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

Gene ID: 361700, updated on 27-Nov-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
EnsemblRapid: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 H3K36 demethylase activity; unmethylated CpG binding activity; and zinc ion binding activity. Predicted to be involved in double-strand break repair via nonhomologous end joining; regulation of circadian rhythm; and regulation of gene expression. Predicted to act upstream of or within several processes, including epithelial tube morphogenesis; neuroepithelial cell differentiation; and regulation of gene expression. 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, Nov 2024]
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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See Kdm2a in Genome Data Viewer
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 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 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 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
located_in 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
    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
    Related
    ENSRNOP00000097302.1, ENSRNOT00000098321.2

  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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