NKX2-3 NK2 homeobox 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NKX2-3provided by HGNC
Official Full Name: NK2 homeobox 3provided by HGNC
Primary source: HGNC:HGNC:7836
See related: Ensembl:ENSG00000119919 MIM:606727; AllianceGenome:HGNC:7836
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: CSX3; NK2.3; NKX2C; NKX2.3; NKX4-3
Summary: This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]
Expression: Biased expression in spleen (RPKM 11.9), small intestine (RPKM 4.8) and 5 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.2

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (99532942..99536524)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (100408890..100418489)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (101292699..101296281)

Chromosome 10 - NC_000010.11 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Quantitative Analysis of NKX2-3 Expression in Human Colon: An Immunohistochemical Study.
Title: Quantitative Analysis of NKX2-3 Expression in Human Colon: An Immunohistochemical Study.
Transcription factor Nkx2-3 maintains the self-renewal of hematopoietic stem cells by regulating mitophagy.
Title: Transcription factor Nkx2-3 maintains the self-renewal of hematopoietic stem cells by regulating mitophagy.
NKL Homeobox Genes NKX2-3 and NKX2-4 Deregulate Megakaryocytic-Erythroid Cell Differentiation in AML.
Title: NKL Homeobox Genes NKX2-3 and NKX2-4 Deregulate Megakaryocytic-Erythroid Cell Differentiation in AML.
Identification of novel, clonally stable, somatic mutations targeting transcription factors PAX5 and NKX2-3, the epigenetic regulator LRIF1, and BRAF in a case of atypical B-cell chronic lymphocytic leukemia harboring a t(14;18)(q32;q21).
Title: Identification of novel, clonally stable, somatic mutations targeting transcription factors PAX5 and NKX2-3, the epigenetic regulator LRIF1, and BRAF in a case of atypical B-cell chronic lymphocytic leukemia harboring a t(14;18)(q32;q21).
Development and Validation of an Autophagy-Related Signature for Head and Neck Squamous Cell Carcinoma.
Title: Development and Validation of an Autophagy-Related Signature for Head and Neck Squamous Cell Carcinoma.
Mutations in RPSA and NKX2-3 link development of the spleen and intestinal vasculature.
Title: Mutations in RPSA and NKX2-3 link development of the spleen and intestinal vasculature.
Studies suggest oncogenic NK2 homeobox 3 homeobox protein (NKX2-3) in lymphomagenesis, and show a mouse model for studying the biology and therapy of human marginal-zone B-cell lymphomas.
Title: Homeobox NKX2-3 promotes marginal-zone lymphomagenesis by activating B-cell receptor signalling and shaping lymphocyte dynamics.
NKX2-3 is a key mediator for maintaining myofibroblast characteristics, and our results show that colorectal myofibroblasts, as defined by the expression of AOC3, NKX2-3, and other markers, are a distinctly different cell type from TGFbeta-activated fibroblasts
Title: Myofibroblasts are distinguished from activated skin fibroblasts by the expression of AOC3 and other associated markers.
The persons with a NKX2-3 G or T allele may have a moderately increased risk of CD.
Title: Contribution of NKX2-3 polymorphisms to inflammatory bowel diseases: a meta-analysis of 35358 subjects.
NKX2-3 may play different roles in ulcerative colitis and Crohn's disease pathogenesis by differential regulation of EGR1.
Title: Genes differentially regulated by NKX2-3 in B cells between ulcerative colitis and Crohn's disease patients and possible involvement of EGR1.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association identifies multiple ulcerative colitis susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS of dental caries patterns in the permanent dentition. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Seventy-five genetic loci influencing the human red blood cell. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-147590 (e-PCR)
- UniSTS:172839

NKX2-3_1975 (e-PCR)
- UniSTS:463269

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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 sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within CD4-positive, alpha-beta T cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Peyer's patch development	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell fate specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within digestive tract development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within gland morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within leukocyte homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within leukocyte migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lymph node development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within macrophage differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mucosa-associated lymphoid tissue development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within odontogenesis of dentin-containing tooth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within plasma cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-embryonic development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-embryonic digestive tract morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of epithelial cell proliferation	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 saliva secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within spleen development	IEA Inferred from Electronic Annotation more info
acts_upstream_of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within triglyceride metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Nkx-2.3

Names: NK2 transcription factor related, locus 3; homeobox protein NK-2 homolog C

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

NG_016854.1 RefSeqGene

Range

5010..8592

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_145285.3 → NP_660328.2 homeobox protein Nkx-2.3

See identical proteins and their annotated locations for NP_660328.2

Status: REVIEWED

Source sequence(s)

AL353719, BC025788, BI764885

Consensus CDS

CCDS41558.1

UniProtKB/Swiss-Prot

B4DUZ4, Q8TAU0, Q9NYS6

Related

ENSP00000342828.7, ENST00000344586.9

Conserved Domains (1) summary

smart00389
Location:148 → 204

HOX; Homeodomain

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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

99532942..99536524

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011539370.2 → XP_011537672.1 homeobox protein Nkx-2.3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060934.1 Alternate T2T-CHM13v2.0

Range

100408890..100418489

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054364924.1 → XP_054220899.1 homeobox protein Nkx-2.3 isoform X1
XM_054364923.1 → XP_054220898.1 homeobox protein Nkx-2.3 isoform X2

UniProtKB/Swiss-Prot

B4DUZ4, Q8TAU0, Q9NYS6