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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
  • EC 1.14.11 61
  • 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 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin organization. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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 TMP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1.

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

Genomics for KDM3A Gene

Regulatory Elements for KDM3A Gene

Enhancers for KDM3A 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
GH02F086193 1.2 ENCODE 10.1 -245.2 -245200 3.9 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 IMMT SNORD94 LOC102724642 ENSG00000231259 LOC100420889 LOC100996506 TMEM150A LOC105374845 C2orf68 ATOH8
GH02F086392 1.1 Ensembl ENCODE 10.6 -46.9 -46933 1.6 HDAC1 PKNOX1 ZNF133 ARID4B FEZF1 ZEB1 GATA2 FOS EGR2 ZNF362 REEP1 ENSG00000251974 KDM3A ENSG00000202537 RNU6-640P CHMP3 POLR1A MRPL35 GC02P086411
GH02F086216 1.1 Ensembl ENCODE 10.1 -223.5 -223516 1.0 HDAC1 TBL1XR1 GATA2 ZEB2 MAFF RAD51 KLF16 SMARCA4 PBX2 IKZF1 IMMT ENSG00000251974 REEP1 ENSG00000202537 KDM3A POLR1A GC02M086172 MRPL35
GH02F086184 1 Ensembl ENCODE 9.8 -254.9 -254916 3.2 PKNOX1 SP2 FEZF1 REST ZFHX2 GATA3 ZNF366 IKZF1 ZNF341 ZNF512 IMMT SNORD94 KDM3A ENSG00000251974 POLR1A MIR4779 GC02M086160 ENSG00000200241
GH02F086189 1 ENCODE 9.8 -251.0 -250981 1.3 HDGF PKNOX1 ATF1 ARNT CREB3L1 ELK1 GATA2 NCOA1 SMARCA4 PBX2 IMMT LOC100420889 C2orf68 ENSG00000231259 LOC102724642 SNORD94 KDM3A POLR1A MIR4779 GC02M086160
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM3A on UCSC Golden Path with GeneCards custom track

Promoters for KDM3A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000593912 1253 3001 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3

Genomic Location for KDM3A Gene

Chromosome:
2
Start:
86,440,647 bp from pter
End:
86,492,716 bp from pter
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

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 Lys 851, Lys 895, Lys 905, and Lys 918
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for KDM3A (Lysine (K)-specific Demethylase 3A/KDM3A)

Domains & Families for KDM3A Gene

Gene Families for KDM3A Gene

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.
  • Contains 1 JmjC domain.
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 TMP1 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

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:0001047 core promoter binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
GO:0005506 iron ion binding IMP 16603237
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 Model Products

Inhibitory RNA Products

Flow Cytometry Products

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

Gene Ontology (GO) - Cellular Components for KDM3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA --
GO:0005634 nucleus IEA,IDA 16603237
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IDA 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

Gene Ontology (GO) - Biological Process for KDM3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
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

Transcripts for KDM3A Gene

Unigene Clusters for KDM3A Gene

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

Inhibitory RNA Products

Flow Cytometry Products

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 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, PaxDb, 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
genes like me logo Genes that share expression patterns with KDM3A: view

Primer Products

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 and mRNA Expression by UniProt/SwissProt 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 35
  • 99.52 (n)
dog
(Canis familiaris)
Mammalia KDM3A 34 35
  • 92.02 (n)
cow
(Bos Taurus)
Mammalia KDM3A 34 35
  • 90.41 (n)
mouse
(Mus musculus)
Mammalia Kdm3a 34 16 35
  • 89.23 (n)
rat
(Rattus norvegicus)
Mammalia Kdm3a 34
  • 88.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM3A 35
  • 77 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM3A 35
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM3A 34 35
  • 71.52 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm3a 34
  • 62.84 (n)
Str.15267 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.2818 34
fruit fly
(Drosophila melanogaster)
Insecta JHDM2 35
  • 39 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7055 35
  • 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)

Paralogs for KDM3A Gene

Paralogs for KDM3A Gene

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

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 Sequence Context AA Info Type
VAR_035940 A breast cancer sample
rs193921056 Uncertain significance 86,482,108(+) GTATG(-/TGTT)TGTTT intron-variant
rs10180036 -- 86,440,266(+) GCATC(G/T)ATAAT upstream-variant-2KB
rs10180819 -- 86,444,225(+) AGCTG(C/T)GGAGG intron-variant
rs10496321 -- 86,456,586(+) AACTC(G/T)TTGTA 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)

Relevant External Links for KDM3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM3A

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

Disorders for KDM3A Gene

Relevant External Links for KDM3A

Genetic Association Database (GAD)
KDM3A
Human Genome Epidemiology (HuGE) Navigator
KDM3A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM3A

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 Res. 1998) 2 3 4 64
  2. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PMID: 20378615) Aston K.I. … Carrell D.T. (Hum. Reprod. 2010) 3 46 64
  3. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. (PMID: 16603237) Yamane K. … Zhang Y. (Cell 2006) 3 4 64
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier L.W. … Wilson R.K. (Nature 2005) 3 4 64
  5. Regulation of c-Myc expression by the histone demethylase JMJD1A is essential for prostate cancer cell growth and survival. (PMID: 26279298) Fan L. … Qi J. (Oncogene 2016) 3 64

Products for KDM3A Gene

Sources for KDM3A Gene

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