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

Gene ID: 7080, updated on 4-Jan-2025

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; AllianceGenome:HGNC:11825
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
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Genomic context

See NKX2-1 in Genome Data Viewer
Location:
14q13.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (36516397..36520232, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (30705671..30709516, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (36985602..36989437, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene DPPA3 pseudogene 2 Neighboring gene RNA, U7 small nuclear 93 pseudogene Neighboring gene VISTA enhancer hs1538 Neighboring gene VISTA enhancer hs704 Neighboring gene surfactant associated 3 Neighboring gene VISTA enhancer hs1166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:36974689-36975264 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:36977998-36978653 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:36983846-36984473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:36986696-36987694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:36988853-36989852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:36989853-36990852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:36990853-36991852 Neighboring gene uncharacterized LOC105370453 Neighboring gene NKX2-1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:36994071-36995009 Neighboring gene phosphorylase kinase regulatory subunit beta pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:37025714-37025870 Neighboring gene ribosomal protein L29 pseudogene 3

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding PubMed 
enables DNA-binding transcription factor activity PubMed 
enables DNA-binding transcription factor activity PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific  
enables DNA-binding transcription factor activity, RNA polymerase II-specific  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding PubMed 
enables enzyme binding PubMed 
enables intronic transcription regulatory region sequence-specific DNA binding PubMed 
enables intronic transcription regulatory region sequence-specific DNA binding  
enables protein binding PubMed 
enables transcription cis-regulatory region binding PubMed 
enables transcription cis-regulatory region binding PubMed 
Items 1 - 25 of 43
Process Evidence Code Pubs
involved_in Leydig cell differentiation  
involved_in anatomical structure formation involved in morphogenesis  
involved_in axon guidance  
involved_in brain development PubMed 
involved_in cell differentiation  
involved_in cerebral cortex GABAergic interneuron differentiation  
involved_in cerebral cortex cell migration  
involved_in club cell differentiation  
involved_in developmental induction  
involved_in endoderm development  
involved_in epithelial tube branching involved in lung morphogenesis PubMed 
involved_in forebrain development PubMed 
involved_in forebrain dorsal/ventral pattern formation  
involved_in forebrain neuron fate commitment  
involved_in gene expression  
involved_in globus pallidus development PubMed 
involved_in hippocampus development  
involved_in hypothalamus development  
involved_in interneuron migration  
involved_in locomotory behavior  
involved_in lung development PubMed 
involved_in lung saccule development  
involved_in negative regulation of DNA-templated transcription  
involved_in negative regulation of cell migration PubMed 
involved_in negative regulation of epithelial to mesenchymal transition PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transforming growth factor beta receptor signaling pathway PubMed 
involved_in oligodendrocyte differentiation  
involved_in phospholipid metabolic process  
involved_in pituitary gland development  
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription  
involved_in positive regulation of circadian rhythm  
involved_in positive regulation of gene expression PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in regulation of DNA-templated transcription PubMed 
involved_in regulation of transcription by RNA polymerase II  
involved_in response to hormone PubMed 
involved_in rhythmic process  
involved_in thyroid gland development PubMed 
involved_in thyroid gland development PubMed 
involved_in type II pneumocyte differentiation  
Items 1 - 25 of 43
Component Evidence Code Pubs
located_in chromatin  
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus PubMed 
part_of transcription regulator complex PubMed 

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)

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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
    4994..8829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001079668.3NP_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
    ENSP00000346879.6, ENST00000354822.7
    Conserved Domains (1) summary
    pfam00046
    Location:194247
    Homeobox; Homeobox domain
  2. NM_003317.4NP_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
    D3DSA3, O14954, O14955, P43699, Q7KZF6, Q9BRJ8
    Related
    ENSP00000429607.2, ENST00000498187.6
    Conserved Domains (1) summary
    pfam00046
    Location:164217
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    36516397..36520232 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    30705671..30709516 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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