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

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, Dec 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: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration.
Title: Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration.
Hypothalamic TTF-1 orchestrates the sensitivity of leptin.
Title: Hypothalamic TTF-1 orchestrates the sensitivity of leptin.
Optimized thyroid transcription factor-1 core promoter-driven microRNA-7 expression effectively inhibits the growth of human non-small-cell lung cancer cells.
Title: Optimized thyroid transcription factor-1 core promoter-driven microRNA-7 expression effectively inhibits the growth of human non-small-cell lung cancer cells.
Pax8 and Nkx2-1 haploinsufficiencies differentially affect liver metabolic pathways.
Title: Pax8 and Nkx2-1 haploinsufficiencies differentially affect liver metabolic pathways.
Blastocyst complementation reveals that NKX2-1 establishes the proximal-peripheral boundary of the airway epithelium.
Title: Blastocyst complementation reveals that NKX2-1 establishes the proximal-peripheral boundary of the airway epithelium.
Transcriptional profiling of sequentially generated septal neuron fates.
Title: Transcriptional profiling of sequentially generated septal neuron fates.
Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo.
Title: Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo.
Tsc1 haploinsufficiency in Nkx2.1 cells upregulates hippocampal interneuron mTORC1 activity, impairs pyramidal cell synaptic inhibition, and alters contextual fear discrimination and spatial working memory in mice.
Title: Tsc1 haploinsufficiency in Nkx2.1 cells upregulates hippocampal interneuron mTORC1 activity, impairs pyramidal cell synaptic inhibition, and alters contextual fear discrimination and spatial working memory in mice.
Nkx2.1 downregulation is involved in brain abnormality induced by excess retinoic acid.
Title: Nkx2.1 downregulation is involved in brain abnormality induced by excess retinoic acid.
The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development.
Title: The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development.

Submit: New GeneRIF Correction See all GeneRIFs (83)

Variation

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (3) 1 citation
Targeted (12) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

Nkx2-1 (e-PCR), detects polymorphism
- UniSTS:536832

Nkx2-1 (e-PCR), detects polymorphism
- UniSTS:546582

D6Wox28 (e-PCR)
- UniSTS:518786

Titf1 (e-PCR), detects polymorphism
- UniSTS:226179

PMC152810P1 (e-PCR)
- UniSTS:271243

D6Wox31 (e-PCR)
- UniSTS:518795

Titf1 (e-PCR), detects polymorphism
- UniSTS:497301

Nkx2-1 (e-PCR), detects polymorphism
- UniSTS:534422

Titf1 (e-PCR), detects polymorphism
- UniSTS:464797

AV026640 (e-PCR)
- UniSTS:165823

UniSTS:225218 (e-PCR)
- UniSTS:225218

Nkx2-1 (e-PCR), detects polymorphism
- UniSTS:507093

AA858694 (e-PCR)
- UniSTS:243417

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

Go to the top of the page Help

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)

Go to the top of the page Help

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)

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

Status: VALIDATED

Source sequence(s)

AC160393

UniProtKB/TrEMBL

Q6PFE0
NM_009385.4 → NP_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:164 → 217

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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

56578741..56583570 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

Q6PFE0

Conserved Domains (1) summary

pfam00046
Location:194 → 248

Homeobox; Homeobox domain
XM_036157377.1 → XP_036013270.1 homeobox protein Nkx-2.1 isoform X1

UniProtKB/TrEMBL

Q6PFE0

Conserved Domains (1) summary

pfam00046
Location:215 → 269

Homeobox; Homeobox domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001146198.1: Suppressed sequence

Description

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