LOCUS       NM_001364841            2395 bp    mRNA    linear   PRI 29-OCT-2022
DEFINITION  Homo sapiens NK6 homeobox 3 (NKX6-3), transcript variant 1, mRNA.
ACCESSION   NM_001364841 XM_017013143
VERSION     NM_001364841.2
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 2395)
  AUTHORS   Valsesia A, Wang QP, Gheldof N, Carayol J, Ruffieux H, Clark T,
            Shenton V, Oyston LJ, Lefebvre G, Metairon S, Chabert C, Walter O,
            Mironova P, Lau P, Descombes P, Viguerie N, Langin D, Harper ME,
            Astrup A, Saris WH, Dent R, Neely GG and Hager J.
  TITLE     Genome-wide gene-based analyses of weight loss interventions
            identify a potential role for NKX6.3 in metabolism
  JOURNAL   Nat Commun 10 (1), 540 (2019)
   PUBMED   30710084
  REMARK    GeneRIF: These results identify genetic variants associated with
            the efficacy of weight loss in obese subjects and identify a role
            for NKX6.3 in lipid metabolism, and thereby possibly weight
            control.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2395)
  AUTHORS   Yoon JH, Lee YS, Kim O, Ashktorab H, Smoot DT, Nam SW and Park WS.
  TITLE     NKX6.3 protects against gastric mucosal atrophy by downregulating
            beta-amyloid production
  JOURNAL   World J Gastroenterol 25 (3), 330-345 (2019)
   PUBMED   30686901
  REMARK    GeneRIF: NKX6.3 inhibits gastric mucosal atrophy by regulating
            amyloid beta accumulation and inflammatory reaction in gastric
            epithelial cells.
REFERENCE   3  (bases 1 to 2395)
  AUTHORS   Yoon JH, Kim O, Eun JW, Choi SS, Ashktorab H, Smoot DT, Nam SW and
            Park WS.
  TITLE     Multiple genetic mutations caused by NKX6.3 depletion contribute to
            gastric tumorigenesis
  JOURNAL   Sci Rep 8 (1), 17609 (2018)
   PUBMED   30514953
  REMARK    GeneRIF: These results indicate that NKX6.3 depletion in gastric
            epithelial cells activates AICDA/APOBEC family, leading to
            accumulation of genetic mutations and eventually driving the
            development of gastric cancers.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2395)
  AUTHORS   Yoon JH, Kim O, Nam SW, Lee JY and Park WS.
  TITLE     NKX6.3 Regulates Reactive Oxygen Species Production by Suppressing
            NF-kB and DNMT1 Activities in Gastric Epithelial Cells
  JOURNAL   Sci Rep 7 (1), 2807 (2017)
   PUBMED   28584243
  REMARK    GeneRIF: these results suggest that NKX6.3 inhibits ROS production
            by inducing the expression of Hace1 via down-regulating NF-kB and
            DNMT1 activity in gastric epithelial cells.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2395)
  AUTHORS   Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S,
            Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A,
            Ginno PA, 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 2395)
  AUTHORS   Yoon JH, Eun JW, Choi WS, Kim O, Nam SW, Lee JY and Park WS.
  TITLE     NKX6.3 Is a Transcription Factor for Wnt/beta-catenin and
            Rho-GTPase Signaling-Related Genes to Suppress Gastric Cancer
            Progression
  JOURNAL   EBioMedicine 9, 97-109 (2016)
   PUBMED   27333045
  REMARK    GeneRIF: The expression level of NKX6.3 is involved in regulation
            of gastric cancer progression and expression of Wnt/beta-catenin
            and Rho-GTPase pathway-related genes in clinical samples.
REFERENCE   7  (bases 1 to 2395)
  AUTHORS   Yoon JH, Choi SS, Kim O, Choi WS, Park YK, Nam SW, Lee JY and Park
            WS.
  TITLE     Inactivation of NKX6.3 in the stomach leads to abnormal expression
            of CDX2 and SOX2 required for gastric-to-intestinal
            transdifferentiation
  JOURNAL   Mod Pathol 29 (2), 194-208 (2016)
   PUBMED   26743476
  REMARK    GeneRIF: Suggest that NKX6.3 might function as a master regulator
            of gastric differentiation by affecting SOX2 and CDX2 expression
            and the NKX6.3 inactivation may result in intestinal metaplasia in
            gastric epithelial cells.
REFERENCE   8  (bases 1 to 2395)
  AUTHORS   Yoon JH, Choi WS, Kim O, Choi SS, Lee EK, Nam SW, Lee JY and Park
            WS.
  TITLE     NKX6.3 controls gastric differentiation and tumorigenesis
  JOURNAL   Oncotarget 6 (29), 28425-28439 (2015)
   PUBMED   26314965
  REMARK    GeneRIF: Data suggest that NK6 homeobox 3 (NKX6.3) may control the
            fate of gastric mucosal cells and function as a gastric tumor
            suppressor.
REFERENCE   9  (bases 1 to 2395)
  AUTHORS   Vaquerizas JM, Kummerfeld SK, Teichmann SA and Luscombe NM.
  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   10 (bases 1 to 2395)
  AUTHORS   Alanentalo T, Chatonnet F, Karlen M, Sulniute R, Ericson J,
            Andersson E and Ahlgren U.
  TITLE     Cloning and analysis of Nkx6.3 during CNS and gastrointestinal
            development
  JOURNAL   Gene Expr Patterns 6 (2), 162-170 (2006)
   PUBMED   16326147
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC113133.5 and AC009630.14.
            
            On May 17, 2019 this sequence version replaced NM_001364841.1.
            
            Summary: The NKX family of homeodomain proteins controls numerous
            developmental processes. Members of the NKX6 subfamily, including
            NKX6-3, are involved in development of the central nervous system
            (CNS), gastrointestinal tract, and pancreas (Alanentalo et al.,
            2006 [PubMed 16326147]).[supplied by OMIM, Mar 2008].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments from cross species transcripts such
            as DQ093570.1 and RNA-Seq data.
            
            ##Evidence-Data-START##
            RNAseq introns :: single sample supports all introns SAMEA2142586,
                              SAMEA2144835 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            inferred exon combination :: based on alignments, homology
            MANE Ensembl match        :: ENST00000518699.4/ ENSP00000428361.2
            RefSeq Select criteria    :: based on manual assertion,
                                         conservation, expression, longest
                                         protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-707               AC113133.5         3146-3852           c
            708-877             AC009630.14        390-559
            878-2395            AC009630.14        1931-3448
FEATURES             Location/Qualifiers
     source          1..2395
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="8"
                     /map="8p11.21"
     gene            1..2395
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /note="NK6 homeobox 3"
                     /db_xref="GeneID:157848"
                     /db_xref="HGNC:HGNC:26328"
                     /db_xref="MIM:610772"
     exon            1..707
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /inference="alignment:Splign:2.1.0"
     CDS             326..1123
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     homeobox protein Nkx-6.3; NK6 transcription factor
                     related, locus 3"
                     /codon_start=1
                     /product="homeobox protein Nkx-6.3 isoform 1"
                     /protein_id="NP_001351770.1"
                     /db_xref="CCDS:CCDS94289.1"
                     /db_xref="GeneID:157848"
                     /db_xref="HGNC:HGNC:26328"
                     /db_xref="MIM:610772"
                     /translation="MESNLQGTFLLNNTPLAQFPEMKAPVCQYSVQNSFYKLSPPGLG
                     PQLAAGTPHGITDILSRPVAAPNNSLLSGYPHVAGFGGLSSQGVYYSPQVGNFSKAGN
                     EYPTRTRNCWADTGQDWRGGRQCSNTPDPLSDSIHKKKHTRPTFTGHQIFALEKTFEQ
                     TKYLAGPERARLAYSLGMTESQVKVWFQNRRTKWRKKSALEPSSSTPRAPGGAGAGAG
                     GDRAPSENEDDEYNKPLDPDSDDEKIRLLLRKHRAAFSVLSLGAHSV"
     exon            708..877
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /inference="alignment:Splign:2.1.0"
     exon            878..2395
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2374..2379
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /note="hexamer: AATAAA"
     polyA_site      2395
                     /gene="NKX6-3"
                     /gene_synonym="NKX6.3"
                     /note="major polyA site"
ORIGIN      
        1 taaaacttct catggagggt cccccgactc agaggcagaa agggggtctg agctgaggct
       61 tagggggcca ccctgtccgg ccagggcaag gagagaggcc aggagccctg gggaggcctc
      121 ccacctgccc cgagcacctg acttccgagc agctgatcgg gtgccggttc ctgggccagg
      181 gcctggccca tgccttaggt gggaggcagt caggagctcg gagacggtcc taagcctcca
      241 ggcctgccat gagatttggg gctagagagt gggctcttgg gttttagggg cctggagaag
      301 ccttccctgt cctgactggg agatcatgga gtccaacctg caggggacgt tcctgctgaa
      361 caacacgccg ctggctcagt ttccggagat gaaggccccg gtgtgccagt actctgtgca
      421 gaactccttc tacaagctca gccccccagg gctgggcccc cagctggccg ccggaacccc
      481 ccacgggatc acggacatcc tgagcaggcc cgtggctgcg ccgaacaaca gcctcctctc
      541 cggctacccc cacgtggcag gctttggggg gctcagctcg cagggggtct actacagccc
      601 ccaggtaggg aatttttcca aggctgggaa cgagtacccg acccggaccc ggaactgctg
      661 ggcggacacg ggccaagact ggcgaggcgg gcggcagtgc agcaacaccc cagaccccct
      721 gagtgacagc atacacaaga agaagcacac ccggcccacc ttcacggggc accagatctt
      781 tgccctggag aaaacctttg agcagaccaa gtacttggct ggccccgaga gggcacggct
      841 ggcatactca ctgggcatga ccgagtcgca ggtcaaggtg tggttccaga accgcaggac
      901 caagtggcgg aagaagagcg ccctggagcc ctcgtcctcc acgccccggg ccccgggcgg
      961 cgcgggtgca ggcgcaggcg gggaccgcgc accctcggag aacgaggacg acgagtacaa
     1021 caagccgctg gaccccgact cggacgacga gaagatccgc ctgctgctgc gcaagcaccg
     1081 cgccgccttc tcggtgctca gcctgggagc gcacagcgtc tgacgcccgc cgtccaggcc
     1141 cgggatcctg gctgcagcct gcggggggac gccgaggagc ctaccttccc ctccccttcc
     1201 ccacgctcct gggggcgcag ggactgagtc tttctttgga tgaggggcgc gtggaggagg
     1261 agcagcaggt gcaggggagg aggaggggag gcgggggagg aggaggaaaa ggagggaaag
     1321 gggacaggca tcctagctaa gggaggagga ggccaggagg gaggcacagc actcctgaga
     1381 cctggaagcc gctgcccctt gcacctcctc gggcctcgcc tgccagttct gcagattcac
     1441 aagtggacag aggactaaaa tgaccaggct ctgcagccaa gaaactggct gtggggtccc
     1501 agacatgcca ctgtgatcca gctgttgggg cggggggagt gggcaggact tcccagggag
     1561 ggaggcagct ggctggggag tcagaagtcc agagtcttgg gccccaagcc agctgctggc
     1621 tgcagaagaa aagacaggtg agtggccagg tgcactcctc agacctgtgc acaggaaggg
     1681 tcccactgga ggggccagag ctgagcacct aacccaggct gcaggaaatc tgcctccagg
     1741 aggggaagtg ggacatccca gtggagaaaa aatgcccctg acactgcagg atgacggccc
     1801 ctgagctgcg gaaatccccc tggcctcctt tctccgattt accctcaggg tcaatacctc
     1861 tgagaccgct gtgccctcct catcctgaca gccggggaaa aggggagggt gcagggagag
     1921 gggaggcggg gacggtgtgc ccaagggcca cccacctggg catcatttgg tgctgatata
     1981 aggacaggcc cacccagaga gaaaaagcat cccacctggg gaggaaagga agggctggga
     2041 aagaccccag aacggcaccc ctccaacaag gcaggaaggg agaaggacag cccctccggc
     2101 tgggtggagg atgccaggaa ggggctgaac cacggcctgc tgggaatcac ggcccttcct
     2161 ttcctcagat cgccttgcgg cctggcactg gagctggtgc tgacagggac gctggccaac
     2221 agggtggtat ttttcacccg ggtgatctga gctgctggca ggtagggggt gggctggggg
     2281 aggcgggtga gggctggtct tagataggaa tgcagcccag aagggaccaa gcacttgccc
     2341 atcctcactg gctttcaaaa aataaacagt aaaaataaaa gtcccatgaa cctta
//
