LOCUS       NM_201057               2239 bp    mRNA    linear   VRT 04-DEC-2022
DEFINITION  Danio rerio iroquois homeobox 2a (irx2a), mRNA.
ACCESSION   NM_201057
VERSION     NM_201057.1
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 2239)
  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 2239)
  AUTHORS   Marra AN, Cheng CN, Adeeb B, Addiego A, Wesselman HM, Chambers BE,
            Chambers JM and Wingert RA.
  TITLE     Iroquois transcription factor irx2a is required for multiciliated
            and transporter cell fate decisions during zebrafish pronephros
            development
  JOURNAL   Sci Rep 9 (1), 6454 (2019)
   PUBMED   31015532
  REMARK    GeneRIF: Iroquois transcription factor irx2a is required for
            multiciliated and transporter cell fate decisions during zebrafish
            pronephros development.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2239)
  AUTHORS   Lush ME, Diaz DC, Koenecke N, Baek S, Boldt H, St Peter MK,
            Gaitan-Escudero T, Romero-Carvajal A, Busch-Nentwich EM, Perera AG,
            Hall KE, Peak A, Haug JS and Piotrowski T.
  TITLE     scRNA-Seq reveals distinct stem cell populations that drive hair
            cell regeneration after loss of Fgf and Notch signaling
  JOURNAL   Elife 8, e44431 (2019)
   PUBMED   30681411
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2239)
  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   5  (bases 1 to 2239)
  AUTHORS   Wang J, Wu Y, Zhao F, Wu Y, Dong W, Zhao J, Zhu Z and Liu D.
  TITLE     Fgf-signaling-dependent Sox9a and Atoh1a regulate otic neural
            development in zebrafish
  JOURNAL   J Neurosci 35 (1), 234-244 (2015)
   PUBMED   25568117
REFERENCE   6  (bases 1 to 2239)
  AUTHORS   Foucher I, Mione M, Simeone A, Acampora D, Bally-Cuif L and Houart
            C.
  TITLE     Differentiation of cerebellar cell identities in absence of Fgf
            signalling in zebrafish Otx morphants
  JOURNAL   Development 133 (10), 1891-1900 (2006)
   PUBMED   16611693
REFERENCE   7  (bases 1 to 2239)
  AUTHORS   Lecaudey V, Anselme I, Dildrop R, R 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 2239)
  AUTHORS   Dildrop R and R U.
  TITLE     Organization of Iroquois genes in fish
  JOURNAL   Dev Genes Evol 214 (6), 267-276 (2004)
   PUBMED   15133664
REFERENCE   9  (bases 1 to 2239)
  AUTHORS   Feij CG, Manzanares M, de la Calle-Mustienes E, G 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
REFERENCE   10 (bases 1 to 2239)
  AUTHORS   Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, Kaplan S, Jackson
            D, de Sauvage F, Jacob H and Fishman MC.
  TITLE     Zebrafish genetic map with 2000 microsatellite markers
  JOURNAL   Genomics 58 (3), 219-232 (1999)
   PUBMED   10373319
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC056322.1.
            
            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 :: BC056322.1, AY845127.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA4476732 [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2239
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="16"
                     /map="16"
     gene            1..2239
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /note="iroquois homeobox 2a"
                     /db_xref="GeneID:394032"
                     /db_xref="ZFIN:ZDB-GENE-040426-1446"
     exon            1..358
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    131..133
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /note="upstream in-frame stop codon"
     CDS             140..1438
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /note="Iroquois 2a protein; iroquois homeobox protein 2,
                     a"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-2a"
                     /protein_id="NP_957351.1"
                     /db_xref="GeneID:394032"
                     /db_xref="ZFIN:ZDB-GENE-040426-1446"
                     /translation="

MSYPQGYLYQPPGSLALYSCPLAAPRSEDLARSSSGSAFSPYPGSAAFTASANGFSSPLPYSTDPATGFPSYMGSPYDAHTTGMAGAISYHPYGSPGYPYQLNDPAYRKNATRDATATLKAWLQEHRKNPYPTKGQKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWAPRNKSEDEDEDDGDGERKDERTDKNMDNSEASAEDEGISLHVDALTDHSCSVESDGEKVTCRTGDLVCDSGAEIQDKCEATDLGEERQRGASPKPVTSSPLTGVEAPLLTHHHRENSTNKTCLDGQNQTVKPKLWSLAEIATSDPKQQNCPPGVGLLTSSAPGASPAGAVYPATSILGRPLYYTSPFYSNYTNYGNFSPLQGQGILRYNSAAEGLLHKQTGEPLIKTNPNQTEAHFRASNAESKKDPSEVFTVRSQSYLSS"

     misc_feature    order(461..466,470..472,530..532,548..550,587..589,
                     593..598,605..610,614..622,626..631)
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(467..469,596..598,605..610,617..619)
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    506..622
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            359..761
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /inference="alignment:Splign:2.1.0"
     exon            762..1388
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /inference="alignment:Splign:2.1.0"
     exon            1389..1457
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /inference="alignment:Splign:2.1.0"
     exon            1458..2220
                     /gene="irx2a"
                     /gene_synonym="Irx2; zgc:65872; zgc:77209; ziro2a"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atctccatgacggctctctgctgaacgctcctctcgtgcgcgtttatttattttattttattagttcgcgtccggtgcgtcaatgcgctgattccatcgatcagcccgatttcgcgttgtggagagaagctgagtaataatgtcctatcctcagggttacctctaccagcccccgggctctctggcgctttactcgtgtccgctggccgccccgaggagcgaggatttggcccggtcatcctccggttccgcgttcagcccgtaccccgggtcggcggcgttcacagcctccgccaacggattctccagcccgctgccctactccacagatccggccacgggattcccgtcctacatgggctctccgtatgacgcgcacactacgggaatggcaggagccataagttatcacccgtacgggagtcccggttacccgtaccagctcaacgatcccgcttaccggaaaaacgccactcgggacgcaacagcgacgttaaaagcgtggctgcaggagcacaggaaaaacccctatcccactaaaggacagaagatcatgctggccatcatcaccaaaatgaccctcacgcaagtgtccacctggttcgccaatgcacgacggagactcaagaaggagaacaagatgacctgggcaccgcggaataaaagtgaagacgaagacgaagatgacggagatggagagagaaaagacgagcgcacggataaaaacatggacaacagcgaagcgtcagctgaggacgaaggcatcagtttgcacgtcgatgccctgacagaccactcgtgctcggtggagtcggacggggagaaggtcacgtgtcggaccggagaccttgtttgcgattctggagctgaaatccaggacaaatgcgaggcgacggatctcggggaggaaaggcagcgaggcgcgtcacccaaaccggtgacctcttctcctttgaccggggtggaggcgcctctattgacccatcatcaccgggagaacagcaccaacaaaacatgcctggacggtcaaaaccaaaccgtcaagcctaagctgtggtcattagcagagatcgccacttcggaccccaagcagcagaactgtcccccgggtgtcggccttctgacctccagcgcgcccggcgcgtccccggcgggcgcggtttaccccgccacctccatactaggaagacctctttattacacttctccgttttatagtaattacacaaactatggcaacttcagcccgcttcagggccaggggatactgcgctacaactccgccgcagagggactccttcataaacagactggagagccgctaataaagactaatccaaaccagactgaagctcacttcagggcctccaatgcagaatccaaaaaagaccccagcgaggttttcacagtaagatcccaatcttacctgtcgagttaagacgaggaagatcttccaagtaggtgtcacaattgctttgaacaaagcgaacaagccatcaccccttctctctctcccccctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctccccaagctgttttaaactaacatttgctccttatacgcggatcctcttttgtgtgccactgtacacccacggactacagagcacctgcctatacaataacaacaacaacactgcgattgcgggacagaaacgcaaagacaagacaggacaagagaaagaagagcgagtttataaggcacaatagccagtctgctttggacgaactgctgatttattgatgaagtactttatcccaacacatgtgacttttccatgaggaaacttatttctcaggatccttatagtagcttcattgccaccagttgtaaacacgcgtgggacatttattattattaattattattattatagacctcctatgagactttatatgtgctatagaggtgtgaagtgtaaacgagatctcgggactggtataaacttgactaagagtggaatacatttgatatttatttttgtaatgcctataatttatgcaagttgtattgcaatggttgctgaacattgttttgtaaataaattatgatgggtttttattttaaaaaagccgaagttacacaatgttgttaacaaggagacttttactaatttatatctctcgttgtaaataaaaatgcgctagtctgcactggcacaaaaaaaaaaaaaaaaaaaaa

//