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NKX2-1 NK2 homeobox 1 [ Homo sapiens (human) ]

Gene ID: 7080, updated on 9-Dec-2018

Summary

Official Symbol
NKX2-1provided by HGNC
Official Full Name
NK2 homeobox 1provided by HGNC
Primary source
HGNC:HGNC:11825
See related
Ensembl:ENSG00000136352 MIM:600635
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BCH; BHC; NK-2; TEBP; TTF1; NKX2A; NMTC1; T/EBP; TITF1; TTF-1; NKX2.1
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 'TTF1' with another gene, transcription termination factor 1, which plays a role in ribosomal gene transcription. [provided by RefSeq, Feb 2014]
Annotation information
Note: TTF1 (GeneID 7270) and NKX2-1 (GeneID 7080) loci share the TTF1 symbol/alias in common. TTF1 is a widely used alternative name for thyroid transcription factor 1 (NKX2-1) conflicting with the official symbol for transcription termination factor, RNA polymerase I (TTF1). [13 Feb 2013]
Expression
Biased expression in lung (RPKM 35.0) and thyroid (RPKM 29.1) See more
Orthologs

Genomic context

See NKX2-1 in Genome Data Viewer
Location:
14q13.3
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (36516397..36520225, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (36985602..36990894, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs704 Neighboring gene surfactant associated 3 Neighboring gene VISTA enhancer hs1166 Neighboring gene NKX2-1 antisense RNA 1 Neighboring gene uncharacterized LOC105370453 Neighboring gene phosphorylase kinase regulatory subunit beta pseudogene 2 Neighboring gene ribosomal protein L29 pseudogene 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Benign hereditary chorea
MedGen: C0393584 OMIM: 118700 GeneReviews: NKX2-1-Related Disorders
Compare labs
Choreoathetosis, hypothyroidism, and neonatal respiratory distress
MedGen: C1970269 OMIM: 610978 GeneReviews: NKX2-1-Related Disorders
Compare labs
Nonmedullary thyroid carcinoma 1
MedGen: C1853488 OMIM: 188550 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations.
NHGRI GWA Catalog
Genome wide association study of age at menarche in the Japanese population.
NHGRI GWA Catalog
Identification of ten loci associated with height highlights new biological pathways in human growth.
NHGRI GWA Catalog

Pathways from BioSystems

  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • FOXA2 and FOXA3 transcription factor networks, organism-specific biosystem (from Pathway Interaction Database)
    FOXA2 and FOXA3 transcription factor networks, organism-specific biosystem
    FOXA2 and FOXA3 transcription factor networks
  • Preimplantation Embryo, organism-specific biosystem (from WikiPathways)
    Preimplantation Embryo, organism-specific biosystemThe source of this pathway is RNA-Seq data from single-cell pre-implantation embryos (Supplemental Table 1): http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Analysis options for runnin...
  • Tgif disruption of Shh signaling, organism-specific biosystem (from WikiPathways)
    Tgif disruption of Shh signaling, organism-specific biosystemMutations in the Sonic Hedgehog(SHH) gene result in HPE in humans and mice, and the Shh pathway is targeted by other mutations that cause HPE. HPE is a severe human genetic disease affecting craniofa...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
RNA polymerase II distal enhancer sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
intronic transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
intronic transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
Clara cell differentiation IEA
Inferred from Electronic Annotation
more info
 
Leydig cell differentiation IEA
Inferred from Electronic Annotation
more info
 
anatomical structure formation involved in morphogenesis IEA
Inferred from Electronic Annotation
more info
 
axon guidance IEA
Inferred from Electronic Annotation
more info
 
brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cerebral cortex GABAergic interneuron differentiation IEA
Inferred from Electronic Annotation
more info
 
cerebral cortex cell migration IEA
Inferred from Electronic Annotation
more info
 
developmental induction IEA
Inferred from Electronic Annotation
more info
 
endoderm development IEA
Inferred from Electronic Annotation
more info
 
epithelial tube branching involved in lung morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
forebrain development IEP
Inferred from Expression Pattern
more info
PubMed 
forebrain dorsal/ventral pattern formation IEA
Inferred from Electronic Annotation
more info
 
forebrain neuron fate commitment IEA
Inferred from Electronic Annotation
more info
 
globus pallidus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
hippocampus development IEA
Inferred from Electronic Annotation
more info
 
locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
lung development IEP
Inferred from Expression Pattern
more info
PubMed 
lung saccule development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of epithelial to mesenchymal transition IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transforming growth factor beta receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
neuron migration IEA
Inferred from Electronic Annotation
more info
 
oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
phospholipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
pituitary gland development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
response to hormone IEP
Inferred from Expression Pattern
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
thyroid gland development IEP
Inferred from Expression Pattern
more info
PubMed 
thyroid gland development IMP
Inferred from Mutant Phenotype
more info
PubMed 
type II pneumocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
homeobox protein Nkx-2.1
Names
NK-2 homolog A
homeobox protein NK-2 homolog A
thyroid nuclear factor 1
thyroid transcription factor 1
thyroid-specific enhancer-binding protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013365.1 RefSeqGene

    Range
    5001..8829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001079668.2NP_001073136.1  homeobox protein Nkx-2.1 isoform 1

    See identical proteins and their annotated locations for NP_001073136.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
    Source sequence(s)
    AL132857, BM970287, U43203
    Consensus CDS
    CCDS41945.1
    UniProtKB/Swiss-Prot
    P43699
    Related
    ENSP00000346879.5, ENST00000354822.6
    Conserved Domains (1) summary
    pfam00046
    Location:194247
    Homeobox; Homeobox domain
  2. NM_003317.3NP_003308.1  homeobox protein Nkx-2.1 isoform 2

    See identical proteins and their annotated locations for NP_003308.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    BC006221, BM970838, U33749
    Consensus CDS
    CCDS9659.1
    UniProtKB/Swiss-Prot
    P43699
    Related
    ENSP00000429607.2, ENST00000498187.6
    Conserved Domains (1) summary
    pfam00046
    Location:164217
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    36516397..36520225 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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