LOCUS       NM_001030264            1881 bp    mRNA    linear   VRT 02-OCT-2022
DEFINITION  Danio rerio homeobox containing 1a (hmbox1a), mRNA.
ACCESSION   NM_001030264 XM_695104
VERSION     NM_001030264.1
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 1881)
  AUTHORS   Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M,
            Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD,
            Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov
            GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W and
            Hertzano R.
  TITLE     RFX transcription factors are essential for hearing in mice
  JOURNAL   Nat Commun 6, 8549 (2015)
   PUBMED   26469318
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1881)
  AUTHORS   Diotel N, Rodriguez Viales R, Armant O, Marz M, Ferg M, Rastegar S
            and Strahle U.
  TITLE     Comprehensive expression map of transcription regulators in the
            adult zebrafish telencephalon reveals distinct neurogenic niches
  JOURNAL   J Comp Neurol 523 (8), 1202-1221 (2015)
   PUBMED   25556858
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC097126.1.
            
            On Aug 6, 2005 this sequence version replaced XM_695104.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC097126.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           SAMEA2168446, SAMEA2168447
                                           [ECO:0000350]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1881
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="17"
                     /map="17"
     gene            1..1881
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="homeobox containing 1a"
                     /db_xref="GeneID:571508"
                     /db_xref="ZFIN:ZDB-GENE-050913-89"
     exon            1..212
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    82..84
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="upstream in-frame stop codon"
     exon            213..746
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     CDS             214..1539
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="homeobox containing 1"
                     /codon_start=1
                     /product="homeobox-containing protein 1a"
                     /protein_id="NP_001025435.1"
                     /db_xref="GeneID:571508"
                     /db_xref="ZFIN:ZDB-GENE-050913-89"
                     /translation="

MSHYTDEPRFTIEQIDLLQRLRRSGMTKQEILHALDTLDRLDREHVEKFGHRHAHGGTSAINHSSNATTSSNSCTTSSNNLTASSSTTSTATQTGFRGNGLSPSPSNSYETSPPPTAPTSMPVVAPLVQNGPDALASMSNGKLSPPRFTVSNVSSRAFPFEPPDEEMDIDDRVEELMRMDSAIIKEEIKAFLGNRRISQAVVAQVTGISQSRISHWLLQQGSDLSEQKKRAFYRWYQLEKTTPGATLAMRPTPMALEDIVEWRQTPPPISSTQGSFRLRRGSRFTWRKECLAVMESYFNDNQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAILESHGIDVQSPGGHSNSDEIDGNDYGEPVAADQVLGMDDNTGPNEHQDPIALAVEMAAVNHSILALARQGGSASDIKTEVLDDE"

     misc_feature    250..927
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="Hepatocyte nuclear factor 1 (HNF-1), N terminus;
                     Region: HNF-1_N; pfam04814"
                     /db_xref="CDD:461440"
     misc_feature    1051..1269
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="Homeodomain; DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:238039"
     misc_feature    order(1051..1065,1069..1071,1120..1122,1138..1140,
                     1222..1224,1228..1233,1240..1245,1249..1257,1261..1266)
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1057..1059,1066..1068,1231..1233,1240..1245,
                     1252..1254)
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            747..832
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     exon            833..943
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     exon            944..1100
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     exon            1101..1183
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     exon            1184..1279
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     exon            1280..1395
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
     exon            1396..1860
                     /gene="hmbox1a"
                     /gene_synonym="hmbox1; zgc:114064"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

tgttaatatcaatatggcttctgtcagtcagacaaaggcgaatcagtttttgccttgaaatgaaatcaaattaggtaaaggtagcgggagagtcggacatcgtcctgttttgctggttcatgtcaggcgacggggattaaagggccggaaacactgtcagtcgagtggaataaatgctgtggtgcacggaggccccgcacgcgcacaatcagaatgtcccattatacagatgagcctcgttttaccattgagcagatcgacttactgcagaggctgcgtcggagtggcatgacaaagcaagagatcctgcatgctctggacacccttgaccggctggaccgcgaacatgtggagaagtttggccatcggcatgctcacggtgggacctccgccatcaatcacagcagtaacgccaccacctcttccaactcctgcactacctcctccaacaacctcacagcctcttcttcaacgacctctacagccacgcagacgggtttccgtggcaatggcctctccccgtctccgagcaacagctatgaaacctcccctccgccgaccgcccccacctctatgccggttgtagcacccctggtccaaaatggaccggacgccctcgcctctatgtccaatgggaaactctcgccaccccgcttcactgttagcaacgtctcctcacgggcctttcccttcgagccccccgatgaggaaatggacatcgatgaccgagtcgaggagctcatgagaatggacagtgctataattaaagaagagattaaagcgttcttggggaaccggcgaatatcacaggctgtagttgcacaagtgacaggtatcagtcagagcaggatctctcattggcttctccagcagggctcagacctcagcgagcagaagaaaagagctttctaccgctggtaccaactggagaaaacgacacctggtgcgactctagcgatgcgtcccacaccgatggccctggaggacattgtggagtggcgtcagactcctccacccatcagcagcacgcagggcagcttccgtctgcggcgcggcagccgcttcacctggaggaaagagtgtctggccgtcatggagagttacttcaatgacaaccagtacccggacgaagccaaacgagaggaaattgccaacgcctgcaatgcagtaattcagaaaccagggaagaagctttcagatcttgagagggtcacgtctctgaaagtttacaactggttcgccaacagacggaaggaaattaagagaagagccaacatagcaatcctggagagtcatgggattgatgtccaaagcccgggaggtcattctaacagcgacgagattgatggaaatgactacggtgaaccggtagctgctgaccaagttttgggaatggacgacaacactggcccgaatgagcaccaggaccccatcgctctggcagtagagatggccgccgtcaaccacagcattttggcgctggcccgacaaggcggatcagccagcgacatcaagacagaagtgctggatgatgagtgaaacacgcagcgctgttgtcagtgggggggatgctgaacggagaaatgtggggttactgaaatacagccaaaacagaactgttaggagtctggcccggtcacggatgacctaagtgaacgcggagatttctgaagactgttaacccaacattcccctcttccttctcctcctcctcctcattaaggaggtgctgcgttcaaactgatgatgaaacgcgttcacttaaaaaacgtcacgccacacgtcaccctgccatctcacactcggatcgtgagtttttgcctctcggtttctccttctttcaggaagtcttctttgcagaaaaaaaaaaaaaaaaaaaaa

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