LOCUS       NM_001386325             777 bp    mRNA    linear   VRT 11-SEP-2023
DEFINITION  Danio rerio NK3 homeobox 1 (nkx3-1), mRNA.
ACCESSION   NM_001386325 XM_677868
VERSION     NM_001386325.1
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 777)
  AUTHORS   Watson CJ, Tang WJ, Rojas MF, Fiedler IAK, Morfin Montes de Oca E,
            Cronrath AR, Callies LK, Swearer AA, Ahmed AR, Sethuraman V, Addish
            S, Farr GH 3rd, Gomez AE, Rai J, Monstad-Rios AT, Gardiner EM,
            Karasik D, Maves L, Busse B, Hsu YH and Kwon RY.
  TITLE     wnt16 regulates spine and muscle morphogenesis through parallel
            signals from notochord and dermomyotome
  JOURNAL   PLoS Genet 18 (11), e1010496 (2022)
   PUBMED   36346812
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 777)
  AUTHORS   Wada Y, Tsukatani H, Kuroda C, Miyazaki Y, Otoshi M and Kobayashi
            I.
  TITLE     Jagged 2b induces intercellular signaling within somites to
            establish hematopoietic stem cell fate in zebrafish
  JOURNAL   Development 149 (7) (2022)
   PUBMED   35388409
REFERENCE   3  (bases 1 to 777)
  AUTHORS   Ikeda T, Inamori K, Kawanishi T and Takeda H.
  TITLE     Reemployment of Kupffer's vesicle cells into axial and paraxial
            mesoderm via transdifferentiation
  JOURNAL   Dev Growth Differ 64 (3), 163-177 (2022)
   PUBMED   35129208
REFERENCE   4  (bases 1 to 777)
  AUTHORS   Gu Q, Yang X, Lv J, Zhang J, Xia B, Kim JD, Wang R, Xiong F, Meng
            S, Clements TP, Tandon B, Wagner DS, Diaz MF, Wenzel PL, Miller YI,
            Traver D, Cooke JP, Li W, Zon LI, Chen K, Bai Y and Fang L.
  TITLE     AIBP-mediated cholesterol efflux instructs hematopoietic stem and
            progenitor cell fate
  JOURNAL   Science 363 (6431), 1085-1088 (2019)
   PUBMED   30705153
REFERENCE   5  (bases 1 to 777)
  AUTHORS   Ma RC, Jacobs CT, Sharma P, Kocha KM and Huang P.
  TITLE     Stereotypic generation of axial tenocytes from bipartite sclerotome
            domains in zebrafish
  JOURNAL   PLoS Genet 14 (11), e1007775 (2018)
   PUBMED   30388110
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 777)
  AUTHORS   Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M,
            Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD,
            Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov
            GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W and
            Hertzano R.
  TITLE     RFX transcription factors are essential for hearing in mice
  JOURNAL   Nat Commun 6, 8549 (2015)
   PUBMED   26469318
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 777)
  AUTHORS   Kobayashi I, Kobayashi-Sun J, Kim AD, Pouget C, Fujita N, Suda T
            and Traver D.
  TITLE     Jam1a-Jam2a interactions regulate haematopoietic stem cell fate
            through Notch signalling
  JOURNAL   Nature 512 (7514), 319-323 (2014)
   PUBMED   25119047
REFERENCE   8  (bases 1 to 777)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            EH437171.1 and CT676517.2.
            
            On Aug 19, 2020 this sequence version replaced XM_677868.5.
            
            ##Evidence-Data-START##
            Transcript exon combination :: EH437171.1, CT676517.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA4476751 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-630               EH437171.1         12-641
            631-772             EH437171.1         643-784
            773-777             CT676517.2         33-37               c
FEATURES             Location/Qualifiers
     source          1..777
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="8"
                     /map="8"
     gene            1..777
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /note="NK3 homeobox 1"
                     /db_xref="GeneID:555375"
                     /db_xref="ZFIN:ZDB-GENE-081104-238"
     exon            1..217
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /inference="alignment:Splign:2.1.0"
     CDS             88..645
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /codon_start=1
                     /product="homeobox protein Nkx-3.1"
                     /protein_id="NP_001373254.1"
                     /db_xref="GeneID:555375"
                     /db_xref="ZFIN:ZDB-GENE-081104-238"
                     /translation="

MATSNKQLTSFFIEDILSLKEDKKDEDSCNAESDRDDSTDRQTDSADTCRTSEGKTVSSTEMTGGGGKKKRSRAAFTHLQVLELEKKFSRQRYLSAPERTHLASALHLTETQVKIWFQNRRYKTKRRQLTTEHSKDYFQKSNAAAMAATEEDFFRASLLATVYKSSPYRPYVYDLHGLSMWRPAL"

     misc_feature    130..>495
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(295..309,313..315,364..366,382..384,421..423,
                     427..432,439..444,448..456,460..465)
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    301..462
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(301..303,310..312,430..432,439..444,451..453)
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            218..327
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /inference="alignment:Splign:2.1.0"
     exon            328..777
                     /gene="nkx3-1"
                     /gene_synonym="si:ch211-67o1.2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agtcgagctgtgcagagtgaaagtgacaattaccaacccggagaaagaggcttcatctttacctttatcgggagtttagcagcacagatggcgacttctaacaagcagctaacgtcgtttttcatagaggacattttatccttaaaggaggataaaaaagatgaagactcctgtaatgctgagagtgacagagacgacagcactgacagacaaacagattcagcggatacttgtcggacttcagagggtaaaactgtgtcgtcgacagagatgacggggggaggcgggaaaaagaagcggtcgcgcgccgcgttcacgcacctgcaggttttggagctggagaagaagttcagccgtcagcggtacctgagcgcacctgagcgcacacacctggcgagcgcgctgcacctaacagagactcaggtcaaaatctggttccagaacaggagatataaaaccaaacggagacagttaaccacagagcacagcaaggactacttccagaaatcaaatgcggctgctatggctgctacagaagaggactttttcagagcatcgcttttagcgacagtctataaatcctccccttaccggccgtatgtgtatgatttacacggactgagcatgtggagaccagcactgtgatgacaaggacattggactatggggactctctcagattattgttaataatattctttattttggtgatttttctaataaatcttgtgtacagttttgtataccatgtaataaagtatttttttttcaatcaaa

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