KDM3A Gene (Protein Coding)

Lysine Demethylase 3A

GC02P086440
GIFtS:
41
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] See more...

Aliases for KDM3A Gene

Aliases for KDM3A Gene

  • Lysine Demethylase 3A 2 3 5
  • TSGA 2 3 4
  • JmjC Domain-Containing Histone Demethylation Protein 2A 3 4
  • Jumonji C Domain-Containing Histone Demethylase 2A 2 3
  • [Histone H3]-Dimethyl-L-Lysine(9) Demethylase 3A 3 4
  • Jumonji Domain-Containing Protein 1A 3 4
  • Lysine (K)-Specific Demethylase 3A 2 3
  • Lysine-Specific Demethylase 3A 3 4
  • KIAA0742 2 4
  • JHDM2A 3 4
  • JHMD2A 2 3
  • JMJD1A 3 4
  • JMJD1 3 4
  • Jumonji Domain Containing 1A 2
  • Jumonji Domain Containing 1 2
  • Testis-Specific Protein A 3
  • EC 1.14.11.65 4
  • EC 1.14.11 50
  • KDM3A 5

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. Diseases associated with KDM3A include Ewing Sarcoma and Familial Isolated Hypoparathyroidism. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. 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 Summary 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 , Rfam classification and piRNA Summary for KDM3A Gene

Genomics for KDM3A Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for KDM3A Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KDM3A

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

Genomic Locations for KDM3A Gene

Latest Assembly
chr2:86,440,647-86,492,716
(GRCh38/hg38)
Size:
52,070 bases
Orientation:
Plus strand

Previous Assembly
chr2:86,668,494-86,719,839
(GRCh37/hg19 by Entrez Gene)
Size:
51,346 bases
Orientation:
Plus strand

chr2:86,667,770-86,719,839
(GRCh37/hg19 by Ensembl)
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 Structure • Gene Density

RefSeq DNA sequence for KDM3A Gene

Proteins for KDM3A Gene

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  • 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=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for KDM3A Gene

Protein Expression for KDM3A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for KDM3A Gene

Q9Y4C1:
  • GVREMCD
  • SPVFCRF
  • CRFFHFRRL
  • DHDPIHDQSWYLD
  • GTTNLHLDVSDA
  • THTNHEDKLQVKN
  • NVMVYVGIP
  • ILTPVSNNN
  • IITGATVGDFW
  • GVLRVEGFL
  • PESFRKEFG
  • MSTIEPHRQVAWKRAV
  • KCRECRL
  • PGKALYDV
  • VLKLKDWP
  • CDTTIFNLHWVCP
  • DIVHSVR
  • GVQGWAIVQFLGD
  • HEPENLMPTQI
  • NIPLPEYTRR
  • ECWKQGQP
  • KWGIKANCPC
  • EDFVSPEH
  • EKPGALWHIYAAKDTEKIREFLKKV
  • YFVRPDLGPKMYNAYGLIT
  • TSGNVNKENKEK

Post-translational modifications for KDM3A Gene

  • Ubiquitination at Lys851, Lys895, Lys905, and Lys918
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM3A Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for KDM3A Gene

Gene Families for KDM3A Gene

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

Protein Domains for KDM3A Gene

InterPro:

Suggested Antigen Peptide Sequences for KDM3A Gene

GenScript: Design optimal peptide antigens:
  • Jumonji domain containing 1A, isoform CRA_b (D6W5M4_HUMAN)
  • Jumonji domain-containing protein 1A (KDM3A_HUMAN)

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

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  6. Cell Lines for research

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2 2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl(9)-[histone H3] + 2 succinate; Xref=Rhea:RHEA:60188, Rhea:RHEA-COMP:15541, Rhea:RHEA-COMP:15546, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031, ChEBI:CHEBI:61976; EC=1.14.11.65; Evidence={ECO:0000269|PubMed:16603237};.

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:0003682 chromatin binding IEA --
GO:0003712 transcription coregulator activity IBA 21873635
GO:0005506 iron ion binding IMP 16603237
GO:0005515 protein binding IPI 25535969
GO:0016491 oxidoreductase activity IEA --
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 Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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
extracellular 2
cytoskeleton 2
mitochondrion 2
cytosol 2
plasma membrane 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex IBA 21873635
GO:0000785 chromatin IBA 21873635
GO:0005634 nucleus IEA,IDA 16603237
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
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 BioSystems pathway 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:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007283 spermatogenesis IEA --
GO:0007290 spermatid nucleus elongation IEA --
GO:0009755 hormone-mediated signaling pathway IDA 16603237
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

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No Compound Related Data Available

Transcripts for KDM3A Gene

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mRNA/cDNA for KDM3A Gene

2 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

Expression for KDM3A Gene

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

mRNA expression in normal human tissues for KDM3A Gene
mRNA expression by BioGPS for KDM3A GenemRNA expression by GTEx 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KDM3A

SOURCE GeneReport for Unigene cluster for KDM3A Gene:

Hs.557425

Evidence on tissue expression from TISSUES for KDM3A Gene

  • Nervous system(4.8)
  • Skin(2.5)
  • Blood(2.4)
  • Bone marrow(2.4)
  • Muscle(2.3)
  • Heart(2.3)
  • Lung(2.3)
  • Kidney(2.3)
  • Eye(2.2)
  • Intestine(2.2)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with KDM3A: view

Primer products for research

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 29 30
  • 99.52 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia KDM3A 29 30
  • 92.02 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia KDM3A 29 30
  • 90.41 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Kdm3a 29 16 30
  • 89.23 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Kdm3a 29
  • 88.67 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia KDM3A 30
  • 77 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia KDM3A 30
  • 74 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves KDM3A 29 30
  • 71.52 (n)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia kdm3a 29
  • 62.84 (n)
Str.15267 29
African clawed frog
(Xenopus laevis)
 Amphibia Xl.2818 29
Fruit Fly
(Drosophila melanogaster)
 Insecta JHDM2 30
  • 39 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.7055 30
  • 39 (a)
 OneToMany
Species where no ortholog for KDM3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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
Alliance of Genome Resources:
Additional Orthologs for KDM3A

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

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KDM3A Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
835013 Uncertain Significance: not provided 86,466,385(+) AG/A
NM_018433.6(KDM3A):c.1022del (p.Ser341fs) 		FRAMESHIFT
rs1207228552 Likely Benign: not provided 86,451,218(+) A/G
NM_018433.6(KDM3A):c.453+5A>G 		INTRON
rs193921056 Uncertain Significance: Malignant tumor of prostate 86,482,107(+) GTGTT/G
NM_018433.6(KDM3A):c.2685+6TGTT[2] 		INTRON
rs34673273 Benign: not provided 86,482,581(+) C/T
NM_018433.6(KDM3A):c.2809C>T (p.Leu937=) 		SYNONYMOUS
rs569604500 Likely Benign: not provided 86,485,753(+) T/C
NM_018433.6(KDM3A):c.3207T>C (p.Ile1069=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for KDM3A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
Leiden Open Variation Database (LOVD)
KDM3A

SNP Genotyping and Copy Number Assays for research

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

Disorders for KDM3A Gene

MalaCards: The human disease database

(2) MalaCards diseases for KDM3A Gene - From: COP and GCD

Disorder Aliases PubMed IDs
ewing sarcoma
  • es
familial isolated hypoparathyroidism
  • fih
- elite association - COSMIC cancer census association via MalaCards
Search KDM3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for KDM3A

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with KDM3A: view

No data available for 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
  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
  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 40
  4. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. (PMID: 16603237) Yamane K … Zhang Y (Cell 2006) 3 4
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4

ExternalLinks

View latest publications for KDM3A gene in Mastermind

Products for KDM3A Gene

  • Addgene plasmids for KDM3A

Sources for KDM3A Gene