LOCUS       NM_001045227            1922 bp    mRNA    linear   VRT 02-APR-2024
DEFINITION  Danio rerio iroquois homeobox 5a (irx5a), mRNA.
ACCESSION   NM_001045227 NM_131824 XM_681897 XM_703534 XM_703535 XM_703536
VERSION     NM_001045227.1
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 1922)
  AUTHORS   Thiruppathy,M., Fabian,P., Gillis,J.A. and Crump,J.G.
  TITLE     Gill developmental program in the teleost mandibular arch
  JOURNAL   Elife 11, e78170 (2022)
   PUBMED   35762575
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1922)
  AUTHORS   Liu,Y., Kossack,M.E., McFaul,M.E., Christensen,L.N., Siebert,S.,
            Wyatt,S.R., Kamei,C.N., Horst,S., Arroyo,N., Drummond,I.A.,
            Juliano,C.E. and Draper,B.W.
  TITLE     Single-cell transcriptome reveals insights into the development and
            function of the zebrafish ovary
  JOURNAL   Elife 11, e76014 (2022)
   PUBMED   35588359
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1922)
  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   4  (bases 1 to 1922)
  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   5  (bases 1 to 1922)
  AUTHORS   Mitchell,J.M., Sucharov,J., Pulvino,A.T., Brooks,E.P., Gillen,A.E.
            and Nichols,J.T.
  TITLE     The alx3 gene shapes the zebrafish neurocranium by regulating
            frontonasal neural crest cell differentiation timing
  JOURNAL   Development 148 (7) (2021)
   PUBMED   33741714
REFERENCE   6  (bases 1 to 1922)
  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   7  (bases 1 to 1922)
  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   8  (bases 1 to 1922)
  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   9  (bases 1 to 1922)
  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
REFERENCE   10 (bases 1 to 1922)
  AUTHORS   Wang,X., Emelyanov,A., Sleptsova-Friedrich,I., Korzh,V. and Gong,Z.
  TITLE     Expression of two novel zebrafish iroquois homologues (ziro1 and
            ziro5) during early development of axial structures and central
            nervous system
  JOURNAL   Mech Dev 105 (1-2), 191-195 (2001)
   PUBMED   11429297
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BX005202.14.
            
            On or before May 22, 2007 this sequence version replaced
            NM_131824.1, XM_681897.1, XM_703534.1, XM_703535.1, XM_703536.1.
            
            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 :: AY017309.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA4476754, SAMEA4476774
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1922
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="7"
                     /map="7"
     gene            1..1922
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="iroquois homeobox 5a"
                     /db_xref="GeneID:573346"
                     /db_xref="ZFIN:ZDB-GENE-010716-2"
     exon            1..526
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    257..259
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="upstream in-frame stop codon"
     CDS             284..1624
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="iroquois homeobox protein 5; iroquois-class
                     homeodomain protein IRX-5a"
                     /codon_start=1
                     /product="Iroquois homeobox protein 5a"
                     /protein_id="NP_001038692.1"
                     /db_xref="GeneID:573346"
                     /db_xref="ZFIN:ZDB-GENE-010716-2"
                     /translation="

MAYPQGYLYQPSASLALYSCPAYSTSVISGPRTEELGRSSSGSAFAPYAGSTAFTSASPGYNSHLPYSADAAAAATFTSYVSSPYDHTTGMAGSIGYHPYAAPLGSYPYGDPAYRKNATRDATATLKAWLNEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWTPRNRSEDEEEDENIDLEKNDDDEPNKPTDKGDSTDTEADHKLINPGEIPCDRFKDETHSKDLDPPLTDSELKEAEERTDLLAEQAKPTTSSPSVLQRGSDLITQEKPSEPGHAASTGNSNVTSVIHSPPSAPKPKLWSLAEIATSSDRCKGSSEASQAAGLSQSTVIASAASPTRSSPQCPLPNNTVLSRPIYYTSPFYPGYTNYSTFGHLHSSHGTNTSSTAHFNGLSQTVLNRAEALVRESKVRSQTQVDLCKDSPYELKKGMSNI"

     misc_feature    order(626..631,635..637,695..697,713..715,752..754,
                     758..763,770..775,779..787,791..796)
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(632..634,761..763,770..775,782..784)
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    671..787
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     misc_feature    806..1219
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="propagated from UniProtKB/Swiss-Prot (Q1LXU5.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1202..1255
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /note="Motif in Iroquois-class homeodomain proteins
                     (only). Unknown function; Region: IRO; smart00548"
                     /db_xref="CDD:214716"
     exon            527..932
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /inference="alignment:Splign:2.1.0"
     exon            933..1922
                     /gene="irx5a"
                     /gene_synonym="iro5"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      1922
                     /gene="irx5a"
                     /gene_synonym="iro5"
ORIGIN      

ccatctgagagcaaaaaacttgtcccgcgcgctcggcatgagagtcacagagcgctcagagggtgagagagcgcctcgaaaatccgcgagcgagtctgacaacgactgattaacgagtgtgaagtctatgcaatcgtcgttctctttaatttccatcactgctagacgcgaggaggacaggacggaggtctgtttactcggaactctatgagcgagcgcggcgagcgcgtgagagtttgagggagaagaactcaagtgagaagcttatatttggatcttcaccatggcgtaccctcagggctacttgtatcagccatccgcctctttggcactctattcgtgtcctgcctacagtacaagcgtgatttcgggaccccggacagaggagctagggagatcttcctctggctctgctttcgctccctatgccggatctacagcgttcaccagcgcctcgccaggctacaattcccatctcccgtacagtgctgatgcggccgccgctgctactttcacctcttatgtgagctcaccttatgaccacacgacaggcatggccgggtctatagggtatcatccttatgctgctcccctgggctcgtacccgtatggagacccagcttaccgcaagaatgctacccgggacgccacagctactttgaaagcttggcttaacgagcaccggaaaaacccgtaccccaccaaaggcgagaagatcatgctggccatcatcactaaaatgaccctcactcaagtgtccacctggttcgccaacgccaggaggaggctaaaaaaggagaacaagatgacctggaccccacggaaccggagtgaagacgaggaggaggacgaaaacattgatctagagaaaaacgacgacgacgagccaaacaagcccacggacaagggagactccacagacacagaggcagatcacaaactcatcaacccaggggaaataccatgcgacagatttaaagacgagactcattctaaagatcttgatccacctttgacagactcggaattaaaagaagcagaggagcggacggatttgctcgccgagcaagcgaaacccaccacatcctctccctccgttctacagagagggagtgatctcattacgcaagaaaagccctcagaaccgggccacgccgcgagcacgggaaacagcaacgtaacgtctgttattcattctcccccctcggcgcccaaacccaaactctggtctctggccgagatcgccacttcttcggacaggtgcaaagggagcagtgaggcttcacaggccgcgggtctgagtcaaagcacagtcattgccagcgctgcctcgccgacccggtcctcccctcagtgccctctccctaataacactgttctatctcggcctatttactacacgtcccctttttacccaggctacacgaactatagcactttcggacacctccacagcagtcatggcaccaacaccagctcaacggcacatttcaatggattaagccagactgttttaaacagagccgaggctctggtaagagagagcaaagtaagaagccaaacacaggtagatctttgtaaagactcaccttatgagctaaagaaaggtatgtcaaacatttaataccggattcatcgccaatcacacggacatttatttattatttgtggttgcctaaagaagaagcaaaagaagacgcattctgattttaaaaaatccgaggacaattattttctgagtaaatgcttatcctcaaaatcttagtttctgaatggttaatcaagaggatgtaatttctaagaattgtcttaaacgctgcagccgcctgagtctatttgtattaaagactaatatgtatatttaatgtagcattttgtatttaaaatggacaatacactatctttgaagtaaattatgaaaa

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