LOCUS       NM_001023575            2296 bp    mRNA    linear   VRT 07-JUN-2025
DEFINITION  Danio rerio iroquois homeobox 6a (irx6a), mRNA.
ACCESSION   NM_001023575 XM_686269
VERSION     NM_001023575.2
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 2296)
  AUTHORS   Farmer,D.T., Patel,P., Choi,R., Liu,C.Y. and Crump,J.G.
  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 2296)
  AUTHORS   Kohl,S., Llavona,P., Sauer,A., Reuter,P., Weisschuh,N., Kempf,M.,
            Dehmelt,F.A., Arrenberg,A.B., Sliesoraityte,I., Zrenner,E., van
            Schooneveld,M.J., 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 2296)
  AUTHORS   Elkon,R., Milon,B., Morrison,L., Shah,M., Vijayakumar,S.,
            Racherla,M., Leitch,C.C., Silipino,L., Hadi,S., Weiss-Gayet,M.,
            Barras,E., Schmid,C.D., Ait-Lounis,A., Barnes,A., Song,Y.,
            Eisenman,D.J., Eliyahu,E., Frolenkov,G.I., Strome,S.E., Durand,B.,
            Zaghloul,N.A., Jones,S.M., 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 2296)
  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 2296)
  AUTHORS   Tena,J.J., Alonso,M.E., de la Calle-Mustienes,E., Splinter,E., de
            Laat,W., Manzanares,M. and Gomez-Skarmeta,J.L.
  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 2296)
  AUTHORS   McDonald,L.A., Gerrelli,D., Fok,Y., Hurst,L.D. 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 2296)
  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 2296)
  AUTHORS   de la Calle-Mustienes,E., Feijoo,C.G., Manzanares,M., Tena,J.J.,
            Rodriguez-Seguel,E., Letizia,A., Allende,M.L. and
            Gomez-Skarmeta,J.L.
  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 2296)
  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 2296)
  AUTHORS   Feijoo,C.G., Manzanares,M., de la Calle-Mustienes,E.,
            Gomez-Skarmeta,J.L. and Allende,M.L.
  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     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JBMGRA010000007.1.
            
            On Jun 17, 2024 this sequence version replaced NM_001023575.1.
            
            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 :: BC095113.1, SRR32588729.10867269.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA3505370,
                                           SAMEA3505372 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-328               JBMGRA010000007.1  35626537-35626864   c
            329-592             JBMGRA010000007.1  35625504-35625767   c
            593-702             JBMGRA010000007.1  35624979-35625088   c
            703-968             JBMGRA010000007.1  35624616-35624881   c
            969-1607            JBMGRA010000007.1  35623854-35624492   c
            1608-1722           JBMGRA010000007.1  35623502-35623616   c
            1723-2296           JBMGRA010000007.1  35622384-35622957   c
FEATURES             Location/Qualifiers
     source          1..2296
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="7"
                     /map="7"
     gene            1..2296
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="iroquois homeobox 6a"
                     /db_xref="GeneID:474317"
                     /db_xref="ZFIN:ZDB-GENE-040712-5"
     exon            1..328
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    221..223
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="upstream in-frame stop codon"
     CDS             263..1717
                     /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_001018869.2"
                     /db_xref="GeneID:474317"
                     /db_xref="ZFIN:ZDB-GENE-040712-5"
                     /translation="

MVTKEAAMSFSQFGYPYNATSQFFVSATPSTTCCDSISRSVTEGSSASQTAASFCCPSYENRLLASTRTELNAALGMYGSPYAAAAAAAGQNYANYFPYSADPSAIYSSLNPQYEIKEGSGSLHSTITQPATYYPYDHSLGQYQYDRYGTVDFNGSTRRKNATRETTSTLKTWLYEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWSPKNKAGDDRKEDLDSKDSKDEQDLQFSDLDDMEDEDCDKLDSDCEKSGQDDLPTSSPPKRDCNPDIPLHSNFPSFPCGLKSLGPLNPDYLDHLGSKPQQQQPSPQSTSINTVALSHFESSEKPRIWSLARTAAAGVVLGTQHVGDVRTGPVDCQMQGVRLPTVGAVQCGELKGLQDPTNLSNTESLFQEGLQGIHKAYSSGSFKTLQLHSSSYPGLTESCQYSSMEGFPSAGKTETESSELSDTCPTIQEAKTTAFRPVMKR"

     misc_feature    order(734..742,746..748,806..808,824..826,863..865,
                     869..874,881..886,890..898,902..907)
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(734..736,743..745,872..874,881..886,893..895)
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    782..898
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            329..592
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            593..702
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            703..968
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            969..1607
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            1608..1722
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
     exon            1723..2296
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agtcttacgttatcctttaagctttctacagctgtttaacaacaatatttttgtacttgatgaagcttaactctaatttctcatttccttaaggggattatctatacatataaaactagggctggcgtaaacatcctcagtgcttcccagttaagtgcagtcatctattattgagcgaaaggccgagtgtggaaatgtgtgtaagacggtggatttgaagtagatttggtttcaatcgatcagcaggagaagaatattgcttatggtaacaaaagaagcagctatgtccttctctcagtttggatatccttacaatgcaacttctcagtttttcgtgtcggcaacccccagtacgacttgctgcgattcgatatccaggtcggtgacagaaggatcgagcgcatcgcagaccgcagcctccttctgctgtccctcctatgagaaccggctgctggcgagtacacggacggagctcaacgccgcgctcgggatgtacggctccccttacgcagcagcagcggccgcagccgggcagaactacgccaactactttccgtatagcgccgacccctccgccatctactccagcctgaacccacaatatgaaatcaaagaggggtcaggcagtcttcatagcactataacacaaccagccacttactatccatatgaccactcactcggacagtaccagtatgacaggtatgggacagttgattttaatggatcaacacggagaaagaacgccacacgtgagacaacaagtacgcttaaaacatggctttatgagcaccgcaaaaacccttatcctacaaagggtgaaaagatcatgctggccattatcaccaaaatgaccctcacgcaagtgtctacctggtttgccaatgctagaagacgactaaaaaaagaaaacaagatgacttggtcccccaaaaacaaagcaggcgatgacaggaaggaagacctcgactccaaagacagtaaggatgagcaggacctgcagttcagtgacctggatgatatggaggatgaggactgtgacaagctggacagtgactgtgaaaaatcaggtcaggatgacctcccgacctcctcccctccaaagagagactgtaaccctgacatccctctccactccaacttcccatcttttccctgtggtctgaagagtttggggcctctgaacccagactacctagatcatctgggctccaaaccacagcagcaacagccctcacctcagtccacctccataaacactgtggcactctctcactttgagtcatcggagaagccccggatctggtcgttggcacgtacggccgcagcaggggttgtactaggcacacagcatgttggggatgtacggactgggcctgtggactgtcagatgcagggagtccggttacccacagtcggagcagtgcagtgtggggagctgaagggccttcaggaccctacaaacctcagcaatactgaaagcctttttcaagaaggactacaggggatacacaaggcatacagtagcgggagcttcaagacactacaacttcactcttcatcatatcctggactgacagaatcctgccagtactcctcaatggaaggcttccccagtgcaggaaagacagagacagaatccagtgagctcagtgacacatgcccaacaatccaggaggctaagaccactgcattcagacctgtgatgaagaggtgaggcaggactatggaaatgccaataaacatggggaagtttttatgatctacattatgcactatggaatggagtcaatgaggaactttaagcccatggcagcagacacttgaaatagtagcgcaatgactttgtgtgccctttctggaactgtgaaaactggaggcagccataattttgcacaatatgatttaatggtgtcaataactttatgcaatgttttgtgtatgtatgagaataaattgtgattttttatgtctgcattggcaatcgtaggtttagtaattctatttatctatttattgttttatcatccatctgctttatttatctgttaccatgtgtcctctcaaggtttttttgtgtgtgttaagtttaattctctgtggttatgtgcttaatgttatgtgatttacttttttttggaagctggtgtaaaatttagtcagtcttttaacttttatttacttctcaaaaataaatgaggtgcgatactgtgctcctgcggagtgtgatatgtttatataaaaaaaaagttgtgtataaatgtcatgttgttatttataaaatattttataagaa

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