NKX6-3 NK6 homeobox 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NKX6-3provided by HGNC
Official Full Name: NK6 homeobox 3provided by HGNC
Primary source: HGNC:HGNC:26328
See related: Ensembl:ENSG00000165066 MIM:610772; AllianceGenome:HGNC:26328
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NKX6.3
Summary: The NKX family of homeodomain proteins controls numerous developmental processes. Members of the NKX6 subfamily, including NKX6-3, are involved in development of the central nervous system (CNS), gastrointestinal tract, and pancreas (Alanentalo et al., 2006 [PubMed 16326147]).[supplied by OMIM, Mar 2008]
Expression: Biased expression in stomach (RPKM 15.7) and duodenum (RPKM 4.5) See more
Orthologs: mouse all
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Genomic context

Location:: 8p11.21

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (41645177..41650817, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (41918807..41924450, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (41502696..41508336, complement)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These results indicate that NKX6.3 depletion in gastric epithelial cells activates AICDA/APOBEC family, leading to accumulation of genetic mutations and eventually driving the development of gastric cancers.
Title: Multiple genetic mutations caused by NKX6.3 depletion contribute to gastric tumorigenesis.
These results identify genetic variants associated with the efficacy of weight loss in obese subjects and identify a role for NKX6.3 in lipid metabolism, and thereby possibly weight control.
Title: Genome-wide gene-based analyses of weight loss interventions identify a potential role for NKX6.3 in metabolism.
NKX6.3 inhibits gastric mucosal atrophy by regulating amyloid beta accumulation and inflammatory reaction in gastric epithelial cells.
Title: NKX6.3 protects against gastric mucosal atrophy by downregulating β-amyloid production.
these results suggest that NKX6.3 inhibits ROS production by inducing the expression of Hace1 via down-regulating NF-kB and DNMT1 activity in gastric epithelial cells.
Title: NKX6.3 Regulates Reactive Oxygen Species Production by Suppressing NF-kB and DNMT1 Activities in Gastric Epithelial Cells.
The expression level of NKX6.3 is involved in regulation of gastric cancer progression and expression of Wnt/beta-catenin and Rho-GTPase pathway-related genes in clinical samples.
Title: NKX6.3 Is a Transcription Factor for Wnt/β-catenin and Rho-GTPase Signaling-Related Genes to Suppress Gastric Cancer Progression.
Suggest that NKX6.3 might function as a master regulator of gastric differentiation by affecting SOX2 and CDX2 expression and the NKX6.3 inactivation may result in intestinal metaplasia in gastric epithelial cells.
Title: Inactivation of NKX6.3 in the stomach leads to abnormal expression of CDX2 and SOX2 required for gastric-to-intestinal transdifferentiation.
Data suggest that NK6 homeobox 3 (NKX6.3) may control the fate of gastric mucosal cells and function as a gastric tumor suppressor.
Title: NKX6.3 controls gastric differentiation and tumorigenesis.

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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

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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay 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 DNA-binding transcription repressor 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 sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell fate determination	IEA Inferred from Electronic Annotation more info
involved_in enteroendocrine cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of epithelial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	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 transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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

General protein information

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Preferred Names: homeobox protein Nkx-6.3

Names: NK6 transcription factor related, locus 3

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.

mRNA and Protein(s)

NM_001364841.2 → NP_001351770.1 homeobox protein Nkx-6.3 isoform 1

Status: VALIDATED

Source sequence(s)

AC009630, AC113133

Consensus CDS

CCDS94289.1

UniProtKB/Swiss-Prot

A6NJ46, Q96LR0

Related

ENSP00000428361.2, ENST00000518699.4

Conserved Domains (1) summary

pfam00046
Location:142 → 195

Homeobox; Homeobox domain
NM_152568.3 → NP_689781.1 homeobox protein Nkx-6.3 isoform 2

See identical proteins and their annotated locations for NP_689781.1

Status: VALIDATED

Source sequence(s)

AC009630, AK057898

Consensus CDS

CCDS6118.1

UniProtKB/Swiss-Prot

A6NJ46

Related

ENSP00000429553.2, ENST00000524115.2

Conserved Domains (1) summary

cl00084
Location:55 → 66

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.