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

Gene ID: 22992, updated on 6-Jan-2019

Summary

Official Symbol
KDM2Aprovided by HGNC
Official Full Name
lysine demethylase 2Aprovided by HGNC
Primary source
HGNC:HGNC:13606
See related
Ensembl:ENSG00000173120 MIM:605657
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

Genomic context

See KDM2A in Genome Data Viewer
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

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
 
DNA-binding transcription factor activity, RNA polymerase II-specific 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
 
Component Evidence Code Pubs
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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, ENST00000530342.2
    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_012308.3NP_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, AP000729, AP001885, BC047486, BC064360, BE675843
    Consensus CDS
    CCDS44657.1
    UniProtKB/Swiss-Prot
    Q9Y2K7
    UniProtKB/TrEMBL
    I3VM53
    Related
    ENSP00000432786.1, ENST00000529006.6
    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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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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