LOCUS       NM_001020493            1874 bp    mRNA    linear   VRT 30-JUN-2024
DEFINITION  Danio rerio iroquois homeobox 4b (irx4b), mRNA.
ACCESSION   NM_001020493 XM_005170029 XM_009294211
VERSION     NM_001020493.2
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 1874)
  AUTHORS   Ezhkova,D., Schwarzer,S., Spiess,S., Geffarth,M., Machate,A.,
            Zoller,D., Stucke,J., Alexopoulou,D., Lesche,M., Dahl,A. and
            Hans,S.
  TITLE     Transcriptome analysis reveals an Atoh1b-dependent gene set
            downstream of Dlx3b/4b during early inner ear development in
            zebrafish
  JOURNAL   Biol Open 12 (6) (2023)
   PUBMED   37272628
REFERENCE   2  (bases 1 to 1874)
  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   3  (bases 1 to 1874)
  AUTHORS   Clement,Y., Torbey,P., Gilardi-Hebenstreit,P. and Roest Crollius,H.
  TITLE     Enhancer-gene maps in the human and zebrafish genomes using
            evolutionary linkage conservation
  JOURNAL   Nucleic Acids Res 48 (5), 2357-2371 (2020)
   PUBMED   31943068
REFERENCE   4  (bases 1 to 1874)
  AUTHORS   Mullally,M., Albrecht,C., Horton,M., Laboissonniere,L.A.,
            Goetz,J.J., Chowdhury,R., Manning,A., Wester,A.K., Bose,Q. and
            Trimarchi,J.M.
  TITLE     Expression Profiling of Developing Zebrafish Retinal Cells
  JOURNAL   Zebrafish 13 (4), 272-280 (2016)
   PUBMED   26982811
REFERENCE   5  (bases 1 to 1874)
  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   6  (bases 1 to 1874)
  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 1874)
  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   8  (bases 1 to 1874)
  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
            BX571830.6.
            
            On or before Feb 12, 2016 this sequence version replaced
            XM_009294211.1, NM_001020493.1.
            
            Sequence Note: This RefSeq record was created from genomic sequence
            data because no single transcript from the reference strain was
            available for the full length of the gene. The extent of this
            transcript is supported by transcript alignments, RNA-seq data and
            orthologous data.
            
            ##Evidence-Data-START##
            CDS exon combination :: AY845129.1 [ECO:0000331]
            RNAseq introns       :: single sample supports all introns
                                    SAMEA3505376, SAMEA3505385 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-479               BX571830.6         127637-128115       c
            480-719             BX571830.6         126038-126277       c
            720-832             BX571830.6         124979-125091       c
            833-1152            BX571830.6         124562-124881       c
            1153-1874           BX571830.6         122159-122880       c
FEATURES             Location/Qualifiers
     source          1..1874
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="19"
                     /map="19"
     gene            1..1874
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="iroquois homeobox 4b"
                     /db_xref="GeneID:474318"
                     /db_xref="ZFIN:ZDB-GENE-040712-4"
     exon            1..479
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    390..392
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="upstream in-frame stop codon"
     CDS             435..1754
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="iroquois homeobox protein 4b"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-4b"
                     /protein_id="NP_001018329.2"
                     /db_xref="GeneID:474318"
                     /db_xref="ZFIN:ZDB-GENE-040712-4"
                     /translation="

MSFTQFGYSYPAAPQLLMSSNALSTCFESSGSLLDSGVPTSPQNSLYCPVYESRLVASSRHELIPTAVYGNSCSKNHVYDSCSTYGPDSAACYPLGKLNEKDGVQTGHSRVTQSSAYYPYDYPIGQYSYDRYGYGSVDVGTRRKNATRETTSTLKAWLQEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWSPRNKNSDEKECDDDQEDLDEAQEEPIKTEQDFNDNHGKDDTDQLHSDLDDFDLVESDGSECESKPSFVVHVHSETSDHPETHFKDAFHESVTELTRGVHKFSEDRLRAPAEDHQMAKFYLQQGQKTIETKPKIWSLAQTATSLNQVDYSSCMHKRTACPSSNCDSDSEMTKRKQESPVATLRNWVDGVFHDPLFRHNNLNQTFSNSTELWTDAISSQNNYHEHSGTPITSSHA"

     misc_feature    <840..>1076
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(858..866,870..872,930..932,948..950,987..989,
                     993..998,1005..1010,1014..1022,1026..1031)
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(858..860,867..869,996..998,1005..1010,1017..1019)
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    906..1022
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     misc_feature    1068..>1232
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="Spt5 transcription elongation factor, acidic
                     N-terminal; Region: Spt5_N; pfam11942"
                     /db_xref="CDD:463406"
     misc_feature    <1440..1478
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /note="Motif in Iroquois-class homeodomain proteins
                     (only). Unknown function; Region: IRO; smart00548"
                     /db_xref="CDD:214716"
     exon            480..719
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /inference="alignment:Splign:2.1.0"
     exon            720..832
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /inference="alignment:Splign:2.1.0"
     exon            833..1152
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /inference="alignment:Splign:2.1.0"
     exon            1153..1874
                     /gene="irx4b"
                     /gene_synonym="ziro4b"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggctgctggcggcaggggaactgaacacgtcctcattaatgtgcgcgagaccccgcgggctcttcacgaggacacccgcgcatcacccgggactctcaactcgtacggcgcatatataaactgttccgctgtctgaacaataactttcgttgttattcgcgtttgttatctggacctttaaatctgctcccgtgacgtcagcgccgccggtgtttaaaacaacgtgcaaactgaggcaacgtttgttatgaatttttttccaacttcagctcaagcacgttatgttcgtgtcatgctgcggtctgtggtggctttagtgtaaagagacgaacagaaacaggaaaaggacgcttatctccagttgatggaagatattggtgataaactgatgacccgccgcgggactgcagctttctctgtgcaggacactcatcatgtcatttacacagtttggttattcataccctgcagcaccacagcttttaatgtcttctaatgctctgagcacctgctttgagtctagtggttctctgctagactctggagtgccgacttctcctcaaaactcactttactgccccgtgtacgaaagtaggcttgtggcctccagccggcatgagctgatccctactgcggtctatggcaactcctgttcaaaaaatcatgtttacgactcctgcagcacttacggtccagattcagccgcatgctatcctctgggtaaactcaatgagaaagatggagtgcaaactggacattcaagagttacccaaagctctgcatattatccctacgactacccaattggacaatactcatatgatcgatatggatatggatctgtagatgtggggacaagaagaaagaatgccaccagagagaccaccagcacattgaaagcatggttgcaggaacataaaaagaatccgtatcctacaaagggtgagaagatcatgttggctatcatcactaagatgacccttacgcaggtctccacctggtttgccaacgcacgccggagactcaagaaggagaataagatgacgtggtcaccacgtaacaagaactcagatgagaaggagtgtgacgacgaccaagaagatctggatgaagcgcaggaggagccaataaaaactgaacaagatttcaatgacaaccatggaaaggacgatacagatcaacttcacagcgatctggatgatttcgatctagtggaatcggatggctctgagtgcgaatcgaaaccatcttttgttgtgcacgttcactcagaaaccagcgaccacccagaaacccactttaaagatgcttttcatgaatccgttaccgagcttacaagaggtgtccacaaatttagcgaagaccgtctgagagcacctgctgaggatcaccaaatggcaaagttttaccttcaacaaggccaaaagaccattgagaccaagccgaaaatctggtcgcttgcacagaccgctacatcgttaaaccaagtcgattattcatcatgcatgcataaacgaacagcctgcccttcttcaaactgtgactccgattcagaaatgacaaagaggaaacaagagtctccagtagctactctgaggaactgggtggatggagtgtttcacgatcccctattcaggcacaacaacctaaaccaaactttcagcaactccacagagttatggactgatgccatttcctcacagaataactaccatgaacactcaggaacacctattacttcctctcatgcttaatagtggtgtttttttcatacattttgtagcaccatcacaaaattaacatgttagccaatctcattagtttcatcctgtaagcttttgtcatttaagaaatcttgagagtcatgaacttta

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