LOCUS       NM_001001405            1231 bp    mRNA    linear   VRT 04-DEC-2022
DEFINITION  Danio rerio iroquois homeobox 5b (irx5b), mRNA.
ACCESSION   NM_001001405
VERSION     NM_001001405.1
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 1231)
  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 1231)
  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, K 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 1231)
  AUTHORS   Pasquier J, Cabau C, Nguyen T, Jouanno E, Severac D, Braasch I,
            Journot L, Pontarotti P, Klopp C, Postlethwait JH, Guiguen Y and
            Bobe J.
  TITLE     Gene evolution and gene expression after whole genome duplication
            in fish: the PhyloFish database
  JOURNAL   BMC Genomics 17, 368 (2016)
   PUBMED   27189481
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1231)
  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 1231)
  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   6  (bases 1 to 1231)
  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   7  (bases 1 to 1231)
  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   8  (bases 1 to 1231)
  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
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AY512587.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY512587.1, BC160654.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505372
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1231
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="25"
                     /map="25"
     gene            1..1231
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="iroquois homeobox 5b"
                     /db_xref="GeneID:405792"
                     /db_xref="ZFIN:ZDB-GENE-040628-5"
     exon            1..262
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    2..4
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="upstream in-frame stop codon"
     CDS             38..1153
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="iroquois homeobox protein 5b"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-5b"
                     /protein_id="NP_001001405.1"
                     /db_xref="GeneID:405792"
                     /db_xref="ZFIN:ZDB-GENE-040628-5"
                     /translation="

MAFPQGYLYQSSLSLYSCPPYGSTGITAPRTDDLGRSSSGSAFSPYASTAFTNTTVAFSSLQYSPESAAPFTSYGGSPYDPSPGMTGSIGYHPYAGPLGPYPFGDPAYRKNATRDATATLKAWLNEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWTPRTRSEDEDEEDSIDLEKNDEDDEPMKTAESTKDSETRAEDHDDSTDSVIIDCGEEEENRTESPVPTTSSPQDELSESTIKPLSGNCKPTSVIPSPNPKPKLWSLAEIATSDKGREEVSHTSRAGSPQCTFPARHLYYASPFFVGFSNYGAFGHLNGCGGGNSTHLNGINQAVLHRTRDSKLTLEMCKELTFEHKRANI"

     misc_feature    <83..>418
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="Sec24-related protein; Provisional; Region:
                     PTZ00395"
                     /db_xref="CDD:185594"
     misc_feature    order(362..367,371..373,431..433,449..451,488..490,
                     494..499,506..511,515..523,527..532)
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(368..370,497..499,506..511,518..520)
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    407..523
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     misc_feature    836..889
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /note="Motif in Iroquois-class homeodomain proteins
                     (only). Unknown function; Region: IRO; smart00548"
                     /db_xref="CDD:214716"
     exon            263..659
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /inference="alignment:Splign:2.1.0"
     exon            660..1225
                     /gene="irx5b"
                     /gene_synonym="iro5b; ziro5b"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atgagagtacagaggtgactgtagcggtaatctggtcatggcgtttccacagggatacttgtaccagtcgtcgctgtctctgtactcgtgtccgccgtacggctccaccgggataacggcaccgcgaacggacgatctgggacggtcctccagtggatctgctttttccccgtatgcgtccacagccttcacgaacaccaccgtcgccttcagctccctccagtacagcccagaatccgcagcccccttcacttcatacgggggctccccatatgacccttctccaggcatgaccggctccatcggctatcacccgtacgccggtcccctgggcccgtacccgttcggggaccccgcttaccggaaaaacgcaacgcgcgacgccaccgccaccctgaaggcctggctcaacgagcaccgcaaaaacccttatcccaccaaaggagagaagatcatgctggccatcatcaccaaaatgaccctcactcaagtgtccacctggttcgccaacgcgcgcaggaggctgaaaaaggaaaacaagatgacgtggacgcccaggacgcggagcgaggatgaggatgaagaggacagcattgatttggagaaaaatgatgaagatgatgagcccatgaagacagccgagagcaccaaagattcagaaacccgtgcggaagaccacgacgactccacggacagtgtgataatcgactgcggggaagaagaggaaaaccggacagagtctccggtgcccacgacctcctctccccaagacgaactgagtgaaagcacgattaagcccctcagcggaaactgcaagcccacatctgtcatcccctccccgaaccccaaacccaaactctggtctctggcagaaatcgctacgtcggataaagggcgcgaggaggtgtcacatacgtcacgcgcggggtcaccacagtgcacgtttcccgccagacatttgtactacgcgtctccatttttcgtgggtttctcgaactatggcgcctttggacatttgaacggctgcggtggcgggaactcgacacacctgaacggaataaaccaggcggtgttacacagaaccagagacagcaaactgactctggagatgtgcaaagaactcactttcgagcacaagagggcgaatatttagcttttcttttaattttttttgtatttattgtttccagaatgaaacgaacaagcgttgtgcttttaaactgtaaaaaaa

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