Nkx2-9 NK2 homeobox 9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nkx2-9provided by MGI
Official Full Name: NK2 homeobox 9provided by MGI
Primary source: MGI:MGI:1270158
See related: Ensembl:ENSMUSG00000058669 AllianceGenome:MGI:1270158
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: Nkx2-8; Nkx2.9; tinman; Nkx-2.9
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within axonogenesis; lung development; and negative regulation of epithelial cell proliferation. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; embryo ectoderm; embryo mesoderm; liver; and lung epithelium. Orthologous to human NKX2-8 (NK2 homeobox 8). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in cerebellum adult (RPKM 1.1), CNS E11.5 (RPKM 0.9) and 11 other tissues See more
Orthologs: human all
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Genomic context

Location:: 12 C1; 12 24.47 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (56658174..56660354, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (56611389..56613569, complement)

Chromosome 12 - NC_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nkx2.9 Contributes to Mid-Hindbrain Patterning by Regulation of mdDA Neuronal Cell-Fate and Repression of a Hindbrain-Specific Cell-Fate.
Title: Nkx2.9 Contributes to Mid-Hindbrain Patterning by Regulation of mdDA Neuronal Cell-Fate and Repression of a Hindbrain-Specific Cell-Fate.
FKBP8 variants are risk factors for spina bifida.
Title: FKBP8 variants are risk factors for spina bifida.
that Nkx2.2 and Nkx2.9 proteins play no role in the development of branchiovisceral motor neurons in hindbrain rostral to rhombomere 4.
Title: Nkx2.2 and Nkx2.9 are the key regulators to determine cell fate of branchial and visceral motor neurons in caudal hindbrain.
Nkx2.9 controls SACMN axon exit from the mammalian spinal cord by regulating Robo-Slit signaling
Title: Motor axon exit from the mammalian spinal cord is controlled by the homeodomain protein Nkx2.9 via Robo-Slit signaling.
Data argue that the Nkx2.2 and Nkx2.9 transcription factors contribute crucially to the formation of neuronal networks that function as central pattern generators for locomotor activity in the spinal cord.
Title: The transcription factors Nkx2.2 and Nkx2.9 play a novel role in floor plate development and commissural axon guidance.
The homeodomain protein Tinman activates Hand expression in Drosophlla hematopoiesis and cardiogenesis.
Title: Hand is a direct target of Tinman and GATA factors during Drosophila cardiogenesis and hematopoiesis.
role in development of the spinal accessory nerve
Title: Targeted disruption of the homeobox gene Nkx2.9 reveals a role in development of the spinal accessory nerve.
A murine Nkx2.8 was isolated from the Hepal-6 cell line and showed oligonucleotide binding competitive with fetoprotein transcription factor.
Title: Regulation of alpha-fetoprotein expression by Nkx2.8.

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Variation

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Alleles

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

Targeted (2) 1 citation
Endonuclease-mediated (1)

General gene information

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Markers

Nkx2-9 (e-PCR), detects polymorphism
- UniSTS:144028

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation 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	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 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	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lung development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation 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 respiratory tube development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein Nkx-2.8

Names: Drosophila NK2 transcription factor related, locus 9; NK2 transcription factor related, locus 9; homeobox protein NK-2 homolog H; homeobox protein Nkx-2.9

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.