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NKX3-2 NK3 homeobox 2 [ Homo sapiens (human) ]

Gene ID: 579, updated on 1-Mar-2024

Summary

Official Symbol
NKX3-2provided by HGNC
Official Full Name
NK3 homeobox 2provided by HGNC
Primary source
HGNC:HGNC:951
See related
Ensembl:ENSG00000109705 MIM:602183; AllianceGenome:HGNC:951
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
SMMD; BAPX1; NKX3B; NKX3.2
Summary
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; negative regulation of chondrocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; embryonic skeletal system development; and intestinal epithelial cell development. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in spleen (RPKM 1.5), ovary (RPKM 0.7) and 10 other tissues See more
Orthologs
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Genomic context

See NKX3-2 in Genome Data Viewer
Location:
4p15.33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (13540830..13547744, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (13520522..13527516, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (13542454..13546132, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900669 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:13524914-13526113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21325 Neighboring gene long intergenic non-protein coding RNA 1097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:13548258-13548758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:13548759-13549259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15288 Neighboring gene Sharpr-MPRA regulatory region 12016 Neighboring gene long intergenic non-protein coding RNA 1096 Neighboring gene biorientation of chromosomes in cell division 1 like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:13600786-13601286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:13601287-13601787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15289 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:13628778-13629508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:13629509-13630239 Neighboring gene microRNA 5091

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

Associated conditions

Description Tests
Spondylo-megaepiphyseal-metaphyseal dysplasia
MedGen: C2750066 OMIM: 613330 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC138171

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in animal organ formation IEA
Inferred from Electronic Annotation
more info
 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in determination of left/right symmetry IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
involved_in intestinal epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in middle ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in pancreas development 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 skeletal system development TAS
Traceable Author Statement
more info
PubMed 
involved_in skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in spleen development IEA
Inferred from Electronic Annotation
more info
 
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
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-3.2
Names
bagpipe homeobox protein homolog 1
homeobox protein NK-3 homolog B

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_023192.1 RefSeqGene

    Range
    4983..8661
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001189.4NP_001180.1  homeobox protein Nkx-3.2

    See identical proteins and their annotated locations for NP_001180.1

    Status: REVIEWED

    Source sequence(s)
    AC006445, BC111966
    Consensus CDS
    CCDS3410.1
    UniProtKB/Swiss-Prot
    P78367, Q2M2I7
    Related
    ENSP00000371875.5, ENST00000382438.6
    Conserved Domains (1) summary
    pfam00046
    Location:209262
    Homeobox; Homeobox domain

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    13540830..13547744 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416050.1XP_047272006.1  homeobox protein Nkx-3.2 isoform X1

    UniProtKB/Swiss-Prot
    P78367, Q2M2I7
  2. XM_047416049.1XP_047272005.1  homeobox protein Nkx-3.2 isoform X1

    UniProtKB/Swiss-Prot
    P78367, Q2M2I7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    13520522..13527516 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350659.1XP_054206634.1  homeobox protein Nkx-3.2 isoform X1

    UniProtKB/Swiss-Prot
    P78367, Q2M2I7