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    KDM2A lysine demethylase 2A [ Homo sapiens (human) ]

    Gene ID: 22992, updated on 8-Apr-2018
    Official Symbol
    KDM2Aprovided by HGNC
    Official Full Name
    lysine demethylase 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:13606
    See related
    Ensembl:ENSG00000173120 MIM:605657; Vega:OTTHUMG00000167103
    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
    FBL7; CXXC8; FBL11; FBXL11; JHDM1A; LILINA
    Summary
    This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
    Expression
    Ubiquitous expression in testis (RPKM 25.2), bone marrow (RPKM 22.4) and 25 other tissues See more
    Orthologs
    Location:
    11q13.2
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (67119269..67258082)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66886740..67025553)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ras homolog family member D Neighboring gene translation initiation factor IF-2-like Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene ankyrin repeat domain 13D

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
      HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ00115, FLJ46431, KIAA1004, DKFZp434M1735

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA
    Inferred from Sequence Alignment
    more info
     
    histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    histone demethylase activity (H3-K36 specific) IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone H3-K36 demethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    lysine-specific demethylase 2A
    Names
    CXXC-type zinc finger protein 8
    F-box and leucine-rich repeat protein 11
    F-box/LRR-repeat protein 11
    [Histone-H3]-lysine-36 demethylase 1A
    jmjC domain-containing histone demethylation protein 1A
    jumonji C domain-containing histone demethylase 1A
    lysine (K)-specific demethylase 2A
    NP_001243334.1
    NP_036440.1
    XP_006718543.1
    XP_011543162.1
    XP_011543163.1
    XP_016872880.1
    XP_016872881.1

    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_001256405.1NP_001243334.1  lysine-specific demethylase 2A isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several 5' exons but contains an alternate 5' exon, uses an internal downstream promoter, and differs in its 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b, also known as SF-KDM2A or short-form KDM2A) has a distinct and shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AB490246, AI185920, AL117517, DR001963
      Consensus CDS
      CCDS58148.1
      UniProtKB/Swiss-Prot
      Q9Y2K7
      Related
      ENSP00000435776.1, OTTHUMP00000235170, ENST00000530342.2, OTTHUMT00000393148
      Conserved Domains (5) summary
      cd09293
      Location:493699
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:137170
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:491515
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:180236
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:457497
      F-box-like; F-box-like
    2. NM_012308.2NP_036440.1  lysine-specific demethylase 2A isoform a

      See identical proteins and their annotated locations for NP_036440.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AF179221, AP001885, BC047486, BC064360, BE675843
      Consensus CDS
      CCDS44657.1
      UniProtKB/Swiss-Prot
      Q9Y2K7
      UniProtKB/TrEMBL
      I3VM53
      Related
      ENSP00000432786.1, OTTHUMP00000235169, ENST00000529006.6, OTTHUMT00000393140
      Conserved Domains (6) summary
      pfam02008
      Location:576609
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:930954
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:619675
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:896934
      F-box-like; F-box-like
      cl21464
      Location:199299
      cupin_like; Conserved domain found in cupin and related proteins
      cl28166
      Location:9321138
      AMN1; Antagonist of mitotic exit network protein 1

    RNA

    1. NR_027473.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AP001885, BC047486, BE675843
      Related
      ENST00000398645.6, OTTHUMT00000393139

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

      Range
      67119269..67258082
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544860.3XP_011543162.1  lysine-specific demethylase 2A isoform X2

      Conserved Domains (6) summary
      cd09293
      Location:9041110
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:548581
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:902926
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:591647
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:868908
      F-box-like; F-box-like
      cl21464
      Location:199299
      cupin_like; Conserved domain found in cupin and related proteins
    2. XM_017017391.1XP_016872880.1  lysine-specific demethylase 2A isoform X1

      UniProtKB/TrEMBL
      I3VM54
      Related
      ENSP00000309302.6, ENST00000308783.9
      Conserved Domains (6) summary
      pfam02008
      Location:559592
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:913937
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:602658
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:879917
      F-box-like; F-box-like
      cl21464
      Location:182282
      cupin_like; Conserved domain found in cupin and related proteins
      cl28166
      Location:9151121
      AMN1; Antagonist of mitotic exit network protein 1
    3. XM_017017392.1XP_016872881.1  lysine-specific demethylase 2A isoform X1

      UniProtKB/TrEMBL
      I3VM54
      Conserved Domains (6) summary
      pfam02008
      Location:559592
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:913937
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:602658
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:879917
      F-box-like; F-box-like
      cl21464
      Location:182282
      cupin_like; Conserved domain found in cupin and related proteins
      cl28166
      Location:9151121
      AMN1; Antagonist of mitotic exit network protein 1
    4. XM_006718480.3XP_006718543.1  lysine-specific demethylase 2A isoform X3

      Conserved Domains (6) summary
      cd09293
      Location:8371043
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:481514
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:835859
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:524580
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:801841
      F-box-like; F-box-like
      cl21464
      Location:104204
      cupin_like; Conserved domain found in cupin and related proteins
    5. XM_011544861.1XP_011543163.1  lysine-specific demethylase 2A isoform X4

      UniProtKB/Swiss-Prot
      Q9Y2K7
      Conserved Domains (5) summary
      cd09293
      Location:626832
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:270303
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:624648
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:313369
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam12937
      Location:590630
      F-box-like; F-box-like
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