LOCUS       NM_001189               2259 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens NK3 homeobox 2 (NKX3-2), mRNA.
ACCESSION   NM_001189
VERSION     NM_001189.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2259)
  AUTHORS   Ripmeester,E.G.J., Welting,T.J.M., van den Akker,G.G.H.,
            Surtel,D.A.M., Steijns,J.S.J., Cremers,A., van Rhijn,L.W. and
            Caron,M.M.J.
  TITLE     BMP7 increases protein synthesis in SW1353 cells and determines
            rRNA levels in a NKX3-2-dependent manner
  JOURNAL   PLoS One 17 (2), e0263430 (2022)
   PUBMED   35139106
  REMARK    GeneRIF: BMP7 increases protein synthesis in SW1353 cells and
            determines rRNA levels in a NKX3-2-dependent manner.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2259)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 2259)
  AUTHORS   Simsek-Kiper,P.O., Kosukcu,C., Akgun-Dogan,O., Gocmen,R.,
            Utine,G.E., Soyer,T., Korkmaz-Toygar,A., Nishimura,G.,
            Alikasifoglu,M. and Boduroglu,K.
  TITLE     A novel NKX3-2 mutation associated with perinatal lethal phenotype
            of spondylo-megaepiphyseal-metaphyseal dysplasia in a neonate
  JOURNAL   Eur J Med Genet 62 (1), 21-26 (2019)
   PUBMED   29704686
  REMARK    GeneRIF: A novel NKX3-2 mutation causes perinatal lethal
            spondylo-megaepiphyseal-metaphyseal dysplasia.
REFERENCE   4  (bases 1 to 2259)
  AUTHORS   Nagel,S., Meyer,C., Kaufmann,M., Zaborski,M., MacLeod,R.A.F. and
            Drexler,H.G.
  TITLE     Aberrant activity of NKL homeobox gene NKX3-2 in a T-ALL subset
  JOURNAL   PLoS One 13 (5), e0197194 (2018)
   PUBMED   29746601
  REMARK    GeneRIF: NKL homeobox gene NKX2-5 was activated by NKX3-2 in
            CCRF-CEM and by FOXG1 in PEER, representing mutually inhibitory
            activators of this translocated oncogene.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2259)
  AUTHORS   Yin,Y., Morgunova,E., Jolma,A., Kaasinen,E., Sahu,B.,
            Khund-Sayeed,S., Das,P.K., Kivioja,T., Dave,K., Zhong,F.,
            Nitta,K.R., Taipale,M., Popov,A., Ginno,P.A., Domcke,S., Yan,J.,
            Schubeler,D., Vinson,C. and Taipale,J.
  TITLE     Impact of cytosine methylation on DNA binding specificities of
            human transcription factors
  JOURNAL   Science 356 (6337) (2017)
   PUBMED   28473536
REFERENCE   6  (bases 1 to 2259)
  AUTHORS   Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M.
  TITLE     A census of human transcription factors: function, expression and
            evolution
  JOURNAL   Nat Rev Genet 10 (4), 252-263 (2009)
   PUBMED   19274049
  REMARK    Review article
REFERENCE   7  (bases 1 to 2259)
  AUTHORS   Rodrigo,I., Bovolenta,P., Mankoo,B.S. and Imai,K.
  TITLE     Meox homeodomain proteins are required for Bapx1 expression in the
            sclerotome and activate its transcription by direct binding to its
            promoter
  JOURNAL   Mol Cell Biol 24 (7), 2757-2766 (2004)
   PUBMED   15024065
  REMARK    GeneRIF: Data show that Meox1 activates the Bapx1 promoter in a
            dose-dependent manner and that this activity is enhanced in the
            presence of Pax1 and/or Pax9.
REFERENCE   8  (bases 1 to 2259)
  AUTHORS   Tribioli,C. and Lufkin,T.
  TITLE     Molecular cloning, chromosomal mapping and developmental expression
            of BAPX1, a novel human homeobox-containing gene homologous to
            Drosophila bagpipe
  JOURNAL   Gene 203 (2), 225-233 (1997)
   PUBMED   9426254
REFERENCE   9  (bases 1 to 2259)
  AUTHORS   Yoshiura,K.I. and Murray,J.C.
  TITLE     Sequence and chromosomal assignment of human BAPX1, a
            bagpipe-related gene, to 4p16.1: a candidate gene for skeletal
            dysplasia
  JOURNAL   Genomics 45 (2), 425-428 (1997)
   PUBMED   9344671
REFERENCE   10 (bases 1 to 2259)
  AUTHORS   Tribioli,C., Frasch,M. and Lufkin,T.
  TITLE     Bapx1: an evolutionary conserved homologue of the Drosophila
            bagpipe homeobox gene is expressed in splanchnic mesoderm and the
            embryonic skeleton
  JOURNAL   Mech Dev 65 (1-2), 145-162 (1997)
   PUBMED   9256352
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC006445.11 and BC111966.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_001189.3.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by 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 :: AF009801.1, BC111966.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA1970526
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000382438.6/ ENSP00000371875.5
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-18                AC006445.11        108367-108384
            19-1129             BC111966.1         1-1111
            1130-2259           AC006445.11        110916-112045
FEATURES             Location/Qualifiers
     source          1..2259
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="4"
                     /map="4p15.33"
     gene            1..2259
                     /gene="NKX3-2"
                     /gene_synonym="BAPX1; NKX3.2; NKX3B; SMMD"
                     /note="NK3 homeobox 2"
                     /db_xref="GeneID:579"
                     /db_xref="HGNC:HGNC:951"
                     /db_xref="MIM:602183"
     exon            1..560
                     /gene="NKX3-2"
                     /gene_synonym="BAPX1; NKX3.2; NKX3B; SMMD"
                     /inference="alignment:Splign:2.1.0"
     CDS             95..1096
                     /gene="NKX3-2"
                     /gene_synonym="BAPX1; NKX3.2; NKX3B; SMMD"
                     /note="homeobox protein NK-3 homolog B; bagpipe homeobox
                     protein homolog 1"
                     /codon_start=1
                     /product="homeobox protein Nkx-3.2"
                     /protein_id="NP_001180.1"
                     /db_xref="CCDS:CCDS3410.1"
                     /db_xref="GeneID:579"
                     /db_xref="HGNC:HGNC:951"
                     /db_xref="MIM:602183"
                     /translation="MAVRGANTLTSFSIQAILNKKEERGGLAAPEGRPAPGGTAASVA
                     AAPAVCCWRLFGERDAGALGGAEDSLLASPAGTRTAAGRTAESPEGWDSDSALSEENE
                     SRRRCADARGASGAGLAGGSLSLGQPVCELAASKDLEEEAAGRSDSEMSASVSGDRSP
                     RTEDDGVGPRGAHVSALCSGAGGGGGSGPAGVAEEEEEPAAPKPRKKRSRAAFSHAQV
                     FELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRRYKTKRRQMAADLLASAPA
                     AKKVAVKVLVRDDQRQYLPGEVLRPPSLLPLQPSYYYPYYCLPGWALSTCAAAAGTQ"
     exon            561..2259
                     /gene="NKX3-2"
                     /gene_synonym="BAPX1; NKX3.2; NKX3B; SMMD"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2237..2242
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NKX3-2"
                     /gene_synonym="BAPX1; NKX3.2; NKX3B; SMMD"
                     /note="hexamer: TATAAA"
     polyA_site      2259
                     /gene="NKX3-2"
                     /gene_synonym="BAPX1; NKX3.2; NKX3B; SMMD"
                     /note="major polyA site"
ORIGIN      
        1 actcgcgctg cggccgccgg cgctctctgt cccgctcgga gctgctcggc gccccagctg
       61 cccgccccgc cggccgctcc tgcccgcggc gcagatggct gtgcgcggcg ccaacacctt
      121 gacgtccttc tccatccagg cgatcctcaa caagaaagag gagcgcggcg ggctggccgc
      181 gccagagggg cgcccggcgc ccgggggcac agcggcatcg gtggccgcgg ctcccgctgt
      241 ctgctgttgg cggctctttg gggagaggga cgcgggcgcg ttggggggcg ccgaggactc
      301 tctgctggcg tctcctgccg gtaccagaac agctgcgggg cggactgcgg agagcccgga
      361 aggctgggac tcggactccg cgctcagcga ggagaacgag agcaggcggc gctgcgcgga
      421 cgcgcggggg gccagcgggg ccggccttgc ggggggatcc ttgagcctcg gccagccggt
      481 ctgtgagctg gccgcttcca aagacctaga ggaggaagcc gcgggccgga gcgacagcga
      541 gatgtccgcc agcgtctcag gcgaccgcag cccaaggacc gaggacgacg gtgttggccc
      601 cagaggtgca cacgtgtccg cgctgtgcag cggggccggc ggcgggggcg gcagcgggcc
      661 ggcaggcgtc gcggaggagg aggaggagcc ggcggcgccc aagccacgca agaagcgctc
      721 gcgggccgct ttctcccacg cgcaggtctt cgagctggag cgccgcttta accaccagcg
      781 ctacctgtcc gggcccgagc gcgcagacct ggccgcgtcg ctgaagctca ccgagacgca
      841 ggtgaaaatc tggttccaga accgtcgcta caagacaaag cgccggcaga tggcagccga
      901 cctgctggcc tcggcgcccg ccgccaagaa ggtggccgta aaggtgctgg tgcgcgacga
      961 ccagagacaa tacctgcccg gcgaagtgct gcggccaccc tcgcttctgc cactgcagcc
     1021 ctcctactat tacccgtact actgcctccc aggctgggcg ctctccacct gcgcagctgc
     1081 cgcaggcacc cagtgaaccc gcttgggctg aggcagcgag tgattcccgc gctccggctc
     1141 cggaccggcg ctgacagctg taggctgtag cctgcacggg gcgccccgcc aaggaggcac
     1201 ctggaggtga aacccagctc cagctcccgt tagccaggac ttgtcccctg gcagctgggc
     1261 tgagtctgcc ctgagggggc gcctttttct aatttgaaca gaggcaccct atggcctagg
     1321 ggccctgatc gcccacctgc ctggaagccc ctgggctcta tttattatca tgacaatgtt
     1381 ggaattaaat tttgattcga atatgtctgc ctgggggtgg ggttttccct gagcggcaac
     1441 tcctggagac cacatagcct gaatcctcag aatttcaggc ctgctgggag ctttctgcac
     1501 taggccacac tagttcatgg tatccatgct accaatctat gtgtatctac atatctttta
     1561 tttttggaaa ttgcatttgt aaccaagggg tgcgaaaccc tggcagtccc aggcagcacc
     1621 aggccagggg ttgatttgaa acgtgaagga ttgggttttc aggccctctg ctccacccct
     1681 cctgtgtgtc agagctaggg tgggggtgcc cgattcgggt gctgaatgta aggaggggag
     1741 cctccaagtg tggtgcaagc cgggggtctc cacatcttcc ttctctgaag tccaggtacc
     1801 tgcacaagca ggaagcgcct gggagtcccg gaaggaggag agcgcacacc caggcagccc
     1861 tctgcggaaa ctttccttgg tttcttttta tttgtgtaaa ggaggttaag acgtgtcgca
     1921 cttttcagtt gtttgtattc aaatgacgat tatttttcta ctcaatgtga atatccctgg
     1981 ccagcctttc cacggcgccc accgcagtgc cgctgcctgg ccctcagtgt ctaccttctg
     2041 ccctctgcga ctccagtgct ctggcccggg actcccctat ccgcccctca cttaccctta
     2101 aacaggtgat cccacctgtc ttgtcaacct cgccgctttt cgcctcctta atggcactgt
     2161 gcactcaact agagtattaa ctgtaaaaag atttgtgaag tttggaagct ctattcgctg
     2221 tattttttct ttaatttata aacttttagt ttaacatgc
//
