Kdm5a lysine demethylase 5A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm5aprovided by MGI
Official Full Name: lysine demethylase 5Aprovided by MGI
Primary source: MGI:MGI:2136980
See related: Ensembl:ENSMUSG00000030180 AllianceGenome:MGI:2136980
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: RBP2; Rbbp2; Jarid1a
Summary: Enables several functions, including chromatin DNA binding activity; histone H3K4 demethylase activity; and transcription coactivator activity. Involved in circadian regulation of gene expression and facultative heterochromatin formation. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleus. Part of protein-DNA complex. Is expressed in several structures, including 1st branchial arch; central nervous system; early conceptus; genitourinary system; and sensory organ. Human ortholog(s) of this gene implicated in ankylosing spondylitis. Orthologous to human KDM5A (lysine demethylase 5A). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 4.9), placenta adult (RPKM 3.8) and 26 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 6 F1; 6 56.95 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (120341060..120421535)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (120364099..120444574)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Abeta-induced mitochondrial dysfunction in neural progenitors controls KDM5A to influence neuronal differentiation.
Title: Aβ-induced mitochondrial dysfunction in neural progenitors controls KDM5A to influence neuronal differentiation.
KDM5A mutations identified in autism spectrum disorder using forward genetics.
Title: KDM5A mutations identified in autism spectrum disorder using forward genetics.
C/EBPbeta knockdown impaired the recruitment of KDM5A to the Wnt6 promoter
Title: Histone demethylase KDM5A is transactivated by the transcription factor C/EBPβ and promotes preadipocyte differentiation by inhibiting Wnt/β-catenin signaling.
Our results uncover a regulatory mechanism in which HDAC1 negatively regulates RBPJ binding on mitotic chromatin in a KDM5A-dependent manner. We propose that relative chromatin affinity of a minimal regulatory complex, reflecting a specific transcription program, renders selective RBPJ binding on mitotic chromatin.
Title: HDAC1 negatively regulates selective mitotic chromatin binding of the Notch effector RBPJ in a KDM5A-dependent manner.
Conditional, systemic ablation of RBP2 in pituitary or thyroid tumor-bearing Rb1(+/-) mice is sufficient to slow tumor growth and significantly extend survival without causing obvious toxicity to the host. These findings show that established Rb1-null tumors require RBP2 for growth.
Title: Autochthonous tumors driven by Rb1 loss have an ongoing requirement for the RBP2 histone demethylase.
KDM5A-mediated H3K4me3 modification participated in the etiology of osteoporosis and may provide new strategies to improve the clinical efficacy of BMP2 in osteoporotic conditions.
Title: KDM5A controls bone morphogenic protein 2-induced osteogenic differentiation of bone mesenchymal stem cells during osteoporosis.
Kdm5a associates with p50 and binds to the Socs1 promoter region in resting natural killer cells.
Title: H3K4me3 Demethylase Kdm5a Is Required for NK Cell Activation by Associating with p50 to Suppress SOCS1.
Data show that NP23 and NJL belong to a subset of chromatin-modifying fusion oncoproteins causing leukemia.
Title: NUP98-PHF23 is a chromatin-modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader function.
Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A.
Title: Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A.
In terminally differentiated cells, common KDM5A and E2F4 gene targets were bound by the pRB-related protein p130, a DREAM complex component.
Title: Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (6) 1 citation
Targeted (3) 1 citation

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

NoName (e-PCR)
- UniSTS:235543

RH142775 (e-PCR)
- UniSTS:232022

RH124853 (e-PCR)
- UniSTS:161675

RH126075 (e-PCR)
- UniSTS:162787

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription cis-regulatory region binding	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in facultative heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
involved_in male gonad development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in protein modification process	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in 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
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-DNA complex	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: RBBP-2; [histone H3]-trimethyl-L-lysine(4) demethylase 5A; histone demethylase JARID1A; jumonji, AT rich interactive domain 1A (Rbp2 like); jumonji/ARID domain-containing protein 1A; lysine (K)-specific demethylase 5A; retinoblastoma binding protein 2

NP_666109.2

EC 1.14.11.67

XP_011239583.1

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.

mRNA and Protein(s)

NM_145997.2 → NP_666109.2 lysine-specific demethylase 5A

Status: VALIDATED

Source sequence(s)

AC078896, AC155720

Consensus CDS

CCDS51889.1

UniProtKB/Swiss-Prot

Q3TM94, Q3UMI5, Q3UXZ9, Q66JZ3

Related

ENSMUSP00000005108.8, ENSMUST00000005108.10

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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

120341060..120421535

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011241281.4 → XP_011239583.1 lysine-specific demethylase 5A isoform X1

UniProtKB/TrEMBL

A0A0N4SVA7

Related

ENSMUSP00000145021.2, ENSMUST00000135802.8

Conserved Domains (6) summary

smart00545
Location:18 → 59

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

pfam02373
Location:470 → 586

JmjC; JmjC domain, hydroxylase

cd16873
Location:84 → 175

ARID_KDM5A; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A)

pfam02928
Location:676 → 728

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:741 → 813

PLU-1; PLU-1-like protein

cl22851
Location:295 → 343

PHD_SF; PHD finger superfamily