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Aliases for NKX3-2 Gene

Aliases for NKX3-2 Gene

  • NK3 Homeobox 2 2 3 5
  • Bagpipe Homeobox Protein Homolog 1 3 4
  • Homeobox Protein NK-3 Homolog B 3 4
  • BAPX1 3 4
  • NKX3B 3 4
  • Bagpipe Homeobox Homolog 1 (Drosophila) 2
  • Homeobox Protein Nkx-3.2 3
  • NKX3.2 3
  • SMMD 3

External Ids for NKX3-2 Gene

Previous HGNC Symbols for NKX3-2 Gene

  • BAPX1

Previous GeneCards Identifiers for NKX3-2 Gene

  • GC04M013152
  • GC04M012880

Summaries for NKX3-2 Gene

Entrez Gene Summary for NKX3-2 Gene

  • This gene encodes a member of the NK family of homeobox-containing proteins. The encoded protein may play a role in skeletal development. [provided by RefSeq, Jul 2008]

GeneCards Summary for NKX3-2 Gene

NKX3-2 (NK3 Homeobox 2) is a Protein Coding gene. Diseases associated with NKX3-2 include Spondylo-Megaepiphyseal-Metaphyseal Dysplasia and Bone Osteosarcoma. Among its related pathways are Endochondral Ossification. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is HMX3.

UniProtKB/Swiss-Prot for NKX3-2 Gene

  • Transcriptional repressor that acts as a negative regulator of chondrocyte maturation. PLays a role in distal stomach development; required for proper antral-pyloric morphogenesis and development of antral-type epithelium. In concert with GSC, defines the structural components of the middle ear; required for tympanic ring and gonium development and in the regulation of the width of the malleus (By similarity).

Additional gene information for NKX3-2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NKX3-2 Gene

Genomics for NKX3-2 Gene

GeneHancer (GH) Regulatory Elements for NKX3-2 Gene

Promoters and enhancers for NKX3-2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J013544 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 663.8 +0.1 117 1.5 PKNOX1 ATF1 ARID4B SIN3A DMAP1 GLIS2 ZFP91 ATF7 ZNF202 SP3 NKX3-2 BOD1L1 LINC01097
GH04J013482 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 17.2 +60.9 60850 2.8 PKNOX1 ARNT ARID4B SIN3A YY1 ZNF213 ZNF207 SP3 SP5 NFYC RAB28 LOC105374495 NKX3-2 BOD1L1 GC04P013478
GH04J013546 Enhancer 0.9 Ensembl ENCODE 8.1 -2.3 -2323 2 KLF1 USF1 SUZ12 BACH1 ZFHX2 GLIS2 POLR2A PATZ1 KLF8 EZH2 LINC01096 NKX3-2
GH04J013656 Enhancer 0.8 Ensembl ENCODE 6.9 -111.9 -111867 1.5 CTCF ZNF654 ZNF362 TRIM22 REST ZNF384 RAD21 YY1 SP1 ZFHX2 LINC01182 NKX3-2 GC04P013713
GH04J013647 Enhancer 0.2 Ensembl 7.2 -102.1 -102051 0.2 RPL32P12 NKX3-2 LOC100288683
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NKX3-2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NKX3-2 gene promoter:
  • Arnt
  • Sox9

Genomic Locations for NKX3-2 Gene

Genomic Locations for NKX3-2 Gene
chr4:13,540,830-13,545,050
(GRCh38/hg38)
Size:
4,221 bases
Orientation:
Minus strand
chr4:13,542,454-13,546,674
(GRCh37/hg19)
Size:
4,221 bases
Orientation:
Minus strand

Genomic View for NKX3-2 Gene

Genes around NKX3-2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKX3-2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKX3-2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKX3-2 Gene

Proteins for NKX3-2 Gene

  • Protein details for NKX3-2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78367-NKX32_HUMAN
    Recommended name:
    Homeobox protein Nkx-3.2
    Protein Accession:
    P78367
    Secondary Accessions:
    • Q2M2I7

    Protein attributes for NKX3-2 Gene

    Size:
    333 amino acids
    Molecular mass:
    34814 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NKX3-2 Gene

Post-translational modifications for NKX3-2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKX3-2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for NKX3-2
  • Boster Bio Antibodies for NKX3-2
  • Santa Cruz Biotechnology (SCBT) Antibodies for NKX3-2

No data available for DME Specific Peptides for NKX3-2 Gene

Domains & Families for NKX3-2 Gene

Gene Families for NKX3-2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for NKX3-2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P78367

UniProtKB/Swiss-Prot:

NKX32_HUMAN :
  • Belongs to the NK-3 homeobox family.
Family:
  • Belongs to the NK-3 homeobox family.
genes like me logo Genes that share domains with NKX3-2: view

Function for NKX3-2 Gene

Molecular function for NKX3-2 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor that acts as a negative regulator of chondrocyte maturation. PLays a role in distal stomach development; required for proper antral-pyloric morphogenesis and development of antral-type epithelium. In concert with GSC, defines the structural components of the middle ear; required for tympanic ring and gonium development and in the regulation of the width of the malleus (By similarity).

Gene Ontology (GO) - Molecular Function for NKX3-2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with NKX3-2: view
genes like me logo Genes that share phenotypes with NKX3-2: view

Human Phenotype Ontology for NKX3-2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NKX3-2 Gene

MGI Knock Outs for NKX3-2:

Animal Model Products

CRISPR Products

Targeted motifs for NKX3-2 Gene
HOMER Transcription Factor Regulatory Elements motif NKX3-2
  • Consensus sequence: TTRAGTGSYK Submotif: canonical Cell Type: VertebralCol GEO ID: GSE36672

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX3-2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog and Transcription Factor Targets for NKX3-2 Gene

Localization for NKX3-2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKX3-2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NKX3-2 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NKX3-2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with NKX3-2: view

Pathways & Interactions for NKX3-2 Gene

SuperPathways for NKX3-2 Gene

SuperPathway Contained pathways
1 Endochondral Ossification
genes like me logo Genes that share pathways with NKX3-2: view

Pathways by source for NKX3-2 Gene

1 BioSystems pathway for NKX3-2 Gene

Gene Ontology (GO) - Biological Process for NKX3-2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001501 skeletal system development TAS,IEA 9344671
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 9344671
genes like me logo Genes that share ontologies with NKX3-2: view

No data available for SIGNOR curated interactions for NKX3-2 Gene

Drugs & Compounds for NKX3-2 Gene

No Compound Related Data Available

Transcripts for NKX3-2 Gene

mRNA/cDNA for NKX3-2 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(5) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NKX3-2 Gene

NK3 homeobox 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX3-2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NKX3-2 Gene

No ASD Table

Relevant External Links for NKX3-2 Gene

GeneLoc Exon Structure for
NKX3-2
ECgene alternative splicing isoforms for
NKX3-2

Expression for NKX3-2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NKX3-2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NKX3-2 Gene

This gene is overexpressed in Colon - Sigmoid (x19.2), Colon - Transverse (x8.4), and Stomach (x4.2).

SOURCE GeneReport for Unigene cluster for NKX3-2 Gene:

Hs.590927

mRNA Expression by UniProt/SwissProt for NKX3-2 Gene:

P78367-NKX32_HUMAN
Tissue specificity: Expressed at highest levels in cartilage, bone (osteosarcoma) and gut (small intestine and colon), whereas moderate expression is seen in trachea and brain. Expressed in visceral mesoderm and embryonic skeleton.

Phenotype-based relationships between genes and organs from Gene ORGANizer for NKX3-2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • eye
  • head
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
Pelvis:
  • pelvis
  • testicle
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with NKX3-2: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES for NKX3-2 Gene

Orthologs for NKX3-2 Gene

This gene was present in the common ancestor of animals.

Orthologs for NKX3-2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NKX3-2 34 33
  • 99.38 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NKX3-2 34 33
  • 89.7 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NKX3-2 34 33
  • 87.71 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nkx3-2 16 34 33
  • 83.98 (n)
oppossum
(Monodelphis domestica)
Mammalia NKX3-2 34
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nkx3-2 33
  • 66.67 (n)
African clawed frog
(Xenopus laevis)
Amphibia bapx1-A 33
zebrafish
(Danio rerio)
Actinopterygii nkx3.2 34 33
  • 67.49 (n)
OneToOne
bapx1 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6919 33
fruit fly
(Drosophila melanogaster)
Insecta bap 34
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-27 34
  • 19 (a)
ManyToMany
Species where no ortholog for NKX3-2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NKX3-2 Gene

ENSEMBL:
Gene Tree for NKX3-2 (if available)
TreeFam:
Gene Tree for NKX3-2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NKX3-2: view image

Paralogs for NKX3-2 Gene

Paralogs for NKX3-2 Gene

genes like me logo Genes that share paralogs with NKX3-2: view

Variants for NKX3-2 Gene

Sequence variations from dbSNP and Humsavar for NKX3-2 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs606231352 pathogenic, Spondylo-megaepiphyseal-metaphyseal dysplasia 13,544,078(-) CCCCCC/CCCCCCC coding_sequence_variant, frameshift
rs606231353 pathogenic, Spondylo-megaepiphyseal-metaphyseal dysplasia 13,544,078(-) CC/A coding_sequence_variant, frameshift
rs606231354 pathogenic, Spondylo-megaepiphyseal-metaphyseal dysplasia 13,544,305(-) CCGGGCGCCGGGCGCC/CCGGGCGCC coding_sequence_variant, frameshift
rs536700699 uncertain-significance, not specified 13,544,236(-) G/A/T coding_sequence_variant, missense_variant
rs758464634 uncertain-significance, not specified 13,543,931(-) C/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NKX3-2 Gene

Variant ID Type Subtype PubMed ID
nsv1014473 CNV gain 25217958
nsv593750 CNV gain 21841781

Variation tolerance for NKX3-2 Gene

Gene Damage Index Score: 1.68; 32.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NKX3-2 Gene

Human Gene Mutation Database (HGMD)
NKX3-2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NKX3-2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKX3-2 Gene

Disorders for NKX3-2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NKX3-2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

NKX32_HUMAN
  • Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD) [MIM:613330]: A skeletal dysplasia characterized by disproportionate short stature with a short and stiff neck and trunk, relatively long limbs that may show flexion contractures of the distal joints, delayed and impaired ossification of the vertebral bodies, the presence of large epiphyseal ossification centers and wide growth plates in the long tubular bones, and numerous pseudoepiphyses of the short tubular bones in hands and feet. {ECO:0000269 PubMed:20004766}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NKX3-2

genes like me logo Genes that share disorders with NKX3-2: view

No data available for Genatlas for NKX3-2 Gene

Publications for NKX3-2 Gene

  1. Sequence and chromosomal assignment of human BAPX1, a bagpipe-related gene, to 4p16.1: a candidate gene for skeletal dysplasia. (PMID: 9344671) Yoshiura KI … Murray JC (Genomics 1997) 2 3 4 58
  2. Bapx1: an evolutionary conserved homologue of the Drosophila bagpipe homeobox gene is expressed in splanchnic mesoderm and the embryonic skeleton. (PMID: 9256352) Tribioli C … Lufkin T (Mechanisms of development 1997) 3 4 22 58
  3. Homozygous inactivating mutations in the NKX3-2 gene result in spondylo-megaepiphyseal-metaphyseal dysplasia. (PMID: 20004766) Hellemans J … Mortier G (American journal of human genetics 2009) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Molecular cloning, chromosomal mapping and developmental expression of BAPX1, a novel human homeobox-containing gene homologous to Drosophila bagpipe. (PMID: 9426254) Tribioli C … Lufkin T (Gene 1997) 3 4 58

Products for NKX3-2 Gene

Sources for NKX3-2 Gene

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