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    Nkx2-1 NK2 homeobox 1 [ Mus musculus (house mouse) ]

    Gene ID: 21869, updated on 3-Dec-2024

    Summary

    Official Symbol
    Nkx2-1provided by MGI
    Official Full Name
    NK2 homeobox 1provided by MGI
    Primary source
    MGI:MGI:108067
    See related
    Ensembl:ENSMUSG00000001496 AllianceGenome:MGI:108067
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    T/EBP; Titf1; Ttf-1; Nkx2.1
    Summary
    Enables DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and intronic transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including hypothalamus development; positive regulation of circadian rhythm; and regulation of DNA-templated transcription. Acts upstream of or within several processes, including lung development; nervous system development; and regulation of transcription by RNA polymerase II. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; brain; neural ectoderm; respiratory system; and sensory organ. Human ortholog(s) of this gene implicated in choreatic disease and papillary thyroid carcinoma. Orthologous to human NKX2-1 (NK2 homeobox 1). [provided by Alliance of Genome Resources, Nov 2024]
    Annotation information
    Note: Ttf1 (GeneID 22130) and Nkx2-1 (GeneID 21869) 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 adult (RPKM 102.7), whole brain E14.5 (RPKM 11.8) and 1 other tissue See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Nkx2-1 in Genome Data Viewer
    Location:
    12 C1; 12 24.42 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (56578741..56583570, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (56531935..56536908, complement)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_32209 Neighboring gene predicted gene, 18027 Neighboring gene surfactant associated 3 Neighboring gene Nkx2-1 Hedgehog-responsive enhancer Neighboring gene STARR-seq mESC enhancer starr_32210 Neighboring gene predicted gene, 25760 Neighboring gene STARR-seq mESC enhancer starr_32211 Neighboring gene expressed sequence C87198

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables TBP-class protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables core promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables enzyme binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within GABAergic neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within Leydig cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within anatomical structure formation involved in morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within animal organ morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within brain development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within cerebral cortex GABAergic interneuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cerebral cortex cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cerebral cortex neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within cerebral cortex neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within club cell differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within developmental induction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within endoderm development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in epithelial tube branching involved in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in feeding behavior ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within forebrain dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within forebrain neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within forebrain neuron fate commitment IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within forebrain neuron fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within globus pallidus development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in globus pallidus development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within hippocampus development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hypothalamus development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within interneuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within lung development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within lung development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within lung saccule development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within menarche IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of epithelial to mesenchymal transition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of epithelial to mesenchymal transition ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neuron fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within oligodendrocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within pattern specification process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within phospholipid metabolic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within pituitary gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of blood volume by renin-angiotensin ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to hormone IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to lipopolysaccharide ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within telencephalon cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within telencephalon development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within thyroid gland development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within thyroid gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within thyroid gland development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in thyroid gland development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within type II pneumocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    homeobox protein Nkx-2.1
    Names
    thyroid nuclear factor 1
    thyroid transcription factor 1
    thyroid-specific enhancer-binding protein
    tinman

    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.

    mRNA and Protein(s)

    1. NM_001403580.1NP_001390509.1  homeobox protein Nkx-2.1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC160393
      UniProtKB/TrEMBL
      Q6PFE0
    2. NM_009385.4NP_033411.3  homeobox protein Nkx-2.1 isoform 1

      See identical proteins and their annotated locations for NP_033411.3

      Status: VALIDATED

      Source sequence(s)
      AC160393
      Consensus CDS
      CCDS25922.1
      UniProtKB/Swiss-Prot
      P50220
      UniProtKB/TrEMBL
      Q6PFE0
      Related
      ENSMUSP00000001536.8, ENSMUST00000001536.9
      Conserved Domains (1) summary
      pfam00046
      Location:164217
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000078.7 Reference GRCm39 C57BL/6J

      Range
      56578741..56583570 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006515791.3XP_006515854.1  homeobox protein Nkx-2.1 isoform X2

      UniProtKB/TrEMBL
      Q6PFE0
      Conserved Domains (1) summary
      pfam00046
      Location:194248
      Homeobox; Homeobox domain
    2. XM_036157377.1XP_036013270.1  homeobox protein Nkx-2.1 isoform X1

      UniProtKB/TrEMBL
      Q6PFE0
      Conserved Domains (1) summary
      pfam00046
      Location:215269
      Homeobox; Homeobox domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001146198.1: Suppressed sequence

      Description
      NM_001146198.1: This RefSeq was removed because currently there is insufficient support for the transcript.