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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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