Human Gene NKX2-1 (uc001wtu.3) Description and Page Index
  Description: Homo sapiens NK2 homeobox 1 (NKX2-1), transcript variant 1, mRNA.
RefSeq Summary (NM_001079668): 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 'TTF1' with another gene, transcription termination factor 1, which plays a role in ribosomal gene transcription. [provided by RefSeq, Feb 2014].
Transcript (Including UTRs)
   Position: hg19 chr14:36,985,604-36,989,430 Size: 3,827 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr14:36,986,483-36,989,334 Size: 2,852 Coding Exon Count: 3 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr14:36,985,604-36,989,430)mRNA (may differ from genome)Protein (401 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NKX2-1
CDC HuGE Published Literature: NKX2-1
Positive Disease Associations: Body Height , height , Menarch|Obesity|POF - Premature ovarian failure|POLYCYSTIC OVARIAN SYNDROME|Polycystic Ovary Syndrome|Primary Ovarian Insufficiency|Puberty, Delayed|Puberty, Precocious , Sleep , thyroid cancer , Triglycerides
Related Studies:
  1. Body Height
    Guillaume Lettre et al. Nature genetics 2008, Identification of ten loci associated with height highlights new biological pathways in human growth., Nature genetics. [PubMed 18391950]
  2. height
    Lettre ,et al. 2008, Identification of ten loci associated with height highlights new biological pathways in human growth, Nature genetics 2008 40- 5 : 584-91. [PubMed 18391950]
  3. Menarch|Obesity|POF - Premature ovarian failure|POLYCYSTIC OVARIAN SYNDROME|Polycystic Ovary Syndrome|Primary Ovarian Insufficiency|Puberty, Delayed|Puberty, Precocious
    He C et al. 2010, A large-scale candidate gene association study of age at menarche and age at natural menopause., Human genetics 128(5) : 515-27 2010. [PubMed 20734064]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NKX2-1
Diseases sorted by gene-association score: chorea, hereditary benign* (1691), choreoathetosis, hypothyroidism, and neonatal respiratory distress* (1650), thyroid cancer, nonmedullary, 1* (875), nkx2-1-related disorders* (100), thyroid cancer (52), congenital hypothyroidism (47), hypothyroidism (36), papillary adenocarcinoma (32), pulmonary blastoma (30), pulmonary sclerosing hemangioma (26), sclerosing hemangioma (26), bronchiolo-alveolar adenocarcinoma (25), dyskinetic cerebral palsy (24), large cell carcinoma (24), struma ovarii (23), merkel cell carcinoma (20), carcinoid tumors, intestinal (19), pituicytoma (18), neuroendocrine cell hyperplasia of infancy (18), congenital diaphragmatic hernia (17), lung benign neoplasm (17), malignant pleural mesothelioma (17), papillary carcinoma (16), pleomorphic carcinoma (16), chordoid glioma (16), papillary serous adenocarcinoma (15), thymus cancer (15), thyroglossal duct cyst, familial (15), lung cancer (14), newborn respiratory distress syndrome (14), sarcomatoid mesothelioma (13), hemangioma (13), intestinal perforation (12), hemangioma of lung (12), blastoma (12), follicular adenoma (12), neuroendocrine tumor (12), small cell carcinoma (12), lung cancer susceptibility 3 (11), ovarian germ cell teratoma (11), thyroid cancer, anaplastic (11), mesothelioma, somatic (11), lung acinar adenocarcinoma (11), large cell neuroendocrine carcinoma (11), lung adenoid cystic carcinoma (11), mucinous bronchioloalveolar adenocarcinoma (11), athetosis (10), athyreosis* (10), choreatic disease (10), teratoma (9), cystic teratoma (9), hypothyroidism, congenital, due to thyroid dysgenesis or hypoplasia (9), small cell carcinoma of the bladder (9), chromosome 14q11-q22 deletion syndrome (9), papillary adenoma (9), differentiated thyroid carcinoma* (8), multinodular goiter (8), respiratory failure (8), mucinous adenocarcinoma (8), norwegian scabies (8), small cell cancer of the lung, somatic (8), thymoma (8), malignant struma ovarii (8), goiter (8), rete testis adenocarcinoma (7), ovarian cystic teratoma (7), interstitial lung disease (7), cavernous hemangioma (7), respiratory system benign neoplasm (7), thyroid cancer, nonmedullary, 2 (6), horseshoe kidney (6), malignant teratoma (6), benign mesothelioma (6), extraskeletal ewing sarcoma (6), rete testis neoplasm (6), medullary thyroid carcinoma, familial (5), atypical choroid plexus papilloma (5), epidemic typhus (5), hidradenocarcinoma (5), infant botulism (4), cerebral palsy, ataxic, autosomal recessive (4), dystonia-11, myoclonic (4), patent foramen ovale (4), cribriform carcinoma (4), movement disease (2), renal cell carcinoma (2), thyroid gland disease (1), wilms tumor susceptibility-5 (1), cell type cancer (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 133.70 RPKM in Thyroid
Total median expression: 176.31 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.1096-0.314 Picture PostScript Text
3' UTR -240.14879-0.273 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00046 - Homeobox domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P43699-3
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGD  WormBase 
 Protein Sequence  Protein Sequence 
 Alignment  Alignment 

-  Descriptions from all associated GenBank mRNAs
  LQ270674 - Sequence 2 from Patent WO2016071350.
BC006221 - Homo sapiens NK2 homeobox 1, mRNA (cDNA clone MGC:10523 IMAGE:3941576), complete cds.
U43203 - Human thyroid transcription factor 1 (TTF-1) mRNA, complete cds.
LQ270678 - Sequence 6 from Patent WO2016071350.
U33749 - Human thyroid transcription factor-1 (TTF-1) mRNA, complete cds.
JD036419 - Sequence 17443 from Patent EP1572962.
JD042268 - Sequence 23292 from Patent EP1572962.
JD564140 - Sequence 545164 from Patent EP1572962.
JD325810 - Sequence 306834 from Patent EP1572962.
JD264067 - Sequence 245091 from Patent EP1572962.
JD527907 - Sequence 508931 from Patent EP1572962.
JD211429 - Sequence 192453 from Patent EP1572962.
JD146290 - Sequence 127314 from Patent EP1572962.
JD490429 - Sequence 471453 from Patent EP1572962.
JD461184 - Sequence 442208 from Patent EP1572962.
X82850 - H.sapiens mRNA for thyroid transcript factor 1.
D50741 - Homo sapiens mRNA for Thyroid transcriptional factor-1 truncated form, complete cds.
D50740 - Homo sapiens mRNA for thyroid transcriptional factor-1, complete cds.
JD117425 - Sequence 98449 from Patent EP1572962.
JD145839 - Sequence 126863 from Patent EP1572962.
JD203443 - Sequence 184467 from Patent EP1572962.
U19756 - Human thyroid transcription factor 1 mRNA, complete cds.
BT009773 - Homo sapiens thyroid transcription factor 1 mRNA, complete cds.
DQ892964 - Synthetic construct clone IMAGE:100005594; FLH191219.01X; RZPDo839A1177D thyroid transcription factor 1 (TITF1) gene, encodes complete protein.
DQ896211 - Synthetic construct Homo sapiens clone IMAGE:100010671; FLH191215.01L; RZPDo839A1167D thyroid transcription factor 1 (TITF1) gene, encodes complete protein.
AB590511 - Synthetic construct DNA, clone: pFN21AB8975, Homo sapiens NKX2-1 gene for NK2 homeobox 1, without stop codon, in Flexi system.
LF212489 - JP 2014500723-A/19992: Polycomb-Associated Non-Coding RNAs.
LF383584 - JP 2014500723-A/191087: Polycomb-Associated Non-Coding RNAs.
JD150330 - Sequence 131354 from Patent EP1572962.
LQ932411 - Sequence 2 from Patent WO2014187881.
MA619161 - JP 2018138019-A/191087: Polycomb-Associated Non-Coding RNAs.
MA448066 - JP 2018138019-A/19992: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NKX2A, NM_001079668, NP_001073136, P43699-3, TITF1, TTF1
UCSC ID: uc001wtu.3
RefSeq Accession: NM_001079668
Protein: P43699-3, splice isoform of P43699 CCDS: CCDS41945.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NKX2-1:
nkx2-1-dis (NKX2-1-Related Disorders)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001079668.2
exon count: 3CDS single in 3' UTR: no RNA size: 2197
ORF size: 1206CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2512.00frame shift in genome: no % Coverage: 99.27
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.