LOCUS       NM_001045371            1446 bp    mRNA    linear   VRT 05-AUG-2023
DEFINITION  Danio rerio H6 family homeobox 4 (hmx4), mRNA.
ACCESSION   NM_001045371
VERSION     NM_001045371.1
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 1446)
  AUTHORS   Spead O, Weaver CJ, Moreland T and Poulain FE.
  TITLE     Live imaging of retinotectal mapping reveals topographic map
            dynamics and a previously undescribed role for Contactin 2 in map
            sharpening
  JOURNAL   Development 148 (22) (2021)
   PUBMED   34698769
REFERENCE   2  (bases 1 to 1446)
  AUTHORS   England SJ, Cerda GA, Kowalchuk A, Sorice T, Grieb G and Lewis KE.
  TITLE     Hmx3a Has Essential Functions in Zebrafish Spinal Cord, Ear and
            Lateral Line Development
  JOURNAL   Genetics 216 (4), 1153-1185 (2020)
   PUBMED   33077489
REFERENCE   3  (bases 1 to 1446)
  AUTHORS   Song P and Perkins BD.
  TITLE     Developmental expression of the zebrafish Arf-like small GTPase
            paralogs arl13a and arl13b
  JOURNAL   Gene Expr Patterns 29, 82-87 (2018)
   PUBMED   30009987
REFERENCE   4  (bases 1 to 1446)
  AUTHORS   Kelly LE and El-Hodiri HM.
  TITLE     Xenopus laevis Nkx5.3 and sensory organ homeobox (SOHo) are
            expressed in developing sensory organs and ganglia of the head and
            anterior trunk
  JOURNAL   Dev Genes Evol 226 (6), 423-428 (2016)
   PUBMED   27392729
REFERENCE   5  (bases 1 to 1446)
  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   6  (bases 1 to 1446)
  AUTHORS   Feng Y and Xu Q.
  TITLE     Pivotal role of hmx2 and hmx3 in zebrafish inner ear and lateral
            line development
  JOURNAL   Dev Biol 339 (2), 507-518 (2010)
   PUBMED   20043901
REFERENCE   7  (bases 1 to 1446)
  AUTHORS   Wotton KR, Weierud FK, Juarez-Morales JL, Alvares LE, Dietrich S
            and Lewis KE.
  TITLE     Conservation of gene linkage in dispersed vertebrate NK homeobox
            clusters
  JOURNAL   Dev Genes Evol 219 (9-10), 481-496 (2009)
   PUBMED   20112453
REFERENCE   8  (bases 1 to 1446)
  AUTHORS   French CR, Erickson T, Callander D, Berry KM, Koss R, Hagey DW,
            Stout J, Wuennenberg-Stapleton K, Ngai J, Moens CB and Waskiewicz
            AJ.
  TITLE     Pbx homeodomain proteins pattern both the zebrafish retina and
            tectum
  JOURNAL   BMC Dev Biol 7, 85 (2007)
   PUBMED   17634100
  REMARK    Publication Status: Online-Only
REFERENCE   9  (bases 1 to 1446)
  AUTHORS   Asai-Coakwell M, French CR, Berry KM, Ye M, Koss R, Somerville M,
            Mueller R, van Heyningen V, Waskiewicz AJ and Lehmann OJ.
  TITLE     GDF6, a novel locus for a spectrum of ocular developmental
            anomalies
  JOURNAL   Am J Hum Genet 80 (2), 306-315 (2007)
   PUBMED   17236135
REFERENCE   10 (bases 1 to 1446)
  AUTHORS   Adamska M, Wolff A, Kreusler M, Wittbrodt J, Braun T and Bober E.
  TITLE     Five Nkx5 genes show differential expression patterns in anlagen of
            sensory organs in medaka: insight into the evolution of the gene
            family
  JOURNAL   Dev Genes Evol 211 (7), 338-349 (2001)
   PUBMED   11466530
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC122454.1.
            
            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 :: BC122454.1, CN502217.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505373, SAMEA3505388
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1446
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="1"
                     /map="1"
     gene            1..1446
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /note="H6 family homeobox 4"
                     /db_xref="GeneID:751654"
                     /db_xref="ZFIN:ZDB-GENE-060825-142"
     exon            1..282
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    27..29
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /note="upstream in-frame stop codon"
     CDS             78..794
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /note="homeobox transcription factor; hmx3b; zfSOHo"
                     /codon_start=1
                     /product="H6 family homeobox 4"
                     /protein_id="NP_001038836.2"
                     /db_xref="GeneID:751654"
                     /db_xref="ZFIN:ZDB-GENE-060825-142"
                     /translation="

MSKEDASCRPASLKFTIDNILNSKTSSRNFDSCHSRASLVVCRDGCLHHPGESEDPCKEGSDARLHGIDKLNREGDATVDALKAVDMRSESADSCDDAQQKNNGKKNKLMTKKKTRTIFSKRQIFQLESTFDMKRYLSSAERACLANSLQLTETQVKIWFQNRRNKLKRQLSTELEGPNSEFGDIGKTVPLPALYKENNLLGRCMLPMPLPVVYPGGSAPYFYFSNASKYFSLFDGDI"

     misc_feature    order(420..428,432..434,483..485,501..503,540..542,
                     546..551,558..563,567..575,579..584)
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    420..581
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(420..422,429..431,549..551,558..563,570..572)
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            283..1420
                     /gene="hmx4"
                     /gene_synonym="Hmx1; soho; wu:fc21b03; zgc:154104"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gttcggagaatcgagacgctagtttatgaaacgggggaaaaagaggcacagacacggacccgcatctaacggagaatatgagcaaggaggacgcgtcatgtcgacccgcttctttgaagttcaccattgacaatatcctcaactccaagacgagcagcagaaactttgacagctgtcattcaagggcatcgctcgtggtgtgtcgggatggctgtcttcatcaccccggagagagcgaggatccatgtaaagaagggtcagatgcaagattgcatggcattgataaactcaacagagagggggatgcgactgtggacgcgctcaaagccgtcgacatgcgcagcgagagcgcggacagctgcgacgacgcgcagcaaaagaacaacggcaagaagaataaactgatgacgaagaagaaaacgcgcactatattttcaaaaagacagatcttccaactggaatctacgtttgacatgaagcgctacctgagcagcgcggagcgcgcgtgcttggcgaactccttgcagcttaccgagactcaagtcaaaatctggtttcagaatcgacggaataaattaaaaagacaactgtctactgaacttgaaggaccgaacagcgagttcggtgatattggaaagacggtgccgcttccagctttatataaagagaataatctgctcggaaggtgcatgcttccaatgcctttaccagtcgtgtatcctggaggtagcgcgccttacttttatttctcaaatgccagcaagtatttcagcctgtttgatggagatatatgacttagtaaagatcctctcacaggggacaccgtttccttagctctcataacaaaatcgacaacacgacccaactcaaattttaataagcattatcacccttttgtgtgttttgctgagaacatcgttgagctatcggtcagtaaaaaagctggcttgtatttctatgcaaaacttattttatttattctatgctgtacaaaattttatatataaaacaagaacacatagcatattatacccaggcaaccccgtcatacagtgcatcacagtgagcagccatactggcagaaatgccacagccaatcatcccgtcttcacatggaagaaagttttaacagatgttttgctgtttacattattattattttttacatatccgctaaagattttcgatgcatgcatttgtatttttaaatggccctcttttttcaaaatgagcaattaaacctatttaagtgaatgtattggttattttacatctaacgcatgtttgtatgtttataccttttagattttatcgttttaattccttttcagcataacctggccgattattaggctaccagtatttacatcatttatcgagtgtcattaaatattctgttttacactttcttcaaacgaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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