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Aliases for KDM3A Gene

Aliases for KDM3A Gene

  • Lysine Demethylase 3A 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 2A 3 4
  • Jumonji C Domain-Containing Histone Demethylase 2A 2 3
  • Jumonji Domain-Containing Protein 1A 3 4
  • Lysine (K)-Specific Demethylase 3A 2 3
  • JMJD1A 3 4
  • JHDM2A 3 4
  • JMJD1 3 4
  • TSGA 3 4
  • Lysine-Specific Demethylase 3A 3
  • Jumonji Domain Containing 1A 2
  • Jumonji Domain Containing 1 2
  • Testis-Specific Protein A 3
  • EC 1.14.11.- 4
  • KIAA0742 4
  • JHMD2A 3

External Ids for KDM3A Gene

Previous HGNC Symbols for KDM3A Gene

  • JMJD1
  • JMJD1A

Previous GeneCards Identifiers for KDM3A Gene

  • GC02P086521
  • GC02P086667

Summaries for KDM3A Gene

Entrez Gene Summary for KDM3A Gene

  • This gene encodes a zinc finger protein that contains a jumonji domain and may play a role in hormone-dependent transcriptional activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

GeneCards Summary for KDM3A Gene

KDM3A (Lysine Demethylase 3A) is a Protein Coding gene. Among its related pathways are Coregulation of Androgen receptor activity and Chromatin organization. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and core promoter binding. An important paralog of this gene is KDM3B.

UniProtKB/Swiss-Prot for KDM3A Gene

  • Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code. Preferentially demethylates mono- and dimethylated H3 Lys-9 residue, with a preference for dimethylated residue, while it has weak or no activity on trimethylated H3 Lys-9. Demethylation of Lys residue generates formaldehyde and succinate. Involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes, resulting in H3 Lys-9 demethylation and transcriptional activation. Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TNP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1.

Additional gene information for KDM3A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM3A Gene

Genomics for KDM3A Gene

GeneHancer (GH) Regulatory Elements for KDM3A Gene

Promoters and enhancers for KDM3A 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
GH02J086440 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 680.1 +1.4 1378 3.6 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 KDM3A GC02M086437 LOC102724642 SNORD94 C2orf68 ENSG00000231259 USP39 LOC100420889 LOC105374845 PTCD3
GH02J086439 Enhancer 0.9 ENCODE dbSUPER 661.2 -0.6 -613 0.1 SMARCA5 ARNT ZMYM3 ZEB2 KLF5 ZNF507 CHAMP1 ZNF280A ZNF217 CBX5 KDM3A GC02M086437 LOC102724642 SNORD94 GC02P086423 GC02M086423 GC02M086424
GH02J085536 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 34.8 -900.9 -900887 6.9 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 GC02M085541 PARTICL PIR40998 PIR39955 MAT2A USP39 SNORD94 C2orf68 LOC100996506 KDM3A
GH02J086193 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 32.9 -245.2 -245199 3.9 ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 IMMT GC02P086196 MRPL35 ENSG00000273080 LOC102724642 SNORD94 ENSG00000231259 LOC100420889 KDM3A USP39
GH02J085740 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.7 -697.1 -697146 5.4 PKNOX1 FOXA2 SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF416 DEK REST SNORD94 KDM3A POLR1A USP39 LOC100996506 C2orf68 LOC105374845 ELMOD3 PTCD3 MAT2A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KDM3A gene promoter:
  • STAT3
  • Egr-3
  • CUTL1
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • NF-Y
  • CBF(2)

Genomic Locations for KDM3A Gene

Genomic Locations for KDM3A Gene
chr2:86,440,647-86,492,716
(GRCh38/hg38)
Size:
52,070 bases
Orientation:
Plus strand
chr2:86,667,770-86,719,839
(GRCh37/hg19)
Size:
52,070 bases
Orientation:
Plus strand

Genomic View for KDM3A Gene

Genes around KDM3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM3A Gene

Proteins for KDM3A Gene

  • Protein details for KDM3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4C1-KDM3A_HUMAN
    Recommended name:
    Lysine-specific demethylase 3A
    Protein Accession:
    Q9Y4C1
    Secondary Accessions:
    • D6W5M3
    • Q53S72
    • Q68D47
    • Q68UT9
    • Q6N050
    • Q8IY08

    Protein attributes for KDM3A Gene

    Size:
    1321 amino acids
    Molecular mass:
    147341 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA34462.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for KDM3A Gene

Post-translational modifications for KDM3A Gene

  • Ubiquitination at isoforms=918, Lys905, Lys895, and isoforms=851
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for KDM3A Gene

Domains & Families for KDM3A Gene

Gene Families for KDM3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for KDM3A Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for KDM3A Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y4C1

UniProtKB/Swiss-Prot:

KDM3A_HUMAN :
  • The JmjC domain and the C6-type zinc-finger are required for the demethylation activity.
  • Belongs to the JHDM2 histone demethylase family.
Domain:
  • The JmjC domain and the C6-type zinc-finger are required for the demethylation activity.
  • Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors.
Family:
  • Belongs to the JHDM2 histone demethylase family.
genes like me logo Genes that share domains with KDM3A: view

Function for KDM3A Gene

Molecular function for KDM3A Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code. Preferentially demethylates mono- and dimethylated H3 Lys-9 residue, with a preference for dimethylated residue, while it has weak or no activity on trimethylated H3 Lys-9. Demethylation of Lys residue generates formaldehyde and succinate. Involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes, resulting in H3 Lys-9 demethylation and transcriptional activation. Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TNP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1.

Enzyme Numbers (IUBMB) for KDM3A Gene

Phenotypes From GWAS Catalog for KDM3A Gene

Gene Ontology (GO) - Molecular Function for KDM3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IBA --
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005506 iron ion binding IMP 16603237
GO:0005515 protein binding IPI 25535969
genes like me logo Genes that share ontologies with KDM3A: view
genes like me logo Genes that share phenotypes with KDM3A: view

Animal Models for KDM3A Gene

MGI Knock Outs for KDM3A:

Animal Model Products

Clone Products

  • Addgene plasmids for KDM3A

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM3A Gene

Localization for KDM3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM3A Gene

Cytoplasm. Nucleus. Note=Nuclear in round spermatids. When spermatids start to elongate, localizes to the cytoplasm where it forms distinct foci which disappear in mature spermatozoa (By similarity). {ECO:0000250}.

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 KDM3A gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for KDM3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus IDA,IEA 16603237
GO:0005654 nucleoplasm TAS,IDA --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with KDM3A: view

Pathways & Interactions for KDM3A Gene

genes like me logo Genes that share pathways with KDM3A: view

Pathways by source for KDM3A Gene

1 KEGG pathway for KDM3A Gene

Gene Ontology (GO) - Biological Process for KDM3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA,IBA --
GO:0007283 spermatogenesis IEA --
GO:0007290 spermatid nucleus elongation IEA --
genes like me logo Genes that share ontologies with KDM3A: view

No data available for SIGNOR curated interactions for KDM3A Gene

Drugs & Compounds for KDM3A Gene

No Compound Related Data Available

Transcripts for KDM3A Gene

Unigene Clusters for KDM3A Gene

Lysine (K)-specific demethylase 3A:
Representative Sequences:

Clone Products

  • Addgene plasmids for KDM3A

Alternative Splicing Database (ASD) splice patterns (SP) for KDM3A Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^
SP1: - - - -
SP2: - - - -
SP3:
SP4:
SP5:
SP6:
SP7: - - -
SP8:
SP9:
SP10:

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b · 27c ^ 28 ^ 29 ^ 30 ^ 31
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for KDM3A Gene

GeneLoc Exon Structure for
KDM3A
ECgene alternative splicing isoforms for
KDM3A

Expression for KDM3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM3A Gene

Protein differential expression in normal tissues from HIPED for KDM3A Gene

This gene is overexpressed in Brain (40.0), Breast (7.7), and Lung (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for KDM3A Gene



NURSA nuclear receptor signaling pathways regulating expression of KDM3A Gene:

KDM3A

SOURCE GeneReport for Unigene cluster for KDM3A Gene:

Hs.557425

Evidence on tissue expression from TISSUES for KDM3A Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with KDM3A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM3A Gene

Orthologs for KDM3A Gene

This gene was present in the common ancestor of animals.

Orthologs for KDM3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM3A 34 33
  • 99.52 (n)
OneToOne
dog
(Canis familiaris)
Mammalia KDM3A 34 33
  • 92.02 (n)
OneToOne
cow
(Bos Taurus)
Mammalia KDM3A 34 33
  • 90.41 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm3a 16 34 33
  • 89.23 (n)
rat
(Rattus norvegicus)
Mammalia Kdm3a 33
  • 88.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM3A 34
  • 77 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM3A 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM3A 34 33
  • 71.52 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm3a 33
  • 62.84 (n)
Str.15267 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.2818 33
fruit fly
(Drosophila melanogaster)
Insecta JHDM2 34
  • 39 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7055 34
  • 39 (a)
OneToMany
Species where no ortholog for KDM3A 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for KDM3A Gene

ENSEMBL:
Gene Tree for KDM3A (if available)
TreeFam:
Gene Tree for KDM3A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KDM3A: view image

Paralogs for KDM3A Gene

Paralogs for KDM3A Gene

(4) SIMAP similar genes for KDM3A Gene using alignment to 5 proteins:

  • KDM3A_HUMAN
  • C9J7Q7_HUMAN
  • C9JC73_HUMAN
  • F5H070_HUMAN
  • F8WE62_HUMAN

Pseudogenes.org Pseudogenes for KDM3A Gene

genes like me logo Genes that share paralogs with KDM3A: view

Variants for KDM3A Gene

Sequence variations from dbSNP and Humsavar for KDM3A Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs193921056 uncertain-significance, Malignant tumor of prostate 86,482,108(+) TGTTTGTTTGTT/TGTTTGTT intron_variant
VAR_035940 A breast cancer sample p.Asp187His
rs1000034803 -- 86,480,915(+) C/T intron_variant
rs1000069536 -- 86,446,620(+) G/T intron_variant
rs1000212817 -- 86,469,626(+) AT/ intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KDM3A Gene

Variant ID Type Subtype PubMed ID
nsv1129640 CNV tandem duplication 24896259
nsv2813 CNV insertion 18451855

Variation tolerance for KDM3A Gene

Residual Variation Intolerance Score: 2.95% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.75; 66.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDM3A Gene

Human Gene Mutation Database (HGMD)
KDM3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM3A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM3A Gene

Disorders for KDM3A Gene

Additional Disease Information for KDM3A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for KDM3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM3A Gene

Publications for KDM3A Gene

  1. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  2. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. (PMID: 28262558) Tumber A … Brennan PE (Cell chemical biology 2017) 3 4 58
  3. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PMID: 20378615) Aston KI … Carrell DT (Human reproduction (Oxford, England) 2010) 3 44 58
  4. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. (PMID: 16603237) Yamane K … Zhang Y (Cell 2006) 3 4 58
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58

Products for KDM3A Gene

Sources for KDM3A Gene

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