LOCUS       NM_001023575            2175 bp    mRNA    linear   VRT 17-SEP-2023
DEFINITION  Danio rerio iroquois homeobox 6a (irx6a), mRNA.
ACCESSION   NM_001023575 XM_686269
VERSION     NM_001023575.1
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 2175)
  AUTHORS   Farmer DT, Patel P, Choi R, Liu CY and Crump JG.
  TITLE     A comprehensive series of Irx cluster mutants reveals diverse roles
            in facial cartilage development
  JOURNAL   Development 148 (16) (2021)
   PUBMED   34338288
REFERENCE   2  (bases 1 to 2175)
  AUTHORS   Kohl S, Llavona P, Sauer A, Reuter P, Weisschuh N, Kempf M, Dehmelt
            FA, Arrenberg AB, Sliesoraityte I, Zrenner E, van Schooneveld MJ,
            Rudolph G, Kuhlewein L and Wissinger B.
  TITLE     A duplication on chromosome 16q12 affecting the IRXB gene cluster
            is associated with autosomal dominant cone dystrophy with early
            tritanopic color vision defect
  JOURNAL   Hum Mol Genet 30 (13), 1218-1229 (2021)
   PUBMED   33891002
REFERENCE   3  (bases 1 to 2175)
  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   4  (bases 1 to 2175)
  AUTHORS   Orosz F.
  TITLE     On the tubulin polymerization promoting proteins of zebrafish
  JOURNAL   Biochem Biophys Res Commun 457 (3), 267-272 (2015)
   PUBMED   25576359
REFERENCE   5  (bases 1 to 2175)
  AUTHORS   Tena JJ, Alonso ME, de la Calle-Mustienes E, Splinter E, de Laat W,
            Manzanares M and Gomez-Skarmeta JL.
  TITLE     An evolutionarily conserved three-dimensional structure in the
            vertebrate Irx clusters facilitates enhancer sharing and
            coregulation
  JOURNAL   Nat Commun 2, 310 (2011)
   PUBMED   21556064
REFERENCE   6  (bases 1 to 2175)
  AUTHORS   McDonald LA, Gerrelli D, Fok Y, Hurst LD and Tickle C.
  TITLE     Comparison of Iroquois gene expression in limbs/fins of vertebrate
            embryos
  JOURNAL   J Anat 216 (6), 683-691 (2010)
   PUBMED   20408909
REFERENCE   7  (bases 1 to 2175)
  AUTHORS   Lecaudey V, Anselme I, Dildrop R, Ruther U and Schneider-Maunoury
            S.
  TITLE     Expression of the zebrafish Iroquois genes during early nervous
            system formation and patterning
  JOURNAL   J Comp Neurol 492 (3), 289-302 (2005)
   PUBMED   16217788
REFERENCE   8  (bases 1 to 2175)
  AUTHORS   de la Calle-Mustienes E, Feijoo CG, Manzanares M, Tena JJ,
            Rodriguez-Seguel E, Letizia A, Allende ML and Gomez-Skarmeta JL.
  TITLE     A functional survey of the enhancer activity of conserved
            non-coding sequences from vertebrate Iroquois cluster gene deserts
  JOURNAL   Genome Res 15 (8), 1061-1072 (2005)
   PUBMED   16024824
REFERENCE   9  (bases 1 to 2175)
  AUTHORS   Dildrop R and Ruther U.
  TITLE     Organization of Iroquois genes in fish
  JOURNAL   Dev Genes Evol 214 (6), 267-276 (2004)
   PUBMED   15133664
REFERENCE   10 (bases 1 to 2175)
  AUTHORS   Feijoo CG, Manzanares M, de la Calle-Mustienes E, Gomez-Skarmeta JL
            and Allende ML.
  TITLE     The Irx gene family in zebrafish: genomic structure, evolution and
            initial characterization of irx5b
  JOURNAL   Dev Genes Evol 214 (6), 277-284 (2004)
   PUBMED   15064948
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC095113.1.
            
            On Jan 22, 2011 this sequence version replaced XM_686269.4.
            
            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 :: BC095113.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           SAMEA2168448, SAMEA3505370
                                           [ECO:0000350]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2175
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="7"
                     /map="7"
     gene            1..2175
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="iroquois homeobox 6a"
                     /db_xref="GeneID:474317"
                     /db_xref="ZFIN:ZDB-GENE-040712-5"
     exon            1..190
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    83..85
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="upstream in-frame stop codon"
     misc_feature    125..127
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="upstream_AUG_codon; putative N-terminal extension:
                     MVTKEAA"
     CDS             146..1579
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="iroquois-class homeodomain protein IRX-6a"
                     /codon_start=1
                     /product="Iroquois homeobox protein 6a"
                     /protein_id="NP_001018869.1"
                     /db_xref="GeneID:474317"
                     /db_xref="ZFIN:ZDB-GENE-040712-5"
                     /translation="

MSFSQFGYPYNATSQFFVSATPSTTCCDSISRSVTEGSSASQTAASFCCPSYENRLLASTRTELNAALGMYGSPYAAAAAAAGQNYANYFPYSADPSAIYSSLNPQYEIKEGSGSLHSTITQPATYYPYDHSLGQYQYDRYGTVDFNGSTRRKNATRETTSTLKTWLYEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWSPKNKAGDDRKEDLDSKDSKDEQDLQFSDLDDMEDEDCDKLDSDCEKSGQDDLPTSSPPKRDCNPDIPLHSNFPSFPCGLKSLGPLNPDYLDHLGSKPQQQQPSPQSTSINTVALSHFESSEKPRIWSLARTAAAGVVLGTQHVGDVRTGPVDCQMQGVRLPTVGAVQCGELKGLQDPTNLSNTESLFQEGLQGIHKAYSSGSFKTLQLHSSSYPGLTESCQYSSMEGFPSAGKTETESSELSDTCPTIQEAKTTAFRPVMKR"

     misc_feature    order(596..604,608..610,668..670,686..688,725..727,
                     731..736,743..748,752..760,764..769)
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(596..598,605..607,734..736,743..748,755..757)
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    644..760
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     misc_feature    770..991
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="propagated from UniProtKB/Swiss-Prot (Q503Z8.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1052..1114
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="propagated from UniProtKB/Swiss-Prot (Q503Z8.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            191..454
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            455..564
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            565..830
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            831..1469
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            1470..1584
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            1585..2158
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agtgcttcccagttaagtgcagtcatctattattgagcgaaaggccgagtgtggaaatgtgtgtaagacggtggatttgaagtagatttggtttcaatcgatcagcaggagaagaatattgcttatggtaacaaaagaagcagctatgtccttctctcagtttggatatccttacaatgcaacttctcagtttttcgtgtcggcaacccccagtacgacttgctgcgattcgatatccaggtcggtgacagaaggatcgagcgcatcgcagaccgcagcctccttctgctgtccctcctatgagaaccggctgctggcgagtacacggacggagctcaacgccgcgctcgggatgtacggctccccttacgcagcagcagcggccgcagccgggcagaactacgccaactactttccgtatagcgccgacccctccgccatctactccagcctgaacccacaatatgaaatcaaagaggggtcaggcagtcttcatagcactataacacaaccagccacttactatccatatgaccactcactcggacagtaccagtatgacaggtatgggacagttgattttaatggatcaacacggagaaagaacgccacacgtgagacaacaagtacgcttaaaacatggctttatgagcaccgcaaaaacccttatcctacaaagggtgaaaagatcatgctggccattatcaccaaaatgaccctcacgcaagtgtctacctggtttgccaatgctagaagacgactaaaaaaagaaaacaagatgacttggtcccccaaaaacaaagcaggcgatgacaggaaggaagacctcgactccaaagacagtaaggatgagcaggacctgcagttcagtgacctggatgatatggaggatgaggactgtgacaagctggacagtgactgtgaaaaatcaggtcaggatgacctcccgacctcctcccctccaaagagagactgtaaccctgacatccctctccactccaacttcccatcttttccctgtggtctgaagagtttggggcctctgaacccagactacctagatcatctgggctccaaaccacagcagcaacagccctcacctcagtccacctccataaacactgtggcactctctcactttgagtcatcggagaagccccggatctggtcgttggcacgtacggccgcagcaggggttgtactaggcacacagcatgttggggatgtacggactgggcctgtggactgtcagatgcagggagtccggttacccacagtcggagcagtgcagtgtggggagctgaagggccttcaggaccctacaaacctcagcaatactgaaagcctttttcaagaaggactacaggggatacacaaggcatacagtagcgggagcttcaagacactacaacttcactcttcatcatatcctggactgacagaatcctgccagtactcctcaatggaaggcttccccagtgcaggaaagacagagacagaatccagtgagctcagtgacacatgcccaacaatccaggaggctaagaccactgcattcagacctgtgatgaagaggtgaggcaggactatggaaatgccaataaacatggggaagtttttatgatctacattatgcactatggaatggagtcaatgaggaactttaagcccatggcagcagacacttgaaatagtagcgcaatgactttgtgtgccctttctggaactgtgaaaactggaggcagccataattttgcacaatatgatttaatggtgtcaataactttatgcaatgttttgtgtatgtatgagaataaattgtgattttttatgtctgcattggcaatcgtaggtttagtaattctatttatctatttattgttttatcatccatctgctttatttatctgttaccatgtgtcctctcaaggtttttttgtgtgtgttaagtttaattctctgtggttatgtgcttaatgttatgtgatttacttttttttggaagctggtgtaaaatttagtcagtcttttaacttttatttacttctcaaaaataaatgaggtgcgatactgtgctcctgcggagtgtgatatgtttatataaaaaaaaagttgtgtataaatgtcatgttgttatttataaaatattttataagaaaaaaaaaaaaaaaaaaa

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