAL   Nat Chem Biol 12 (9), 694-701 (2016)
   PUBMED   27376691
REFERENCE   6  (bases 1 to 1644)
  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 1644)
  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   8  (bases 1 to 1644)
  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 1644)
  AUTHORS   Snell EA, Scemama JL and Stellwag EJ.
  TITLE     Genomic organization of the Hoxa4-Hoxa10 region from Morone
            saxatilis: implications for Hox gene evolution among vertebrates
  JOURNAL   J Exp Zool 285 (1), 41-49 (1999)
   PUBMED   10327649
REFERENCE   10 (bases 1 to 1644)
  AUTHORS   Zardoya R, Abouheif E and Meyer A.
  TITLE     Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species
            closely related to the zebrafish
  JOURNAL   Proc Natl Acad Sci U S A 93 (23), 13036-13041 (1996)
   PUBMED   8917540
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from CK864624.1,
            BC071329.1 and CT704711.2.
            
            On Jun 16, 2010 this sequence version replaced NM_131166.1.
            
            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 :: BC071329.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA4476735, SAMEA4476737
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-52                CK864624.1         22-73
            53-1626             BC071329.1         1-1574
            1627-1644           CT704711.2         1-18                c
FEATURES             Location/Qualifiers
     source          1..1644
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="9"
                     /map="9"
     gene            1..1644
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="homeobox D10a"
                     /db_xref="GeneID:30404"
                     /db_xref="ZFIN:ZDB-GENE-990415-116"
     exon            1..838
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    43..45
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="upstream in-frame stop codon"
     CDS             115..1113
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="hox-C10; homeobox protein Hox-C10; homeobox gene
                     D-10; homeo box D10a"
                     /codon_start=1
                     /product="homeobox protein Hox-D10a"
                     /protein_id="NP_571241.2"
                     /db_xref="GeneID:30404"
                     /db_xref="ZFIN:ZDB-GENE-990415-116"
                     /translation="

MSFPNSSPAANTFLVDSLIGACRTDFYSSSNMYMPAATAEMGTYGMQTCGLLPALGKRGEVNHQNMDMTVHSYIPQTDTWADPSRSCRLEQPLNQMSTCTFSQSIKEETNCCMYSDKRAKVSSSEIPAYSSLIPESCSVDSPEIPVPGYFRLSQTYATAKNPDYDNETMSPNTTLMQLNRATPKAQSTPFVEVEKKLAHDRDTRSSSPAQSPEPKVSTLEEKNCSTEASVSSPELPHREGKESKNDTPTSNWLTAKSGRKKRCPYTKHQTLELEKEFLFNMYLTRERRLEISKSVNLTDRQVKIWFQNRRMKLKKMSRENRIRELTSNLTFS"

     misc_feature    694..897
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90469.4);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    724..>1077
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(889..903,907..909,958..960,976..978,1015..1017,
                     1021..1026,1033..1038,1042..1050,1054..1059)
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    895..1056
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(895..897,904..906,1024..1026,1033..1038,1045..1047)
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            839..1627
                     /gene="hoxd10a"
                     /gene_synonym="HOX-D10; hoxd-10; hoxd10; z-82"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggttgcagagagactcgctgggttatacagggattgttttgctagatatgtcagcttacagaggacacttctctgcttcttaaaacaaaaaaagaaaacaaaaaaaaatccaaaatgtcctttcccaacagctctcctgcagcaaacacttttttggtagattccttgattggggcgtgcagaacagatttttattccagcagtaacatgtacatgccagcagccactgcagaaatgggaacctatggaatgcaaacctgtggactcctgccggctcttggcaaacggggggaagtaaaccaccaaaacatggacatgaccgtccactcgtacatacctcaaactgatacctgggcagatccgagcaggtcctgccgattagagcaaccgctcaaccagatgtccacctgcacattttcacaaagcataaaagaagagactaactgttgtatgtactccgacaagagagcaaaggtcagttcgtctgagatacccgcgtactccagcctgattcccgaatcatgttctgttgatagtcctgagattccggtccctggctattttagactgagccaaacttacgcgacggcgaaaaacccggactatgacaacgagacgatgagcccaaacaccacgttaatgcagctgaacagggcgactccaaaggcacagtcaacgccctttgtcgaggtggaaaaaaagcttgcgcacgatcgggacacaaggagctcttccccggcgcagagtccagagcccaaagtcagcacgctggaggagaagaattgctcaactgaggcgtctgtttccagccccgaattgccacacagagaaggcaaagaatctaaaaacgacacaccgacgagcaactggttaaccgcgaagagtggaaggaaaaagagatgtccatacacaaaacaccagaccttggaattagaaaaggagtttttattcaacatgtatctgactcgggagcgccgtctagagataagcaaaagcgtcaacctgactgacagacaagtgaaaatctggttccaaaaccgcaggatgaaactcaagaagatgagcagagaaaaccgtatccgtgaactgacgtccaatctcactttttcgtgagcacgcagacaagtgcaaatcaaaaacctagtccctcatttcggtccatctatgttctcctgtgtaatgatgacatgatggcagtgtgcattgtttttggctactttcacgttgcagtcttgtgatcgtcgctaaatccttgtcatttattgctgcatctttgaaatgtacatttgaaatgtgaagctttgtgtaattatcatgttacacagggtatacaagtggtgttaggtcttaacttataaaagaagatagaaaccggctatttctgacggcttcatttcagcggggatagaagaaaatgtcgcaaacacatttgcgtcagcctctaaaaaacaaaaagtcttggacaagaaagcacatttgaaagtgaagattacccattctttctccagtgaaaacgtacatttgtctcaaaataataatgtatttctgtataataggtgtttaaatatgtctgtataagtgcatgtttgtggcatgtggtcaatagactaataaattgattatgtcaaaaaaaaaaaaaaaaaa

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