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KDM5A Gene

protein-coding GIFtS: 53
GCID: GC12M000389

Lysine (K)-Specific Demethylase 5A

(Previous names: retinoblastoma-binding protein 2, Jumonji, AT rich interactive...)
(Previous symbols: RBBP2, JARID1A)

See KDM5A-related disease
at

MalaCards

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
About This Section

Aliases
Lysine (K)-Specific Demethylase 5A¹ ²		Jumonji, AT Rich Interactive Domain 1A¹
RBBP2¹ ² ³ ⁵		Jumonji, AT Rich Interactive Domain 1A (RBBP2-Like)¹
JARID1A¹ ³ ⁵		Jumonji, AT Rich Interactive Domain 1A (RBP2-Like)²
RBP2² ³ ⁵		Lysine-Specific Demethylase 5A²
Retinoblastoma-Binding Protein 2¹ ³		Retinoblastoma Binding Protein 2²
Histone Demethylase JARID1A² ³		EC 1.14.11.-³
Jumonji/ARID Domain-Containing Protein 1A² ³		EC 1.14.11⁸
RBBP-2² ³

External Ids:	HGNC: 9886¹	Entrez Gene: 5927²	Ensembl: ENSG00000073614⁷	OMIM: 180202⁵	UniProtKB: P29375³

Export aliases for KDM5A gene to outside databases

Previous GC identifer: GC12M000259

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 (K)-specific demethylase 5A) is a protein-coding gene. Diseases associated with KDM5A include retinoblastoma. GO annotations related to this gene include oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is KDM5C.

UniProtKB/Swiss-Prot: KDM5A_HUMAN, P29375

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

Gene Wiki entry for KDM5A (JARID1A) Gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence at NCBI GenBank:

NC_000012.11 NC_018923.2 NT_009759.17

Regulatory elements:

Regulatory transcription factor binding sites in the KDM5A gene promoter:
Pax-2 Pax-2a STAT5A C/EBPalpha HNF-1A E2F Pax-2b E2F-1 HNF-1 FOXO4
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: KDM5A promoter sequence

Search Chromatin IP Primers for KDM5A

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM5A

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12p11 Ensembl cytogenetic band: 12p13.33 HGNC cytogenetic band: 12p13.33

KDM5A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KDM5A gene location

GeneLoc information about chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12M000389: view genomic region (about GC identifiers)

Start:	389,223 bp from pter	End:	498,620 bp from pter
Size:	109,398 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, antibodies-online, and/or GeneTex,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
About This Section

UniProtKB/Swiss-Prot: KDM5A_HUMAN, P29375 (See protein sequence)

Recommended Name: Lysine-specific demethylase 5A

Size: 1690 amino acids; 192095 Da

Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)

Subunit: 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

Sequence caution: Sequence=AAB28544.1; Type=Frameshift; Positions=Several; Sequence=BAE06081.1; Type=Erroneous

initiation;

4 PDB 3D structures from and Proteopedia for KDM5A:

2JXJ (3D)

2KGG (3D)

2KGI (3D)

3GL6 (3D)

Secondary accessions: A8MV76 Q4LE72 Q86XZ1

Alternative splicing: 2 isoforms: P29375-1 P29375-2

Explore the universe of human proteins at neXtProt for KDM5A: NX_P29375

Explore proteomics data for KDM5A at MOPED

Post-translational modifications:

Ubiquitination² at Lys347, Lys392, Lys425, Lys733, Lys1275

Modification sites at PhosphoSitePlus

Selected DME Specific Peptides for KDM5A (P29375) (see all 20)

GEPKTWY

ERWEEKA

YSINYLH

TTCFLSA

See KDM5A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001036068.1

ENSEMBL proteins:

ENSP00000382688 ENSP00000440622 ENSP00000443854 ENSP00000438203 ENSP00000444251

ENSP00000372265

KDM5A Human Recombinant Protein Products:

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	antibodies-online peptides for KDM5A

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	antibodies-online kits for KDM5A (4 products)

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GenesLikeMe)
About This Section

HGNC Gene Families:

KDM: Chromatin-modifying enzymes / K-demethylases

PHF: Zinc fingers, PHD-type

Selected InterPro protein domains (see all 10):

IPR001965 Znf_PHD

IPR013083 Znf_RING/FYVE/PHD

IPR003347 JmjC_dom

IPR013637 Lys_sp_deMease_like_dom

IPR019786 Zinc_finger_PHD-type_CS

Graphical View of Domain Structure for InterPro Entry P29375

ProtoNet protein and cluster: P29375

Selected Blocks protein domains (see all 6):

IPB001606 ARID (AT-rich interaction domain) protein

IPB001965 Zn-finger-like

IPB003347 Transcription factor jumonji

IPB003349 Transcription factor jumonji

IPB004198 Zn-finger

UniProtKB/Swiss-Prot: KDM5A_HUMAN, P29375

Domain: The GSGFP motif is required for the interaction with SUZ12 (By similarity)

Similarity: Belongs to the JARID1 histone demethylase family

Similarity: Contains 1 ARID domain

Similarity: Contains 1 JmjC domain

Similarity: Contains 1 JmjN domain

Similarity: Contains 3 PHD-type zinc fingers

Find genes that share domains with KDM5A About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: KDM5A_HUMAN, P29375

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

Enzyme Numbers (IUBMB): EC 1.14.11.-¹ EC 1.14.11²

Gene Ontology (GO): Selected molecular function terms (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	IEA	--
GO:0003682	chromatin binding	IEA	--
GO:0003700	sequence-specific DNA binding transcription factor activity	TAS	8414517
GO:0005515	protein binding	--	--
GO:0008270	zinc ion binding	IEA	--

Find genes that share ontologies with KDM5A About GenesLikeMe

Phenotypes:
9 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Kdm5a):

behavior/neurological	cellular	endocrine/exocrine gland	growth/size/body	hematopoietic system
immune system	mortality/aging	normal	tumorigenesis

Find genes that share phenotypes with KDM5A About GenesLikeMe

Animal Models:
MGI mouse knock-out Kdm5a^tm1.1Kael for KDM5A

genOway: Develop your customized and physiologically relevant rodent model for KDM5A

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		hsa-miR-582-3p hsa-miR-548j hsa-miR-607 hsa-miR-199a-3p hsa-miR-134 hsa-miR-3916 hsa-miR-409-5p hsa-miR-3116

		SwitchGear 3'UTR luciferase reporter plasmid: KDM5A 3' UTR sequence

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Gene Editing
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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM5A

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Subcellular locations from UniProtKB/Swiss-Prot

KDM5A_HUMAN, P29375: Nucleus, nucleolus. Note=Occupies promoters of genes involved in RNA metabolism and

mitochondrial function (By similarity)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
nucleus	5
cytosol	3

About this image

Gene Ontology (GO): 5 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005622	intracellular	--	--
GO:0005634	nucleus	IDA	--
GO:0005730	nucleolus	IEA	--
GO:0005737	cytoplasm	IDA	--
GO:0019907	colocalizes with cyclin-dependent protein kinase activating kinase holoenzyme complex	IDA	11445587

Find genes that share ontologies with KDM5A About GenesLikeMe

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GenesLikeMe, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

SuperPaths for KDM5A About

See pathways by source

Powered
by

SuperPath

Contained pathways About

Chromatin Regulation / Acetylation

Chromatin Regulation / Acetylation

Find genes that share SuperPaths with KDM5A About GenesLikeMe

Pathways by source See SuperPaths
Show all pathways

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for KDM5A

Visual Cycle in Retinal Rods

1 Cell Signaling Technology (CST) Pathway for KDM5A

Chromatin Regulation / Acetylation

Custom Pathway & Disease-focused RT² Profiler PCR Arrays for KDM5A
Interactions:

GeneGlobe Interaction Network for KDM5A

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for KDM5A (P29375³ ENSP00000382688⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 94)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HIST2H3A	Q71DI3³, ENSP00000385479⁴	I2D: score=1 STRING: ENSP00000385479
HIST2H3C	Q71DI3³	I2D: score=1
HIST2H3D	Q71DI3³	I2D: score=1
NR3C1	P04150³, ENSP00000231509⁴	I2D: score=4 STRING: ENSP00000231509
RARA	P10276³, ENSP00000254066⁴	I2D: score=4 STRING: ENSP00000254066

About this table

Gene Ontology (GO): 5 biological process terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006366	transcription from RNA polymerase II promoter	TAS	8414517
GO:0007275	multicellular organismal development	IEA	--
GO:0016568	chromatin modification	IEA	--
GO:0045893	positive regulation of transcription, DNA-templated	IDA	11358960
GO:0055114	oxidation-reduction process	--	--

Find genes that share ontologies with KDM5A About GenesLikeMe

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, Sets of similar genes according to GenesLikeMe)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for KDM5A

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
About This Section

REFSEQ mRNAs for KDM5A gene (2 alternative transcripts):

NM_001042603.2 NM_005056.2

Unigene Cluster for KDM5A:

Lysine (K)-specific demethylase 5A

Hs.76272 [show with all ESTs]

Unigene Representative Sequence: NM_001042603

12 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000399788(uc021qsr.1 uc001qif.1) ENST00000540838 ENST00000540156

ENST00000544760 ENST00000535269 ENST00000541335 ENST00000540168 ENST00000544777

ENST00000535014 ENST00000536014 ENST00000543507 ENST00000382815(uc010sdn.1 uc010sdo.1)

miRNA Products:		Block miRNA regulation of human, mouse, rat KDM5A using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate KDM5A (see all 98):
		hsa-miR-582-3p hsa-miR-548j hsa-miR-607 hsa-miR-199a-3p hsa-miR-134 hsa-miR-3916 hsa-miR-409-5p hsa-miR-3116

		SwitchGear 3'UTR luciferase reporter plasmid: KDM5A 3' UTR sequence

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		GenScript: all cDNA clones in your preferred vector: KDM5A (NM_001042603)
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		QuantiTect SYBR Green Assays in human, mouse, rat KDM5A
		QuantiFast Probe-based Assays in human, mouse, rat KDM5A

Additional mRNA sequence:

AB209999.1 AF007135.1 AK057703.1 AK225060.1 AK301150.1 AK301273.1 AK307580.1 AK307689.1

AL133026.1 BC048307.1 BC053893.1 BC110916.1 S66431.1

15 DOTS entries:

DT.100780845 DT.87016210 DT.75163122 DT.92044835 DT.110527 DT.100780847 DT.100727224 DT.431815

DT.95331495 DT.121126262 DT.121126263 DT.121126329 DT.121126345 DT.87000478 DT.97785624

Selected AceView cDNA sequences (see all 416):

AI884688 AA460157 BX092553 BQ285911 AW300068 BQ632303 BQ933481 AW058576

AI700672 BM709205 AA469935 BE328608 N80904 AA952997 AA812025 BE301184

CA308399 AA906265 AI672662 BC020867 AI146438 BM833997 BC022392 BQ632596

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM5A (see all 7) About this scheme

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:

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

ECgene alternative splicing isoforms for KDM5A

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GenesLikeMe, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

KDM5A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

KDM5A expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 6) fully expand


Limb (Muscoskeletal System)
Limb Bud

Testis (Reproductive System)
Testis Somatic Cells Primitive Gonad

Gonad (Reproductive System)
Testis Somatic Cells Primitive Gonad

Blood (Hematopoietic System)
pre Conventional Dendritic Cells Peripheral Blood

Eye (Sensory Organs)
Corneal Epithelium

KDM5A Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

KDM5A Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.76272

Custom PCR Arrays for KDM5A

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for KDM5A
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat KDM5A
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		QuantiFast Probe-based Assays in human, mouse, rat KDM5A

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM5A

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

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

Orthologs for KDM5A gene from Selected species (see all 17) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Kdm5a^{1 , 5}	lysine (K)-specific demethylase 5A^{1, 5}	91.74(n)¹ 96.69(a)¹		6 (56.95 cM)⁵ 214899¹ NM_145997.2¹ NP_666109.2¹ 120364124⁵
chicken (Gallus gallus)	Aves	KDM5A¹	lysine (K)-specific demethylase 5A	80.5(n) 92.18(a)		418148 XM_004937924.1 XP_004937981.1
lizard (Anolis carolinensis)	Reptilia	KDM5A⁶	lysine (K)-specific demethylase 5A	91(a)	1 ↔ 1	5(11886209-11931909)
African clawed frog (Xenopus laevis)	Amphibia	BJ029275.1²	--	78.67(n)		BJ029275.1
zebrafish (Danio rerio)	Actinopterygii	kdm5a¹	lysine (K)-specific demethylase 5A	66.02(n) 74.44(a)		100333310 XM_003201640.2 XP_003201688.2
fruit fly (Drosophila melanogaster)	Insecta	lid¹	little imaginal discs	52.58(n) 49.63(a)		33837 NM_001258980.1 NP_001245909.1
worm (Caenorhabditis elegans)	Secernentea	rbr-2⁶	Protein RBR-2 (rbr-2) mRNA, complete cds	29(a)	1 → many	IV(10920107-10926797) WBGene00004319
baker's yeast (Saccharomyces cerevisiae)	Saccharomycetes	JHD2⁶	JmjC domain family histone demethylase specific fo...	29(a)	1 → many	X(644304-646490) YJR119C

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

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68,Sets of similar genes according to GenesLikeMe)
About This Section

Paralogs for KDM5A gene

KDM5C² JARID2² KDM5B² KDM5D²

11 SIMAP similar genes for KDM5A using alignment to 6 protein entries: KDM5A_HUMAN (see all proteins):

PLU-1 KDM5C KDM5B JARID1B JARID1C DKFZp434N0335

KDM5D DKFZp434D0815 DKFZp434I0617 PHF21A DKFZp434I2412

Find genes that share paralogs with KDM5A About GenesLikeMe

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 12 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs201821956^1,2	C	untested¹	495101(+)	`GAAACA/GAAAGC`	2	R C	mis¹		0	--	--	--	--
rs201729922^1,2	C	--	388744(+)	`ACTATA/CCNNNN`	1	--	ds500¹		0	--	--	--	--
rs188571177^1,2		--	388749(+)	`ACAGCC/TTCTAT`	1	--	ds500¹		0	--	--	--	--
rs78481620^1,2	C,F	--	388754(+)	`CTCTAT/CTGTCG`	1	--	ds500¹		1		NA	120
rs77827014^1,2	C,F	--	388758(+)	`ATTGTC/TGTCTT`	1	--	ds500¹		1		NA	120
rs146554708^1,2		--	388759(+)	`TTGTCA/GTCTTT`	1	--	ds500¹		0	--	--	--	--
rs79818234^1,2	C,F	--	388806(+)	`AAATCA/GTCTAT`	1	--	ds500¹		1		EA	120
rs141216541^1,2		--	388810(+)	`CATCTA/GTGTCT`	1	--	ds500¹		0	--	--	--	--
rs144925625^1,2		--	388865(+)	`CTTGCA/TTGTGG`	1	--	ds500¹		0	--	--	--	--
rs12317905^1,2	C,F,A,H	--	388877(+)	`AGGAAG/ACCAAG`	1	--	ds500¹		12		NS EA NA WA CSA	915

HapMap Linkage Disequilibrium report for KDM5A (389223 - 498620 bp)

Structural Variations
Database of Genomic Variants (DGV) Selected variations for KDM5A (see all 13): About this table

Variant ID	Type	Subtype	PubMed ID
esv34939	CNV	Loss	17911159
nsv819688	CNV	Loss	19587683
nsv898564	CNV	Loss	21882294
nsv570	CNV	Loss	18451855
esv33025	CNV	Gain	17666407
nsv898563	CNV	Gain	21882294
esv33918	CNV	Gain	17666407
nsv898565	CNV	Gain	21882294
nsv8883	CNV	Gain+Loss	18304495
nsv442250	CNV	CNV	18776908

Human Gene Mutation Database (HGMD): KDM5A

Site Specific Mutation Identification with PCR Assays

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB, Sets of similar genes according to GenesLikeMe)
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OMIM gene information: 180202 OMIM disorders: --

1 disease for KDM5A:
About MalaCards

retinoblastoma

Find genes that share disorders with KDM5A About GenesLikeMe

1 Novoseek inferred disease relationship for KDM5A gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
retinoblastoma	76.4	11	10942599 (1), 7935440 (1), 8530100 (1), 16419055 (1) (see all 8)

Export disorders for KDM5A gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for KDM5A gene, integrated from 10 sources (see all 55):
(articles sorted by number of sources associating them with KDM5A)

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Cloning of cDNAs for cellular proteins that bind to the retinoblastoma gene product. (PubMed id 1857421)^{1, 2, 3, 9} Defeo-Jones D.... Oliff A. (Nature 1991)
Retinoblastoma-binding protein 2 (Rbp2) potentiates nuclear hormone receptor-mediated transcription. (PubMed id 11358960)^{1, 2, 9} Chan S.W. and Hong W. (J. Biol. Chem. 2001)
T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2. (PubMed id 9129143)^{1, 2, 9} Mao S.... Goorha R.M. (Oncogene 1997)
Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein. (PubMed id 7935440)^{1, 2, 9} Kim Y.W.... Kaye F.J. (Mol. Cell. Biol. 1994)
RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. (PubMed id 17320161)^{1, 2} Christensen J.... Helin K. (Cell 2007)
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)^{1, 2} Olsen J.V....Mann M. (Cell 2006)
Binding of pRB to the PHD protein RBP2 promotes cellular differentiation. (PubMed id 15949438)^{1, 2} Benevolenskaya E.V....Kaelin W.G. Jr. (Mol. Cell 2005)
Characterization of the retinoblastoma binding proteins RBP1 and RBP2. (PubMed id 8414517)^{1, 2} Fattaey A.R....Jones R.E. (Oncogene 1993)
RBP2 is an MRG15 complex component and down-regulates intragenic histone H3 lysine 4 methylation. (PubMed id 17573780)^{1, 9} Hayakawa T....Nakayama J. (amp 2007)
Isolation and regional assignment of human chromosome 12p cDNAs. (PubMed id 8530100)^{1, 9} Baens M....Marynen P. (Genomics 1995)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 5927	HGNC: 9886	AceView: JARID1AandSLC6A13	Ensembl:ENSG00000073614	euGenes: HUgn5927
ECgene: KDM5A	H-InvDB: KDM5A

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for KDM5A	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for KDM5A	Genetics and Cytogenetics in Oncology and Haematology

Intellectual Property for KDM5A gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for KDM5A gene:
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GeneCards and IP:
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KDM5A Gene

Lysine (K)-Specific Demethylase 5A

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KDM5A Gene

Lysine (K)-Specific Demethylase 5A

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