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

Gene ID: 5927, updated on 6-Jan-2019

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
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; 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

Genomic context

See KDM5A in Genome Data Viewer
Location:
12p13.33
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (280057..389455, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (389223..498620, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929384 Neighboring gene solute carrier family 6 member 12 Neighboring gene solute carrier family 6 member 13 Neighboring gene uncharacterized LOC102723544 Neighboring gene uncharacterized LOC105369594 Neighboring gene coiled-coil domain containing 77 Neighboring gene beta-1,4-N-acetyl-galactosaminyltransferase 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
chromatin DNA binding IEA
Inferred from Electronic Annotation
more info
 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone binding IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity TAS
Traceable Author Statement
more info
 
NOT histone demethylase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-dimethyl-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-trimethyl-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-trimethyl-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription regulatory region DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 demethylation, trimethyl-H3-K4-specific IEA
Inferred from Electronic Annotation
more info
 
NOT histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of histone deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-DNA complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
lysine-specific demethylase 5A
Names
Jumonji, AT rich interactive domain 1A (RBP2-like)
histone demethylase JARID1A
jumonji/ARID domain-containing protein 1A
lysine (K)-specific demethylase 5A
retinoblastoma binding protein 2

NCBI Reference Sequences (RefSeq)

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

  1. NG_046993.1 RefSeqGene

    Range
    5001..114399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042603.2NP_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
    P29375
    Related
    ENSP00000382688.2, ENST00000399788.6
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    280057..389455 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. 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.
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