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

    Gene ID: 5927, updated on 27-Nov-2024

    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
    NEW
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    Genomic context

    See KDM5A in Genome Data Viewer
    Location:
    12p13.33
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (280057..389320, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (276885..386174, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (389223..498486, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene solute carrier family 6 member 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:320888-321660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:322433-323204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:329915-330870 Neighboring gene solute carrier family 6 member 13 Neighboring gene uncharacterized LOC102723544 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:415875-417074 Neighboring gene Sharpr-MPRA regulatory region 4015 Neighboring gene uncharacterized LOC105369594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:511068-511620 Neighboring gene Sharpr-MPRA regulatory region 4380 Neighboring gene coiled-coil domain containing 77 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:568273-569256 Neighboring gene uncharacterized LOC124902853 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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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 
    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 
    part_of 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 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

    NCBI Reference Sequences (RefSeq)

    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

    1. NG_046993.1 RefSeqGene

      Range
      5136..114399
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001042603.3NP_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: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_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      280057..389320 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. 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

    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.