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    Kdm2a lysine demethylase 2A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361700, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Kdm2aprovided by RGD
    Official Full Name
    lysine demethylase 2Aprovided by RGD
    Primary source
    RGD:1309419
    See related
    Ensembl:ENSRNOG00000019145 AllianceGenome:RGD:1309419
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Fbxl11
    Summary
    Predicted to enable several functions, including histone H3-methyl-lysine-36 demethylase activity; unmethylated CpG binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including double-strand break repair via nonhomologous end joining; protein demethylation; and regulation of gene expression. Predicted to act upstream of or within several processes, including chordate embryonic development; heart looping; and positive regulation of macromolecule metabolic process. Predicted to be located in chromatin and nucleoplasm. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human KDM2A (lysine demethylase 2A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 215.3), Spleen (RPKM 186.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    1q43
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (211041859..211125749, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (201612427..201682359, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (219566130..219642294, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 13D Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene small nucleolar RNA SNORA32 Neighboring gene uncharacterized LOC134483956 Neighboring gene ras homolog family member D Neighboring gene synaptotagmin 12

    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. Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance. Zuo Y, et al. FASEB J, 2023 Mar. PMID 36723950
    2. Fbxl11 Is a Novel Negative Element of the Mammalian Circadian Clock. Reischl S, et al. J Biol Rhythms, 2015 Aug. PMID 26037310
    3. KDM2A promotes lung tumorigenesis by epigenetically enhancing ERK1/2 signaling. Wagner KW, et al. J Clin Invest, 2013 Dec. PMID 24200691, Free PMC Article
    4. Epigenetic switch at atp2a2 and myh7 gene promoters in pressure overload-induced heart failure. Angrisano T, et al. PLoS One, 2014. PMID 25181347, Free PMC Article
    5. CpG islands recruit a histone H3 lysine 36 demethylase. Blackledge NP, et al. Mol Cell, 2010 Apr 23. PMID 20417597, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Stabilization of nuclear beta-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance.
      Title: Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables histone H3K36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables unmethylated CpG binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within heart looping ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within in utero embryonic development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within multicellular organism growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by competitive promoter binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neural tube closure ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuroepithelial cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein demethylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription initiation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 2A
    Names
    F-box and leucine-rich repeat protein 11
    lysine (K)-specific demethylase 2A
    NP_001101985.1
    XP_038939782.1
    XP_063124291.1
    XP_063124292.1
    XP_063124293.1

    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_001108515.1 → NP_001101985.1  lysine-specific demethylase 2A

      See identical proteins and their annotated locations for NP_001101985.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473953
      UniProtKB/TrEMBL
      A0A8I6ARD6, A6HYX1, D3ZTJ7
      Related
      ENSRNOP00000051732.2, ENSRNOT00000054850.3
      Conserved Domains (6) summary
      cd09293
      Location:931 → 1137
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:576 → 609
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:929 → 953
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:619 → 675
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:895 → 935
      F-box-like; F-box-like
      cl21464
      Location:199 → 299
      cupin_like; Conserved domain found in cupin and related proteins

    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_086019.1 Reference GRCr8

      Range
      211041859..211125749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268221.1 → XP_063124291.1  lysine-specific demethylase 2A isoform X1

      UniProtKB/TrEMBL
      A6HYX1, D3ZTJ7

    2. XM_063268223.1 → XP_063124293.1  lysine-specific demethylase 2A isoform X1

      UniProtKB/TrEMBL
      A6HYX1, D3ZTJ7

    3. XM_063268222.1 → XP_063124292.1  lysine-specific demethylase 2A isoform X1

      UniProtKB/TrEMBL
      A6HYX1, D3ZTJ7

    4. XM_039083854.2 → XP_038939782.1  lysine-specific demethylase 2A isoform X2

      Conserved Domains (6) summary
      cd09293
      Location:458 → 664
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:456 → 480
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:146 → 202
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam02008
      Location:103 → 136
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:422 → 460
      F-box-like
      cl40435
      Location:17 → 44
      CTD_KDM2A_2B-like; C-terminal domain found in lysine-specific demethylase KDM2A, KDM2B, and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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