Free for academic non-profit institutions. Other users need a Commercial license

Aliases for KDM5A Gene

Aliases for KDM5A Gene

  • Lysine Demethylase 5A 2 3 5
  • Jumonji/ARID Domain-Containing Protein 1A 3 4
  • Lysine (K)-Specific Demethylase 5A 2 3
  • Retinoblastoma-Binding Protein 2 2 4
  • Histone Demethylase JARID1A 3 4
  • RBBP-2 3 4
  • RBBP2 3 4
  • RBP2 3 4
  • Jumonji, AT Rich Interactive Domain 1A (RBBP2-Like) 2
  • Jumonji, AT Rich Interactive Domain 1A (RBP2-Like) 3
  • Jumonji, AT Rich Interactive Domain 1A 2
  • Retinoblastoma Binding Protein 2 3
  • Lysine-Specific Demethylase 5A 3
  • EC 1.14.11.- 4
  • EC 1.14.11 61
  • JARID1A 4

External Ids for KDM5A Gene

Previous HGNC Symbols for KDM5A Gene

  • RBBP2
  • JARID1A

Previous GeneCards Identifiers for KDM5A Gene

  • GC12M000259
  • GC12M000389

Summaries for KDM5A Gene

Entrez Gene Summary for KDM5A Gene

  • This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]

GeneCards Summary for KDM5A Gene

KDM5A (Lysine Demethylase 5A) is a Protein Coding gene. Diseases associated with KDM5A include Retinoblastoma and Advanced Sleep Phase Syndrome. 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 transcription coactivator activity. An important paralog of this gene is KDM5B.

UniProtKB/Swiss-Prot for KDM5A Gene

  • Histone demethylase that specifically demethylates Lys-4 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-9, H3 Lys-27, H3 Lys-36, H3 Lys-79 or H4 Lys-20. Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-4. May stimulate transcription mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity).

Gene Wiki entry for KDM5A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM5A Gene

Genomics for KDM5A Gene

Regulatory Elements for KDM5A Gene

Enhancers for KDM5A 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
GH12F000749 1.3 FANTOM5 ENCODE 25.8 -363.2 -363188 7.0 HDGF PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 KDM5A ENSG00000255825 DDX11L8 ENSG00000261799 LOC100288778 RAD52 NINJ2 CCDC77 WNK1 GC12M000753
GH12F000198 1 Ensembl ENCODE 22.8 +190.0 189985 1.5 ATF1 INSM2 KLF17 RAD21 ZEB1 ZNF366 SCRT2 FOS CREM ZNF362 KDM5A LOC101929384 ENSG00000255671
GH12F000948 0.2 ENCODE 22.8 -559.9 -559874 2.6 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 KDM5A ENSG00000261799 LOC100288778 RAD52 PIR51139 GC12P000986
GH12F000264 0.5 Ensembl 18.7 +125.6 125555 0.2 MGA KDM5A CCDC77 SLC6A13 LOC102723544
GH12F000614 1.4 FANTOM5 Ensembl ENCODE 16.2 -229.7 -229746 10.4 PKNOX1 ARID4B ZNF48 SLC30A9 ZNF121 ELK1 FOS SP5 MXD4 MIER2 LOC100049716 NINJ2 KDM5A WNK1 LOC105369595 CCDC77 GC12M000616
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around KDM5A on UCSC Golden Path with GeneCards custom track

Promoters for KDM5A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000086289 955 3801 PKNOX1 CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143

Genomic Location for KDM5A Gene

Chromosome:
12
Start:
280,057 bp from pter
End:
389,455 bp from pter
Size:
109,399 bases
Orientation:
Minus strand

Genomic View for KDM5A Gene

Genes around KDM5A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM5A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM5A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM5A Gene

Proteins for KDM5A Gene

  • Protein details for KDM5A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P29375-KDM5A_HUMAN
    Recommended name:
    Lysine-specific demethylase 5A
    Protein Accession:
    P29375
    Secondary Accessions:
    • A8MV76
    • Q4LE72
    • Q86XZ1

    Protein attributes for KDM5A Gene

    Size:
    1690 amino acids
    Molecular mass:
    192095 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with SUZ12; the interaction is direct (By similarity). Interacts with the viral protein-binding domain of RB1. Interacts with ESR1, MYC, MYCN and LMO2. Interacts with HDAC1 (By similarity). Interacts with ARNTL/BMAL1 and CLOCK.
    SequenceCaution:
    • Sequence=AAB28544.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=BAE06081.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM5A Gene

    Alternative splice isoforms for KDM5A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM5A Gene

Selected DME Specific Peptides for KDM5A Gene

P29375:
  • EAFGFEQA
  • NFAEAVNF
  • QRLNELEA
  • DYFNMPVHMVPTE
  • TFLKKNS
  • RTNQCAGEFV
  • CVFSHEELI
  • EKEFWRLV
  • RPRLETIL
  • SQPDLLHQLVTIMNPN
  • EQSVLAHI
  • LLCDGCDDSYHTFCL
  • HYRRLRR
  • VERKILDL
  • GEPKTWY
  • ERWEEKA
  • YSINYLH
  • TTCFLSA
  • PPPECPVFEPSW
  • PWLYVGM

Post-translational modifications for KDM5A Gene

  • Ubiquitination at Lys 347, Lys 425, Lys 733, and Lys 1275
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM5A Gene

Domains & Families for KDM5A Gene

Suggested Antigen Peptide Sequences for KDM5A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P29375

UniProtKB/Swiss-Prot:

KDM5A_HUMAN :
  • The GSGFP motif is required for the interaction with SUZ12.
  • Belongs to the JARID1 histone demethylase family.
  • Contains 3 PHD-type zinc fingers.
Domain:
  • The GSGFP motif is required for the interaction with SUZ12.
  • Contains 1 ARID domain.
  • Contains 1 JmjC domain.
  • Contains 1 JmjN domain.
Family:
  • Belongs to the JARID1 histone demethylase family.
Similarity:
  • Contains 3 PHD-type zinc fingers.
genes like me logo Genes that share domains with KDM5A: view

Function for KDM5A Gene

Molecular function for KDM5A Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-4 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-9, H3 Lys-27, H3 Lys-36, H3 Lys-79 or H4 Lys-20. Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-4. May stimulate transcription mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity).

Enzyme Numbers (IUBMB) for KDM5A Gene

Gene Ontology (GO) - Molecular Function for KDM5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA,IDA 15640446
GO:0003682 chromatin binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 8414517
GO:0003713 transcription coactivator activity IEA,ISS --
GO:0005515 protein binding IPI 21960634
genes like me logo Genes that share ontologies with KDM5A: view
genes like me logo Genes that share phenotypes with KDM5A: view

Animal Models for KDM5A Gene

MGI Knock Outs for KDM5A:

Animal Model Products

miRNA for KDM5A Gene

miRTarBase miRNAs that target KDM5A

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM5A

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM5A Gene

Localization for KDM5A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM5A Gene

Nucleus, nucleolus. Nucleus. Note=Occupies promoters of genes involved in RNA metabolism and mitochondrial function. {ECO:0000250 UniProtKB:Q3UXZ9}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM5A Gene COMPARTMENTS Subcellular localization image for KDM5A gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for KDM5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
GO:0005737 cytoplasm IDA --
GO:0019907 colocalizes_with cyclin-dependent protein kinase activating kinase holoenzyme complex IDA 11445587
genes like me logo Genes that share ontologies with KDM5A: view

Pathways & Interactions for KDM5A Gene

genes like me logo Genes that share pathways with KDM5A: view

Pathways by source for KDM5A Gene

1 GeneTex pathway for KDM5A Gene
1 Cell Signaling Technology pathway for KDM5A Gene
1 Qiagen pathway for KDM5A Gene

SIGNOR curated interactions for KDM5A Gene

Inactivates:

Gene Ontology (GO) - Biological Process for KDM5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter TAS 8414517
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with KDM5A: view

Drugs & Compounds for KDM5A Gene

(6) Drugs for KDM5A Gene - From: ApexBio and DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
IOX 1 Pharma 0
JIB-04 Pharma Jumonji histone demethylase inihibitor, Pan Jumonji inhibitor; active in vivo 0
ML324 Pharma JMJD2 demethylase inhibitor, potent and cell-permeable 0
SP2509 Pharma Demethylase 1 (LSD1) antagonist, novel Lysine-specific 0
Tranylcypromine hydrochloride Pharma 0

(5) ApexBio Compounds for KDM5A Gene

Compound Action Cas Number
IOX 1 5852-78-8
JIB-04 Jumonji histone demethylase inihibitor 199596-05-9
ML324 JMJD2 demethylase inhibitor, potent and cell-permeable 1222800-79-4
SP2509 Demethylase 1 (LSD1) antagonist, novel Lysine-specific 1423715-09-6
Tranylcypromine hydrochloride 1986-47-6
genes like me logo Genes that share compounds with KDM5A: view

Transcripts for KDM5A Gene

Unigene Clusters for KDM5A Gene

Lysine (K)-specific demethylase 5A:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM5A

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM5A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a ·
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:

ExUns: 24b ^ 25 ^ 26 ^ 27a · 27b · 27c ^ 28 ^ 29 ^ 30
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for KDM5A Gene

GeneLoc Exon Structure for
KDM5A
ECgene alternative splicing isoforms for
KDM5A

Expression for KDM5A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for KDM5A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for KDM5A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (16.5), Blymphocyte (13.9), Liver (10.6), and Bone marrow mesenchymal stem cell (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KDM5A Gene



Protein tissue co-expression partners for KDM5A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of KDM5A Gene:

KDM5A

SOURCE GeneReport for Unigene cluster for KDM5A Gene:

Hs.76272
genes like me logo Genes that share expression patterns with KDM5A: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for KDM5A Gene

Orthologs for KDM5A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM5A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM5A 34 35
  • 99.49 (n)
oppossum
(Monodelphis domestica)
Mammalia KDM5A 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM5A 34 35
  • 93.21 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 92 (a)
OneToMany
-- 35
  • 80 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Kdm5a 34 16 35
  • 91.74 (n)
rat
(Rattus norvegicus)
Mammalia Kdm5a 34
  • 91.03 (n)
cow
(Bos Taurus)
Mammalia KDM5A 34 35
  • 89.92 (n)
chicken
(Gallus gallus)
Aves KDM5A 34 35
  • 80.5 (n)
lizard
(Anolis carolinensis)
Reptilia KDM5A 35
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm5a 34
  • 73.17 (n)
Str.17676 34
zebrafish
(Danio rerio)
Actinopterygii KDM5A 35
  • 70 (a)
OneToOne
kdm5a 34
  • 66.02 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004854 34
  • 52.97 (n)
fruit fly
(Drosophila melanogaster)
Insecta lid 34 35
  • 52.58 (n)
worm
(Caenorhabditis elegans)
Secernentea rbr-2 35
  • 29 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD2 35
  • 29 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 46 (a)
OneToMany
Species where no ortholog for KDM5A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)

Evolution for KDM5A Gene

ENSEMBL:
Gene Tree for KDM5A (if available)
TreeFam:
Gene Tree for KDM5A (if available)

Paralogs for KDM5A Gene

Paralogs for KDM5A Gene

genes like me logo Genes that share paralogs with KDM5A: view

Variants for KDM5A Gene

Sequence variations from dbSNP and Humsavar for KDM5A Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs367537993 untested 293,103(-) GGAAA(C/T)GGAAG reference, missense
rs1001401 -- 335,531(+) AATGT(A/G)GATGT intron-variant
rs1003950 -- 305,943(+) AAGCA(C/G)AGCAA intron-variant
rs10083202 -- 373,277(+) ctgtt(A/T)ttggt intron-variant
rs1011699 -- 385,020(+) ctccg(C/T)ctcta intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM5A Gene

Variant ID Type Subtype PubMed ID
esv2759875 CNV gain+loss 17122850
esv33025 CNV gain 17666407
esv33918 CNV gain 17666407
esv34939 CNV loss 17911159
esv3580008 CNV loss 25503493
esv3628231 CNV gain 21293372
esv3628232 CNV gain 21293372
esv3892121 CNV gain 25118596
nsv1050781 CNV loss 25217958
nsv1050912 CNV gain 25217958
nsv1069629 CNV deletion 25765185
nsv1138089 CNV deletion 24896259
nsv1143399 CNV deletion 24896259
nsv1146752 CNV deletion 26484159
nsv442250 CNV gain 18776908
nsv570 CNV deletion 18451855
nsv819688 CNV loss 19587683
nsv8883 CNV gain+loss 18304495

Variation tolerance for KDM5A Gene

Residual Variation Intolerance Score: 1.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.31; 92.60% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM5A Gene

Human Gene Mutation Database (HGMD)
KDM5A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM5A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM5A Gene

Disorders for KDM5A Gene

MalaCards: The human disease database

(2) MalaCards diseases for KDM5A Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinoblastoma
  • retinoblastoma, trilateral
advanced sleep phase syndrome
  • familial advanced sleep-phase syndrome
- elite association - COSMIC cancer census association via MalaCards
Search KDM5A in MalaCards View complete list of genes associated with diseases

Relevant External Links for KDM5A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM5A
genes like me logo Genes that share disorders with KDM5A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KDM5A Gene

Publications for KDM5A Gene

  1. Cloning of cDNAs for cellular proteins that bind to the retinoblastoma gene product. (PMID: 1857421) Defeo-Jones D. … Oliff A. (Nature 1991) 2 3 4 22 64
  2. Retinoblastoma-binding protein 2 (Rbp2) potentiates nuclear hormone receptor-mediated transcription. (PMID: 11358960) Chan S.W. … Hong W. (J. Biol. Chem. 2001) 3 4 22 64
  3. T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2. (PMID: 9129143) Mao S. … Goorha R.M. (Oncogene 1997) 3 4 22 64
  4. Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein. (PMID: 7935440) Kim Y.W. … Kaye F.J. (Mol. Cell. Biol. 1994) 3 4 22 64
  5. Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clock. (PMID: 21960634) DiTacchio L. … Panda S. (Science 2011) 3 4 64

Products for KDM5A Gene

Sources for KDM5A Gene

Content
Loading form....