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

Gene ID: 159296, updated on 1-Mar-2024

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
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Genomic context

See NKX2-3 in Genome Data Viewer
Location:
10q24.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (99532942..99536524)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (100408890..100418489)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (101292699..101296281)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:101280549-101281428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:101281429-101282308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:101282309-101283188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:101292029-101292920 Neighboring gene long intergenic non-protein coding RNA 1475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:101299909-101300617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:101355523-101356023 Neighboring gene small nucleolar RNA U13 Neighboring gene solute carrier family 25 member 28 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:101379422-101380004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:101380588-101381170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:101381171-101381752 Neighboring gene SLC25A28 divergent transcript

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in CD4-positive, alpha-beta T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in Peyer's patch development IEA
Inferred from Electronic Annotation
more info
 
involved_in biological_process ND
No biological Data available
more info
 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in gland morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte migration IEA
Inferred from Electronic Annotation
more info
 
involved_in lymph node development IEA
Inferred from Electronic Annotation
more info
 
involved_in macrophage differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
involved_in plasma cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in post-embryonic digestive tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in 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
 
involved_in spleen development IEA
Inferred from Electronic Annotation
more info
 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in triglyceride metabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

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

  1. NG_016854.1 RefSeqGene

    Range
    5010..8592
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_145285.3NP_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:148204
    HOX; Homeodomain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    99532942..99536524
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    100408890..100418489
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364924.1XP_054220899.1  homeobox protein Nkx-2.3 isoform X1

  2. XM_054364923.1XP_054220898.1  homeobox protein Nkx-2.3 isoform X2

    UniProtKB/Swiss-Prot
    B4DUZ4, Q8TAU0, Q9NYS6