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

Gene ID: 214899, updated on 18-Apr-2024

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 chromatin DNA binding activity and transcription coactivator activity. Involved in circadian regulation of gene expression and negative regulation of histone deacetylase activity. Acts upstream of or within histone H3-K4 demethylation and 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; early conceptus; genitourinary system; limb; 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, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 4.9), placenta adult (RPKM 3.8) and 26 other tissues See more
Orthologs
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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_000072.7Genomic Context describing neighboring genes Neighboring gene ninjurin 2 Neighboring gene STARR-positive B cell enhancer ABC_E2801 Neighboring gene STARR-positive B cell enhancer ABC_E2802 Neighboring gene predicted gene, 25327 Neighboring gene STARR-positive B cell enhancer ABC_E10405 Neighboring gene STARR-seq mESC enhancer starr_17164 Neighboring gene STARR-positive B cell enhancer ABC_E6477 Neighboring gene beta-1,4-N-acetyl-galactosaminyl transferase 3 Neighboring gene STARR-seq mESC enhancer starr_17178 Neighboring gene STARR-seq mESC enhancer starr_17179 Neighboring gene STARR-seq mESC enhancer starr_17181 Neighboring gene coiled-coil domain containing 77 Neighboring gene STARR-positive B cell enhancer ABC_E3675 Neighboring gene STARR-positive B cell enhancer ABC_E11334 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:120314296-120314483 Neighboring gene predicted gene, 24592 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:120416743-120416991 Neighboring gene STARR-positive B cell enhancer ABC_E685 Neighboring gene STARR-positive B cell enhancer ABC_E10406 Neighboring gene interleukin 17 receptor A Neighboring gene transmembrane protein 121B

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC11659

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 dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
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 ISO
Inferred from Sequence Orthology
more info
 
enables histone binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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
 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
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

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
XP_011239583.1

NCBI Reference Sequences (RefSeq)

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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)

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

    See identical proteins and their annotated locations for NP_666109.2

    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:1859
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:85170
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:470586
    JmjC; JmjC domain, hydroxylase
    cd15602
    Location:295343
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)
    cd15606
    Location:11631215
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15686
    Location:16081659
    PHD3_KDM5A; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A)
    pfam02928
    Location:676728
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:7411070
    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

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    120341060..120421535
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A0N4SVA7
    Related
    ENSMUSP00000145021.2, ENSMUST00000135802.8
    Conserved Domains (6) summary
    smart00545
    Location:1859
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:470586
    JmjC; JmjC domain, hydroxylase
    cd16873
    Location:84175
    ARID_KDM5A; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A)
    pfam02928
    Location:676728
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:741813
    PLU-1; PLU-1-like protein
    cl22851
    Location:295343
    PHD_SF; PHD finger superfamily

RNA

  1. XR_004942930.1 RNA Sequence

  2. XR_004942931.1 RNA Sequence

  3. XR_003956180.2 RNA Sequence

  4. XR_004942932.1 RNA Sequence