KDM5A lysine demethylase 5A [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM5Aprovided by HGNC
Official Full Name: lysine demethylase 5Aprovided by HGNC
Primary source: HGNC:HGNC:9886
See related: Ensembl:ENSG00000073614 MIM:180202; AllianceGenome:HGNC:9886
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RBP2; RBBP2; NEDEHC; RBBP-2
Summary: 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]
Annotation information: Note: RBP2 (Gene ID: 5948) and KDM5A (Gene ID: 5927) share the RBP2 symbol/alias in common. RBP2 is a widely used alternative name for lysine demethylase 5A (KDM5A), which can be confused with the official symbol for retinol binding protein 2 (RBP2). [03 Jul 2018]
Expression: Ubiquitous expression in testis (RPKM 10.6), bone marrow (RPKM 8.6) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 12p13.33

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (280057..389320, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (276885..386174, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (389223..498486, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mechanism of KDM5A-mediated H3K4me3 modification in the osteogenic differentiation of mesenchymal stem cells in steroid-induced osteonecrosis of the femoral head.
Title: Mechanism of KDM5A-mediated H3K4me3 modification in the osteogenic differentiation of mesenchymal stem cells in steroid-induced osteonecrosis of the femoral head.
KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
Title: KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas.
Fbxo22 inhibits metastasis in triple-negative breast cancer through ubiquitin modification of KDM5A and regulation of H3K4me3 demethylation.
Title: Fbxo22 inhibits metastasis in triple-negative breast cancer through ubiquitin modification of KDM5A and regulation of H3K4me3 demethylation.
Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis.
Title: Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis.
Long non-coding RNA tumor protein 73 antisense RNA 1 influences an interaction between lysine demethylase 5A and promoter of tumor protein 73 to enhance the malignancy of colorectal cancer.
Title: Long non-coding RNA tumor protein 73 antisense RNA 1 influences an interaction between lysine demethylase 5A and promoter of tumor protein 73 to enhance the malignancy of colorectal cancer.
KDM5A Inhibits Antitumor Immune Responses Through Downregulation of the Antigen-Presentation Pathway in Ovarian Cancer.
Title: KDM5A Inhibits Antitumor Immune Responses Through Downregulation of the Antigen-Presentation Pathway in Ovarian Cancer.
TSG Targeting KDM5A Affects Osteogenic Differentiation of Bone Mesenchymal Stem Cells Induced by Bone Morphogenetic Protein 2.
Title: TSG Targeting KDM5A Affects Osteogenic Differentiation of Bone Mesenchymal Stem Cells Induced by Bone Morphogenetic Protein 2.
Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma.
Title: Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma.
KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance.
Title: KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance.
Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference.
Title: Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference.

Submit: New GeneRIF Correction See all GeneRIFs (69)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
New loci associated with kidney function and chronic kidney disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

A003M44 (e-PCR)
- UniSTS:53263

SHGC-145012 (e-PCR)
- UniSTS:174376

RH44598 (e-PCR)
- UniSTS:59193

RH47587 (e-PCR)
- UniSTS:71747

STS-R65684 (e-PCR)
- UniSTS:69464

RH66643 (e-PCR)
- UniSTS:20824

RH68615 (e-PCR)
- UniSTS:74082

RH70148 (e-PCR)
- UniSTS:34151

RH75356 (e-PCR)
- UniSTS:91513

RH70779 (e-PCR)
- UniSTS:40357

D12S928 (e-PCR)
- UniSTS:149929

G41014 (e-PCR)
- UniSTS:26542

SHGC-82407 (e-PCR)
- UniSTS:104395

JARID1A_2177 (e-PCR)
- UniSTS:280794

D12S1914 (e-PCR)
- UniSTS:18654

D12S1897 (e-PCR)
- UniSTS:71658

RH11182 (e-PCR)
- UniSTS:40953

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables enzyme inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription cis-regulatory region binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in facultative heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: lysine-specific demethylase 5A

Names: Jumonji, AT rich interactive domain 1A (RBP2-like); [histone H3]-trimethyl-L-lysine(4) demethylase 5A; histone demethylase JARID1A; jumonji/ARID domain-containing protein 1A; lysine (K)-specific demethylase 5A; retinoblastoma binding protein 2

NP_001036068.1

EC 1.14.11.67

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_046993.1 RefSeqGene

Range

5136..114399

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001042603.3 → NP_001036068.1 lysine-specific demethylase 5A

See identical proteins and their annotated locations for NP_001036068.1

Status: REVIEWED

Source sequence(s)

AB209999, AC007406, BU182136, DA211439

Consensus CDS

CCDS41736.1

UniProtKB/Swiss-Prot

A8MV76, P29375, Q4LE72, Q86XZ1

Related

ENSP00000382688.2, ENST00000399788.7

Conserved Domains (8) summary

smart00545
Location:18 → 59

JmjN; Small domain found in the jumonji family of transcription factors

smart01014
Location:85 → 170

ARID; ARID/BRIGHT DNA binding domain

pfam02373
Location:470 → 586

JmjC; JmjC domain, hydroxylase

cd15602
Location:295 → 343

PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)

cd15606
Location:1163 → 1215

PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)

cd15686
Location:1608 → 1659

PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)

pfam02928
Location:676 → 728

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:741 → 1070

PLU-1; PLU-1-like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

280057..389320 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

276885..386174 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_005056.2: Suppressed sequence

Description

NM_005056.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.