LOCUS       NM_131634               2058 bp    mRNA    linear   VRT 12-OCT-2024
DEFINITION  Danio rerio H6 family homeobox 3a (hmx3a), mRNA.
ACCESSION   NM_131634
VERSION     NM_131634.2
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 2058)
  AUTHORS   Olson,H.M., Maxfield,A., Calistri,N.L., Heiser,L.M., Qian,W.,
            Knaut,H. and Nechiporuk,A.V.
  TITLE     RhoA GEF Mcf2lb regulates rosette integrity during collective cell
            migration
  JOURNAL   Development 151 (1) (2024)
   PUBMED   38165177
REFERENCE   2  (bases 1 to 2058)
  AUTHORS   England,S.J., Rusnock,A.K., Mujcic,A., Kowalchuk,A., de Jager,S.,
            Hilinski,W.C., Juarez-Morales,J.L., Smith,M.E., Grieb,G.,
            Banerjee,S. and Lewis,K.E.
  TITLE     Molecular analyses of zebrafish V0v spinal interneurons and
            identification of transcriptional regulators downstream of Evx1 and
            Evx2 in these cells
  JOURNAL   Neural Dev 18 (1), 8 (2023)
   PUBMED   38017520
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2058)
  AUTHORS   Haws,W., England,S., Grieb,G., Susana,G., Hernandez,S., Mirer,H.
            and Lewis,K.
  TITLE     Analyses of binding partners and functional domains for the
            developmentally essential protein Hmx3a/HMX3
  JOURNAL   Sci Rep 13 (1), 1151 (2023)
   PUBMED   36670152
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2058)
  AUTHORS   Shi,T., Beaulieu,M.O., Saunders,L.M., Fabian,P., Trapnell,C.,
            Segil,N., Crump,J.G. and Raible,D.W.
  TITLE     Single-cell transcriptomic profiling of the zebrafish inner ear
            reveals molecularly distinct hair cell and supporting cell subtypes
  JOURNAL   Elife 12, e82978 (2023)
   PUBMED   36598134
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2058)
  AUTHORS   Tan,A.L., Mohanty,S., Guo,J., Lekven,A.C. and Riley,B.B.
  TITLE     Pax2a, Sp5a and Sp5l act downstream of Fgf and Wnt to coordinate
            sensory-neural patterning in the inner ear
  JOURNAL   Dev Biol 492, 139-153 (2022)
   PUBMED   36244503
REFERENCE   6  (bases 1 to 2058)
  AUTHORS   Omata,Y., Nojima,Y., Nakayama,S., Okamoto,H., Nakamura,H. and
            Funahashi,J.
  TITLE     Role of Bone morphogenetic protein 4 in zebrafish semicircular
            canal development
  JOURNAL   Dev Growth Differ 49 (9), 711-719 (2007)
   PUBMED   17908182
REFERENCE   7  (bases 1 to 2058)
  AUTHORS   Lecaudey,V., Ulloa,E., Anselme,I., Stedman,A.,
            Schneider-Maunoury,S. and Pujades,C.
  TITLE     Role of the hindbrain in patterning the otic vesicle: a study of
            the zebrafish vhnf1 mutant
  JOURNAL   Dev Biol 303 (1), 134-143 (2007)
   PUBMED   17137573
REFERENCE   8  (bases 1 to 2058)
  AUTHORS   Kwak,S.J., Vemaraju,S., Moorman,S.J., Zeddies,D., Popper,A.N. and
            Riley,B.B.
  TITLE     Zebrafish pax5 regulates development of the utricular macula and
            vestibular function
  JOURNAL   Dev Dyn 235 (11), 3026-3038 (2006)
   PUBMED   17013878
REFERENCE   9  (bases 1 to 2058)
  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
REFERENCE   10 (bases 1 to 2058)
  AUTHORS   Adamska,M., Leger,S., Brand,M., Hadrys,T., Braun,T. and Bober,E.
  TITLE     Inner ear and lateral line expression of a zebrafish Nkx5-1 gene
            and its downregulation in the ears of FGF8 mutant, ace
  JOURNAL   Mech Dev 97 (1-2), 161-165 (2000)
   PUBMED   11025218
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            EH585322.1 and AL773596.12.
            
            On Oct 15, 2015 this sequence version replaced NM_131634.1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: AF288211.1, GDQH01030455.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA4476733, SAMEA4476746
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-735               EH585322.1         27-761
            736-2058            AL773596.12        165317-166639
FEATURES             Location/Qualifiers
     source          1..2058
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="17"
                     /map="17"
     gene            1..2058
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /note="H6 family homeobox 3a"
                     /db_xref="GeneID:60310"
                     /db_xref="ZFIN:ZDB-GENE-001020-1"
     exon            1..553
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    241..243
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /note="upstream in-frame stop codon"
     CDS             268..1161
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /note="homeobox protein Nkx-5.1; homeobox protein H6
                     family member 3; homeo box (H6 family) 3; H6 family
                     homeobox 3"
                     /codon_start=1
                     /product="homeobox protein HMX3"
                     /protein_id="NP_571709.2"
                     /db_xref="GeneID:60310"
                     /db_xref="ZFIN:ZDB-GENE-001020-1"
                     /translation="

MPETTQDTCASAKDSPFFIKNLLNSDSKPSKPKPILAPTKAGLDGSFSLSQVGEINFPRFELPTQRFALPAYLERASAWWYPYTLSASAHLHRTEAAQKARDSSPTTGTDRDSPELVLKSDPDAKDDEDDNKSGDEIVLEESDTEDGKKEGGIDDWKKSDDGADKKPCRKKKTRTVFSRSQVFQLESTFDMKRYLSSSERAGLAASLHLTETQVKIWFQNRRNKWKRQLAAELEAANLSHAAAQRIVRVPILYHENSASESTNTAGNVPVSQPLLTFPHPVYYSHPIVTSVPLLRPV"

     misc_feature    337..396
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /note="propagated from UniProtKB/Swiss-Prot (Q504H8.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    553..783
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /note="propagated from UniProtKB/Swiss-Prot (Q504H8.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    778..948
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            554..2058
                     /gene="hmx3a"
                     /gene_synonym="hmx3; Nkx5-1; nkx5.1; zgc:109845"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atcattagcatctggcgccagacggtcgcggtgagcatcattttcaccaaggaactctcggaagatgatcagcaagattaatattgtttatctcgatccgcgttattgtctttcgttttaacgtcaatgctgaccgtaaacaaccgcgtttaagttcccattgctggaagagtttaccaaggacttttaaactgtttaaagattttcttttttaacgcgtttttaacgatttataaattgtagtataaacccgaatatcaagccaacatgcccgaaacaacacaggatacgtgtgcttcagcgaaagactctccatttttcattaaaaatcttctcaattctgacagtaagccgtcaaagcctaagcctattttggcacccactaaagcaggacttgatggcagcttctccctttctcaggttggggaaataaactttcctcgctttgagttacccacccagcgctttgcgttaccggcttaccttgagcgtgcctcggcgtggtggtacccgtacacactcagtgcatccgcgcatcttcacagaacagaagcagcacagaaagcgagggactcttcgccgaccacaggcaccgaccgagattcccccgagcttgtgctcaaatcagatccggacgccaaggacgatgaagacgacaacaaaagtggcgacgagattgtcctcgaggagagcgacaccgaagacggtaaaaaagaaggcggcatagacgactggaagaagagtgacgacggcgctgacaagaaaccttgccggaaaaagaaaactcgcacggtgttctcgcggagtcaggtgttccagctggagtccaccttcgacatgaaacgctacctcagcagctcggagcgcgcgggccttgctgcctcccttcacctcacagagactcaagtgaaaatctggtttcagaaccgcagaaacaaatggaaacgtcagctggccgcagagctggaggccgccaacttgagccacgcagcagcacaaaggattgtgagagtacccatcctgtatcacgagaactcggcctctgagagcaccaacacagcgggcaacgttcctgtaagccagccgctgctcactttccctcatccggtttactactcgcaccccatcgtcacctccgtgcccctcctcagaccggtttgagaggacgacagatgtctttttctatgtaactatgtaactaaattttacagagactcgaaagagggaaagagagaaaatgggaaaatgaaaccaagagacaaagatatttttgtttagaaaatacaaaaaaaaaattaaagaaaagaaaaaaatgtacaaagacgcactatcatgcatttgagcccgacattttttgttttgttttacaattcctaaaaatacccataaaactacacataaataaggctgtttagaggcctgtatttcaaatgttgatgttggttggtggtaaatttctgactttgtttattcactttgtcattatacaactactactaataataatattaatattattattattattaataataataataataattattattattattattattgtacctgctacggtttatctgtttatataacaaatcaacttgttcaacttgttgacacgaaaagtctttaatacacacgtttaagtttctttacagcaccgaaaacgcgtacccacagacagccctgaacacggatgtgcaatactactgtgtatgatctgtatatttagacaacattactattcttattttagacacgttttcttaccaaacatttcttaggttaagaagttaaccgttaaaacgatttaactgcttggtcccgcgttcaatagacaatcatatatctgacagacattacagttaaactgaagacaaaaacacgaagaataaatacttttacttttatctatattatttacagatgtatatgtacatgtacagatataacgaaccaaaaggaaaggtgtcatttgtacagtaacagatacgttcttttttacattgtattgctaaattctgttgtgaaataaacgaagactactgaagtcaa

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