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

    Gene ID: 7080, updated on 23-Nov-2023

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NKX2-1 in Genome Data Viewer
    Location:
    14q13.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (36516397..36520232, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (30705671..30709516, complement)
    105.20220307 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: 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Benign hereditary chorea
    MedGen: C0393584 OMIM: 118700 GeneReviews: NKX2-1-Related Disorders
    Compare labs
    Brain-lung-thyroid syndrome
    MedGen: C1970269 OMIM: 610978 GeneReviews: NKX2-1-Related Disorders
    Compare labs
    Thyroid cancer, nonmedullary, 1
    MedGen: C4721429 OMIM: 188550 GeneReviews: Not available
    Compare labs

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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_2023_10

    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)