LOCUS       NM_205698               2101 bp    mRNA    linear   VRT 16-SEP-2024
DEFINITION  Danio rerio iroquois homeobox 4a (irx4a), mRNA.
ACCESSION   NM_205698
VERSION     NM_205698.1
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 2101)
  AUTHORS   Hung JC, Wu JL, Li HC, Chiu HW and Hong JR.
  TITLE     The Proapoptotic Gene Bad Regulates Brain Development via
            p53-Mediated Stress Signals in Zebrafish
  JOURNAL   Cells 10 (11), 2820 (2021)
   PUBMED   34831043
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2101)
  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   3  (bases 1 to 2101)
  AUTHORS   Hung JC, Wu JL and Hong JR.
  TITLE     Proapoptotic Bad Involved in Brain Development, When Severely
            Defected, Induces Dramatic Malformation in Zebrafish
  JOURNAL   Int J Mol Sci 22 (9), 4832 (2021)
   PUBMED   34063300
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2101)
  AUTHORS   Targoff KL, Colombo S, George V, Schell T, Kim SH, Solnica-Krezel L
            and Yelon D.
  TITLE     Nkx genes are essential for maintenance of ventricular identity
  JOURNAL   Development 140 (20), 4203-4213 (2013)
   PUBMED   24026123
REFERENCE   5  (bases 1 to 2101)
  AUTHORS   Zhang Y, Bonilla S, Chong L and Leung YF.
  TITLE     Irx7, a Smarca4-regulated gene for retinal differentiation,
            regulates other genes controlled by Smarca4 in zebrafish retinas
  JOURNAL   Gene Expr Patterns 13 (5-6), 177-182 (2013)
   PUBMED   23557786
REFERENCE   6  (bases 1 to 2101)
  AUTHORS   Carney SA, Chen J, Burns CG, Xiong KM, Peterson RE and Heideman W.
  TITLE     Aryl hydrocarbon receptor activation produces heart-specific
            transcriptional and toxic responses in developing zebrafish
  JOURNAL   Mol Pharmacol 70 (2), 549-561 (2006)
   PUBMED   16714409
REFERENCE   7  (bases 1 to 2101)
  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 2101)
  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 2101)
  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
REFERENCE   10 (bases 1 to 2101)
  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 BC065966.1.
            
            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 :: BC065966.1, AY845128.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA3505372,
                                           SAMEA3505374 [ECO:0006172]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2101
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="16"
                     /map="16"
     gene            1..2101
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /note="iroquois homeobox 4a"
                     /db_xref="GeneID:402999"
                     /db_xref="ZFIN:ZDB-GENE-040426-1825"
     exon            1..321
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    115..117
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /note="upstream in-frame stop codon"
     CDS             277..1599
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /note="Iroquois 4a protein; iroquois homeobox protein 4a"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-4a"
                     /protein_id="NP_991261.1"
                     /db_xref="GeneID:402999"
                     /db_xref="ZFIN:ZDB-GENE-040426-1825"
                     /translation="

MSYPQFGYPYSSAPQFLMTTNSLTSCCESSTRSIPDSSAQTPVYCPVYESRLLATARHELSSAAALGVYGSPYTGGQGYGNYVTYGADASAFYSLGTFDAKDGSASAHAGITPAAAYYPYDPTLGQYQYDRYGSMEGGTRRKNATRETTSTLKAWLQEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWPPRNKGSDEKKYDDDEDGSPEEQIKSETNDDESKDREDKDLQLSDLEDFDPLESESPECELKHRFQISAHMETKDPQKLSIPGLLEEAKSCLKSPEDCELELRHSKACFQQQQQQSHPILDSKPRIWSLAQTATSLNPAEFPSCMLRCPASPSPAGGPDRQQDSPVTTLRNWVDGVFHDPLFRHSSLNQTNTTVSWTNKGSILETGALGRSVADSGKQEAGKDTMTFPKGVNKIFCS"

     misc_feature    order(694..702,706..708,766..768,784..786,823..825,
                     829..834,841..846,850..858,862..867)
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(694..696,703..705,832..834,841..846,853..855)
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    742..858
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            322..561
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /inference="alignment:Splign:2.1.0"
     exon            562..668
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /inference="alignment:Splign:2.1.0"
     exon            669..979
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /inference="alignment:Splign:2.1.0"
     exon            980..2069
                     /gene="irx4a"
                     /gene_synonym="zgc:77362; ziro4a"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

caaaatatgtatttctgacatcaaaggcgacaacactcgcagtttctttcaggatgtgcgctttgtagaagtttatcagtgcgacaggagggataaatcaaagcgtgcatcagttgaacatctcctggaaggcgtttaaagcgaattaaacatgctagaatcgcgcttcgccctataagcgtccggcagctttatgcgttaccaatcaatcggtacagtgaaacacagcagacctgcagtctcgcctgcgttccgcgaaagggggatcactttacaatgtcctatcctcaattcggatacccatactcttctgcaccacagttcctcatgaccaccaactctctgacatcttgctgcgagtcgagcaccagatccatcccggactcatcggcgcagacccccgtgtactgcccggtgtacgagagccggctgttggccaccgccagacacgagctcagctccgccgccgcgctcggggtctacggcagcccgtacaccggcggacaaggctacgggaattacgtgacctacggagctgacgcatcggcgttctactctttgggaacatttgacgccaaagatggaagcgcgtctgcgcatgcggggataacaccggctgccgcatattacccatacgatcccaccctgggacagtaccagtatgacaggtacggctctatggagggcgggacccgcaggaaaaacgctacccgggagaccacgagcacgctgaaggcctggctgcaggagcaccggaaaaacccctacccgaccaaaggagagaagatcatgctggccatcatcaccaagatgaccctcactcaggtgtccacctggttcgccaacgccagaaggagactcaagaaggagaacaagatgacctggccaccgaggaacaagggctcggacgagaagaagtatgatgatgatgaggatggatcaccagaggagcagatcaagagtgaaaccaatgatgacgagagcaaagatcgagaggacaaggatctgcagctgagcgacctggaggacttcgacccactggagtctgagagcccggagtgtgaactcaagcaccgcttccagatcagcgcgcacatggagaccaaagacccgcagaaactctccatccccgggctgctggaggaggccaagagctgcctgaagagcccggaggactgcgagctggagctccggcacagcaaagcgtgtttccagcagcagcagcagcagagccacccgatactggacagcaaaccgcggatctggtctctggcgcagaccgccacctccctgaaccccgcggagttcccgtcctgcatgctccggtgcccggcctcgccctcccccgccggcggccccgacagacagcaggactcaccggtcaccacgctcagaaactgggtagacggagttttccacgaccccttgttcagacacagctcgttaaaccagacgaacactactgtttcttggaccaacaaaggctcgatcctagagacaggagccctgggacgctcggtggcggacagcggcaagcaggaggccggcaaggacactatgacatttccaaagggggtgaataaaatattctgctcctagcacactggacatgactgccagaaagagactgtttggaatagctgtctgcggttttctgtgcgcagactgtgaatccacatgggcccaaaactggttttgttatcgcgggaagttgtgtgtatttattgctgtatgacatctcactggcgacggcattggtttatatatatatattggtttggttgacgcacgttcagattatgtaaatgaactggaagtttatgttctgaaagactgacaaaagtttacagcccagtttggtttcagcttttctttggcatgcatatgttgctagattttctatttgattttattattattatcggtcattcttttagacggactcggaccttgttgcatcgactcacaagtgtcactgttaagaaagtatcgcacacatgcacagatctcctggaatggagaatgttcaacctgatcactctaataaacggtcgatttttccaagcgttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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