LOCUS       NM_001079668            2197 bp    mRNA    linear   PRI 16-JUN-2013
DEFINITION  Homo sapiens NK2 homeobox 1 (NKX2-1), transcript variant 1, mRNA.
ACCESSION   NM_001079668
VERSION     NM_001079668.2  GI:261244895
KEYWORDS    RefSeq.
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 2197)
  AUTHORS   Watanabe,H., Francis,J.M., Woo,M.S., Etemad,B., Lin,W., Fries,D.F.,
            Peng,S., Snyder,E.L., Tata,P.R., Izzo,F., Schinzel,A.C., Cho,J.,
            Hammerman,P.S., Verhaak,R.G., Hahn,W.C., Rajagopal,J., Jacks,T. and
            Meyerson,M.
  TITLE     Integrated cistromic and expression analysis of amplified NKX2-1 in
            lung adenocarcinoma identifies LMO3 as a functional transcriptional
            target
  JOURNAL   Genes Dev. 27 (2), 197-210 (2013)
   PUBMED   23322301
  REMARK    GeneRIF: suggest that LMO3 is a transcriptional signal transducer
            in NKX2-1-amplified lung adenocarcinomas
REFERENCE   2  (bases 1 to 2197)
  AUTHORS   Konishi,T., Kono,S., Fujimoto,M., Terada,T., Matsushita,K.,
            Ouchi,Y. and Miyajima,H.
  TITLE     Benign hereditary chorea: dopaminergic brain imaging in patients
            with a novel intronic NKX2.1 gene mutation
  JOURNAL   J. Neurol. 260 (1), 207-213 (2013)
   PUBMED   22825795
  REMARK    GeneRIF: This study demonistrated that Benign hereditary chorea:
            dopaminergic brain imaging in patients with a novel intronic NKX2.1
            gene mutation.
REFERENCE   3  (bases 1 to 2197)
  AUTHORS   Vincenten,J., Smit,E.F., Vos,W., Grunberg,K., Postmus,P.E.,
            Heideman,D.A., Snijders,P.J., Meijer,G., Kuik,J., Witte,B.I. and
            Thunnissen,E.
  TITLE     Negative NKX2-1 (TTF-1) as temporary surrogate marker for treatment
            selection during EGFR-mutation analysis in patients with
            non-small-cell lung cancer
  JOURNAL   J Thorac Oncol 7 (10), 1522-1527 (2012)
   PUBMED   22982653
  REMARK    GeneRIF: Positive NKX2-1 is associated with EGFR mutation in
            non-small-cell lung cancer.
REFERENCE   4  (bases 1 to 2197)
  AUTHORS   Gras,D., Jonard,L., Roze,E., Chantot-Bastaraud,S., Koht,J.,
            Motte,J., Rodriguez,D., Louha,M., Caubel,I., Kemlin,I.,
            Lion-Francois,L., Goizet,C., Guillot,L., Moutard,M.L., Epaud,R.,
            Heron,B., Charles,P., Tallot,M., Camuzat,A., Durr,A., Polak,M.,
            Devos,D., Sanlaville,D., Vuillaume,I., Billette de Villemeur,T.,
            Vidailhet,M. and Doummar,D.
  TITLE     Benign hereditary chorea: phenotype, prognosis, therapeutic outcome
            and long term follow-up in a large series with new mutations in the
            TITF1/NKX2-1 gene
  JOURNAL   J. Neurol. Neurosurg. Psychiatr. 83 (10), 956-962 (2012)
   PUBMED   22832740
  REMARK    GeneRIF: The TITF1/NKX2-1 gene is essential for organogenesis of
            the basal ganglia, thyroid and lungs. In this study, all patients
            had private mutations, including 7 new ones, 3 previously reported
            mutations & 3 sporadic deletions in the NKX2-1 gene.
REFERENCE   5  (bases 1 to 2197)
  AUTHORS   Runkle,E.A., Rice,S.J., Qi,J., Masser,D., Antonetti,D.A.,
            Winslow,M.M. and Mu,D.
  TITLE     Occludin is a direct target of thyroid transcription factor-1
            (TTF-1/NKX2-1)
  JOURNAL   J. Biol. Chem. 287 (34), 28790-28801 (2012)
   PUBMED   22761434
  REMARK    GeneRIF: TTF-1 transcriptionally regulates occludin, which
            represents another avenue of TTF-1-mediated metastasis suppression
REFERENCE   6  (bases 1 to 2197)
  AUTHORS   Yan,C., Sever,Z. and Whitsett,J.A.
  TITLE     Upstream enhancer activity in the human surfactant protein B gene
            is mediated by thyroid transcription factor 1
  JOURNAL   J. Biol. Chem. 270 (42), 24852-24857 (1995)
   PUBMED   7559607
REFERENCE   7  (bases 1 to 2197)
  AUTHORS   Acebron,A., Aza-Blanc,P., Rossi,D.L., Lamas,L. and Santisteban,P.
  TITLE     Congenital human thyroglobulin defect due to low expression of the
            thyroid-specific transcription factor TTF-1
  JOURNAL   J. Clin. Invest. 96 (2), 781-785 (1995)
   PUBMED   7635972
REFERENCE   8  (bases 1 to 2197)
  AUTHORS   Oguchi,H., Pan,Y.T. and Kimura,S.
  TITLE     The complete nucleotide sequence of the mouse thyroid-specific
            enhancer-binding protein (T/EBP) gene: extensive identity of the
            deduced amino acid sequence with the human protein
  JOURNAL   Biochim. Biophys. Acta 1261 (2), 304-306 (1995)
   PUBMED   7711079
REFERENCE   9  (bases 1 to 2197)
  AUTHORS   Abramowicz,M.J., Vassart,G. and Christophe,D.
  TITLE     Functional study of the human thyroid peroxidase gene promoter
  JOURNAL   Eur. J. Biochem. 203 (3), 467-473 (1992)
   PUBMED   1735431
REFERENCE   10 (bases 1 to 2197)
  AUTHORS   Guazzi,S., Price,M., De Felice,M., Damante,G., Mattei,M.G. and Di
            Lauro,R.
  TITLE     Thyroid nuclear factor 1 (TTF-1) contains a homeodomain and
            displays a novel DNA binding specificity
  JOURNAL   EMBO J. 9 (11), 3631-3639 (1990)
   PUBMED   1976511
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL132857.4, U43203.1 and
            BM970287.1.
            This sequence is a reference standard in the RefSeqGene project.
            On Oct 10, 2009 this sequence version replaced gi:118766338.
            
            Summary: This gene encodes a protein initially identified as a
            thyroid-specific transcription factor. The encoded protein binds to
            the thyroglobulin promoter and regulates the expression of
            thyroid-specific genes but has also been shown to regulate the
            expression of genes involved in morphogenesis. Mutations and
            deletions in this gene are associated with benign hereditary
            chorea, choreoathetosis, congenital hypothyroidism, and neonatal
            respiratory distress, and may be associated with thyroid cancer.
            Multiple transcript variants encoding different isoforms have been
            found for this gene. This gene shares the symbol/alias 'TFF1' with
            another gene, transcription termination factor 1, which plays a
            role in ribosomal gene transcription. [provided by RefSeq, Apr
            2011].
            
            Transcript Variant: This variant (1) encodes the longer protein
            (isoform 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 :: U43203.1, BT009773.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           ERS025091, ERS025093 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-14                AL132857.4         67149-67162
            15-669              U43203.1           1-655
            670-670             AL132857.4         69464-69464
            671-1511            U43203.1           657-1497
            1512-1595           AL132857.4         70306-70389
            1596-2197           BM970287.1         1-602               c
FEATURES             Location/Qualifiers
     source          1..2197
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q13"
     gene            1..2197
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /note="NK2 homeobox 1"
                     /db_xref="GeneID:7080"
                     /db_xref="HGNC:11825"
                     /db_xref="MIM:600635"
     exon            1..173
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /inference="alignment:Splign:1.39.8"
     variation       12
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:2076751"
     misc_feature    13..15
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /note="upstream in-frame stop codon"
     CDS             97..1302
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     thyroid transcription factor 1; homeobox protein Nkx-2.1;
                     NK-2 homolog A; thyroid nuclear factor 1; homeobox protein
                     NK-2 homolog A"
                     /codon_start=1
                     /product="homeobox protein Nkx-2.1 isoform 1"
                     /protein_id="NP_001073136.1"
                     /db_xref="GI:118766339"
                     /db_xref="CCDS:CCDS41945.1"
                     /db_xref="GeneID:7080"
                     /db_xref="HGNC:11825"
                     /db_xref="MIM:600635"
                     /translation="

MWSGGSGKARGWEAAAGGRSSPGRLSRRRIMSMSPKHTTPFSVSDILSPLEESYKKVGMEGGGLGAPLAAYRQGQAAPPTAAMQQHAVGHHGAVTAAYHMTAAGVPQLSHSAVGGYCNGNLGNMSELPPYQDTMRNSASGPGWYGANPDPRFPAISRFMGPASGMNMSGMGGLGSLGDVSKNMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAAQQQLQQDSGGGGGGGGTGCPQQQQAQQQSPRRVAVPVLVKDGKPCQAGAPAPGAASLQGHAQQQAQHQAQAAQAAAAAISVGSGGAGLGAHPGHQPGSAGQSPDLAHHAASPAALQGQVSSLSHLNSSGSDYGTMSCSTLLYGRTW

"
     misc_feature    670..843
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /note="Homeodomain;  DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:28970"
     misc_feature    order(670..684,688..690,739..741,757..759,796..798,
                     802..807,814..819,823..831,835..840)
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:28970"
     misc_feature    order(676..678,685..687,805..807,814..819,826..828)
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:28970"
     exon            174..559
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /inference="alignment:Splign:1.39.8"
     STS             486..648
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /standard_name="Titf1"
                     /db_xref="UniSTS:464797"
     exon            560..2183
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /inference="alignment:Splign:1.39.8"
     STS             1263..1420
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /standard_name="RH79171"
                     /db_xref="UniSTS:28443"
     STS             1389..1592
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /standard_name="SHGC-35528"
                     /db_xref="UniSTS:9695"
     variation       1779
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /replace="c"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:11541294"
     STS             1929..2037
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /standard_name="RH69670"
                     /db_xref="UniSTS:56823"
     variation       1944
                     /gene="NKX2-1"
                     /gene_synonym="BCH; BHC; NK-2; NKX2.1; NKX2A; TEBP; TITF1;
                     TTF-1; TTF1"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:11541293"
ORIGIN      

ctgacagacacgtagaccaacagtgcggccccagggttcgtccccagactcgctcgctcatttgttggcgactggggctcagcgcagcgaagcccgatgtggtccggaggcagtgggaaggcgcggggctgggaggccgcggcgggagggaggagcagccccggcaggctcagccgccgccgaatcatgtcgatgagtccaaagcacacgactccgttctcagtgtctgacatcttgagtcccctggaggaaagctacaagaaagtgggcatggagggcggcggcctcggggctccgctggcggcgtacaggcagggccaggcggcaccgccaacagcggccatgcagcagcacgccgtggggcaccacggcgccgtcaccgccgcctaccacatgacggcggcgggggtgccccagctctcgcactccgccgtggggggctactgcaacggcaacctgggcaacatgagcgagctgccgccgtaccaggacaccatgaggaacagcgcctctggccccggatggtacggcgccaacccagacccgcgcttccccgccatctcccgcttcatgggcccggcgagcggcatgaacatgagcggcatgggcggcctgggctcgctgggggacgtgagcaagaacatggccccgctgccaagcgcgccgcgcaggaagcgccgggtgctcttctcgcaggcgcaggtgtacgagctggagcgacgcttcaagcaacagaagtacctgtcggcgccggagcgcgagcacctggccagcatgatccacctgacgcccacgcaggtcaagatctggttccagaaccaccgctacaaaatgaagcgccaggccaaggacaaggcggcgcagcagcaactgcagcaggacagcggcggcggcgggggcggcgggggcaccgggtgcccgcagcagcaacaggctcagcagcagtcgccgcgacgcgtggcggtgccggtcctggtgaaagacggcaaaccgtgccaggcgggtgcccccgcgccgggcgccgccagcctacaaggccacgcgcagcagcaggcgcagcaccaggcgcaggccgcgcaggcggcggcagcggccatctccgtgggcagcggtggcgccggccttggcgcacacccgggccaccagccaggcagcgcaggccagtctccggacctggcgcaccacgccgccagccccgcggcgctgcagggccaggtatccagcctgtcccacctgaactcctcgggctcggactacggcaccatgtcctgctccaccttgctatacggtcggacctggtgagaggacgccgggccggccctagcccagcgctctgcctcaccgcttccctcctgcccgccacacagaccaccatccaccgctgctccacgcgcttcgacttttcttaacaacctggccgcgtttagaccaaggaacaaaaaaaccacaaaggccaaactgctggacgtctttctttttttccccccctaaaatttgtgggtttttttttttaaaaaaagaaaatgaaaaacaaccaagcgcatccaatctcaaggaatctttaagcagagaagggcataaaacagctttggggtgtctttttttggtgattcaaatgggttttccacgctagggcggggcacagattggagagggctctgtgctgacatggctctggactctaaagaccaaacttcactctgggcacactctgccagcaaagaggactcgcttgtaaataccaggatttttttttttttttgaagggaggacgggagctggggagaggaaagagtcttcaacataacccacttgtcactgacacaaaggaagtgccccctccccggcaccctctggccgcctaggctcagcggcgaccgccctccgcgaaaatagtttgtttaatgtgaacttgtagctgtaaaacgctgtcaaaagttggactaaatgcctagtttttagtaatctgtacattttgttgtaaaaagaaaaaccactcccagtccccagcccttcacattttttatgggcattgacaaatctgtgtatattatttggcagtttggtatttgcggcgtcagtctttttctgttgtaacttatgtagatatttggcttaaatatagttcctaagaagcttctaataaattatacaaattaaaaagattctttttctgattaaaaaaaaaaaaaaaaaa

//

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:7080 -> Molecular function: GO:0003677 [DNA binding] evidence: IMP
            GeneID:7080 -> Molecular function: GO:0003700 [sequence-specific DNA binding transcription factor activity] evidence: IDA
            GeneID:7080 -> Molecular function: GO:0003705 [RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity] evidence: IEA
            GeneID:7080 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:7080 -> Molecular function: GO:0043565 [sequence-specific DNA binding] evidence: IEA
            GeneID:7080 -> Molecular function: GO:0044212 [transcription regulatory region DNA binding] evidence: IDA
            GeneID:7080 -> Biological process: GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] evidence: IEA
            GeneID:7080 -> Biological process: GO:0001764 [neuron migration] evidence: IEA
            GeneID:7080 -> Biological process: GO:0006644 [phospholipid metabolic process] evidence: IEA
            GeneID:7080 -> Biological process: GO:0007411 [axon guidance] evidence: IEA
            GeneID:7080 -> Biological process: GO:0007420 [brain development] evidence: IMP
            GeneID:7080 -> Biological process: GO:0007492 [endoderm development] evidence: IEA
            GeneID:7080 -> Biological process: GO:0007626 [locomotory behavior] evidence: IEA
            GeneID:7080 -> Biological process: GO:0009725 [response to hormone stimulus] evidence: IEP
            GeneID:7080 -> Biological process: GO:0010628 [positive regulation of gene expression] evidence: IDA
            GeneID:7080 -> Biological process: GO:0010719 [negative regulation of epithelial to mesenchymal transition] evidence: IDA
            GeneID:7080 -> Biological process: GO:0021759 [globus pallidus development] evidence: IMP
            GeneID:7080 -> Biological process: GO:0021766 [hippocampus development] evidence: IEA
            GeneID:7080 -> Biological process: GO:0021795 [cerebral cortex cell migration] evidence: IEA
            GeneID:7080 -> Biological process: GO:0021798 [forebrain dorsal/ventral pattern formation] evidence: IEA
            GeneID:7080 -> Biological process: GO:0021877 [forebrain neuron fate commitment] evidence: IEA
            GeneID:7080 -> Biological process: GO:0021892 [cerebral cortex GABAergic interneuron differentiation] evidence: IEA
            GeneID:7080 -> Biological process: GO:0021983 [pituitary gland development] evidence: IEA
            GeneID:7080 -> Biological process: GO:0030324 [lung development] evidence: IEP
            GeneID:7080 -> Biological process: GO:0030336 [negative regulation of cell migration] evidence: IDA
            GeneID:7080 -> Biological process: GO:0030512 [negative regulation of transforming growth factor beta receptor signaling pathway] evidence: IDA
            GeneID:7080 -> Biological process: GO:0030878 [thyroid gland development] evidence: IEP
            GeneID:7080 -> Biological process: GO:0030878 [thyroid gland development] evidence: IMP
            GeneID:7080 -> Biological process: GO:0030900 [forebrain development] evidence: IEP
            GeneID:7080 -> Biological process: GO:0031128 [developmental induction] evidence: IEA
            GeneID:7080 -> Biological process: GO:0033327 [Leydig cell differentiation] evidence: IEA
            GeneID:7080 -> Biological process: GO:0042696 [menarche] evidence: IEA
            GeneID:7080 -> Biological process: GO:0045893 [positive regulation of transcription, DNA-dependent] evidence: IDA
            GeneID:7080 -> Biological process: GO:0045893 [positive regulation of transcription, DNA-dependent] evidence: ISS
            GeneID:7080 -> Biological process: GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] evidence: IDA
            GeneID:7080 -> Biological process: GO:0048646 [anatomical structure formation involved in morphogenesis] evidence: IEA
            GeneID:7080 -> Biological process: GO:0048709 [oligodendrocyte differentiation] evidence: IEA
            GeneID:7080 -> Biological process: GO:0060430 [lung saccule development] evidence: IEA
            GeneID:7080 -> Biological process: GO:0060441 [epithelial tube branching involved in lung morphogenesis] evidence: IEP
            GeneID:7080 -> Biological process: GO:0060486 [Clara cell differentiation] evidence: IEA
            GeneID:7080 -> Biological process: GO:0060510 [Type II pneumocyte differentiation] evidence: IEA
            GeneID:7080 -> Cellular component: GO:0005634 [nucleus] evidence: IDA
            GeneID:7080 -> Cellular component: GO:0005654 [nucleoplasm] evidence: ISS
            GeneID:7080 -> Cellular component: GO:0005667 [transcription factor complex] evidence: IEA