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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. GO annotations related to this gene include RNA polymerase II core promoter proximal region sequence-specific DNA binding and transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding. An important paralog of this gene is NKX3-1.

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).

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

Regulatory Elements for NKX3-2 Gene

Enhancers for NKX3-2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G013625 1.4 ENCODE dbSUPER 10.4 -82.3 -82292 3.1 HDGF FOXA2 PKNOX1 CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A DMAP1 HSP90AB2P NKX3-2 LINC01096 LOC101929048 BOD1L1 PIR58938
GH04G013546 1.2 Ensembl ENCODE 8.1 -2.3 -2324 2.0 RB1 ARID4B FEZF1 RAD21 GLIS2 ZNF143 ZNF207 EGR2 ZNF263 ZNF654 LINC01096 NKX3-2
GH04G013482 1.5 FANTOM5 ENCODE 5.4 +60.9 60850 2.8 PKNOX1 ARNT ARID4B SIN3A YY1 ZNF207 SP3 SP5 ZHX2 NFYC BOD1L1 NKX3-2 RAB28 GC04P013478
GH04G013656 0.9 Ensembl ENCODE 6.9 -111.9 -111868 1.5 CTCF ZNF654 ZNF362 TEAD4 TRIM22 ZNF384 REST RAD21 YY1 ZFHX2 NKX3-2 LINC01182 GC04P013713
GH04G013647 0.4 Ensembl 7.2 -102.1 -102051 0.2 NRF1 NKX3-2 RPL32P12 LOC100288683
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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

Promoters for NKX3-2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000166033 350 1001 PKNOX1 ATF1 CREB3L1 ARID4B DMAP1 GLIS2 ZNF202 SP3 SP5 NFYC

Transcription factor binding sites by QIAGEN in the NKX3-2 gene promoter:

Genomic Location for NKX3-2 Gene

Chromosome:
4
Start:
13,540,830 bp from pter
End:
13,545,050 bp from pter
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:

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

Domains & Families for NKX3-2 Gene

Gene Families for NKX3-2 Gene

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 core promoter proximal region sequence-specific DNA binding IEA --
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific 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

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

Clone Products

No data available for Enzyme Numbers (IUBMB) 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

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 from RNA polymerase II promoter IEA --
GO:0001501 skeletal system development TAS 9344671
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter 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:

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
Organs:
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 35
  • 99.38 (n)
cow
(Bos Taurus)
Mammalia NKX3-2 34 35
  • 89.7 (n)
dog
(Canis familiaris)
Mammalia NKX3-2 34 35
  • 87.71 (n)
mouse
(Mus musculus)
Mammalia Nkx3-2 34 16 35
  • 83.98 (n)
oppossum
(Monodelphis domestica)
Mammalia NKX3-2 35
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nkx3-2 34
  • 66.67 (n)
African clawed frog
(Xenopus laevis)
Amphibia bapx1-A 34
zebrafish
(Danio rerio)
Actinopterygii nkx3.2 34 35
  • 67.49 (n)
bapx1 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6919 34
fruit fly
(Drosophila melanogaster)
Insecta bap 35
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-27 35
  • 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)

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 Sequence Context AA Info Type
rs606231352 Pathogenic 13,544,077(-) GGGGG(-/G)CCAGC reference, frameshift-variant
rs606231353 Pathogenic 13,544,078(-) CGGGG(GG/T)CCAGC reference, frameshift-variant
rs606231354 Pathogenic 13,544,305(-) CCCGG(-/CGCCCGG)GGGCA reference, frameshift-variant
rs536700699 Uncertain significance 13,544,236(+) CGCCC(A/G)CGTCC reference, missense
rs758464634 Uncertain significance 13,543,931(+) ATCCC(A/C/T)GCGAA 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)

Relevant External Links 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: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spondylo-megaepiphyseal-metaphyseal dysplasia
  • smmd
bone osteosarcoma
  • osteosarcoma of bone
otospondylomegaepiphyseal dysplasia
  • chondrodystrophy with sensorineural deafness
- 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.

Relevant External Links for NKX3-2

Human Genome Epidemiology (HuGE) Navigator
NKX3-2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 K. … Murray J.C. (Genomics 1997) 2 3 4 64
  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. (Mech. Dev. 1997) 3 4 22 64
  3. Homozygous inactivating mutations in the NKX3-2 gene result in spondylo-megaepiphyseal-metaphyseal dysplasia. (PMID: 20004766) Hellemans J. … Mortier G. (Am. J. Hum. Genet. 2009) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  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 64

Products for NKX3-2 Gene

Sources for NKX3-2 Gene

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