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Kdm5a lysine demethylase 5A [ Rattus norvegicus (Norway rat) ]

Gene ID: 312678, updated on 30-Mar-2024

Summary

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Official Symbol
Kdm5aprovided by RGD
Official Full Name
lysine demethylase 5Aprovided by RGD
Primary source
RGD:1305429
See related
Ensembl:ENSRNOG00000010591 AllianceGenome:RGD:1305429
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Jarid1a
Summary
Predicted to enable several functions, including DNA binding activity; histone H3-tri/di/monomethyl-lysine-4 demethylase activity; and zinc ion binding activity. Involved in histone H3-K4 demethylation; male gonad development; and spermatogenesis. Predicted to be part of protein-DNA complex. Predicted to be active in nucleus. Biomarker of cryptorchidism. 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
Biased expression in Thymus (RPKM 242.5), Spleen (RPKM 198.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Kdm5a in Genome Data Viewer
Location:
4q42
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (155238124..155316121)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (153565909..153643912)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (152892388..152972196)

Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134486682 Neighboring gene transfer RNA leucine (anticodon AAG) 13 Neighboring gene coiled-coil domain containing 77 Neighboring gene interleukin 17 receptor A Neighboring gene transmembrane protein 121B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. The histone demethylase KDM5A is required for the repression of astrocytogenesis and regulated by the translational machinery in neural progenitor cells. Kong SY, et al. FASEB J, 2018 Feb. PMID 29212818, Free PMC Article
  2. Distinctive changes in histone H3K4 modification mediated via Kdm5a expression in spermatogonial stem cells of cryptorchid testes. Nishio H, et al. J Urol, 2014 May. PMID 24679876
  3. LINC00092 derived from follicular fluid alleviated the symptoms of PCOS through inactivation of phosphatase and tensin homolog by recruiting KDM5A. Zhou Z, et al. Reprod Biol, 2023 Jun. PMID 37084543
  4. Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors. Labadie SS, et al. Bioorg Med Chem Lett, 2016 Sep 15. PMID 27499454
  5. The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif. Tu S, et al. Nat Struct Mol Biol, 2008 Apr. PMID 18270511

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LINC00092 derived from follicular fluid alleviated the symptoms of PCOS through inactivation of phosphatase and tensin homolog by recruiting KDM5A.
    Title: LINC00092 derived from follicular fluid alleviated the symptoms of PCOS through inactivation of phosphatase and tensin homolog by recruiting KDM5A.
  2. These data suggest that KDM5A is a key regulator that maintains neural progenitor cells in an undifferentiated state by repressing astrocytogenesis and that its expression is translationally controlled during astrocyte differentiation.
    Title: The histone demethylase KDM5A is required for the repression of astrocytogenesis and regulated by the translational machinery in neural progenitor cells.
  3. Kdm5a expression was significantly higher in undescended testes.
    Title: Distinctive changes in histone H3K4 modification mediated via Kdm5a expression in spermatogonial stem cells of cryptorchid testes.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Clone Names

  • MGC189432

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables enzyme inhibitor activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K4 demethylase activity ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
enables histone binding ISO
Inferred from Sequence Orthology
more info
  
enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription coactivator activity ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
involved_in facultative heterochromatin formation ISO
Inferred from Sequence Orthology
more info
  
involved_in male gonad development IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in protein modification process IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of protein-DNA complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
lysine-specific demethylase 5A
Names
jumonji, AT rich interactive domain 1A (Rbp2 like)
lysine (K)-specific demethylase 5A
NP_001264106.1
NP_001264107.1

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_001277177.1 → NP_001264106.1  lysine-specific demethylase 5A isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    JAXUCZ010000004
    UniProtKB/TrEMBL
    A0A0G2K454
    Related
    ENSRNOP00000068325.1, ENSRNOT00000075895.3
    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

  2. NM_001277178.1 → NP_001264107.1  lysine-specific demethylase 5A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several exons and its transcription extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    JAXUCZ010000004
    UniProtKB/TrEMBL
    B5DFF8
    Conserved Domains (4) 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 → 552
    JmjC; JmjC domain, hydroxylase
    cd15602
    Location:295 → 343
    PHD1_KDM5A; PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086022.1 Reference GRCr8

    Range
    155238124..155316121
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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