Human Gene KDM2A (uc001ojw.3) Description and Page Index
  Description: Homo sapiens lysine (K)-specific demethylase 2A (KDM2A), transcript variant 1, mRNA.
RefSeq Summary (NM_012308): 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].
Transcript (Including UTRs)
   Position: hg19 chr11:66,886,740-67,025,550 Size: 138,811 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr11:66,888,788-67,022,526 Size: 133,739 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:66,886,740-67,025,550)mRNA (may differ from genome)Protein (1162 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: KDM2A_HUMAN
DESCRIPTION: RecName: Full=Lysine-specific demethylase 2A; EC=1.14.11.27; AltName: Full=CXXC-type zinc finger protein 8; AltName: Full=F-box and leucine-rich repeat protein 11; AltName: Full=F-box protein FBL7; AltName: Full=F-box protein Lilina; AltName: Full=F-box/LRR-repeat protein 11; AltName: Full=JmjC domain-containing histone demethylation protein 1A; AltName: Full=[Histone-H3]-lysine-36 demethylase 1A;
FUNCTION: Histone demethylase that specifically demethylates 'Lys- 36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys- 36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis.
CATALYTIC ACTIVITY: Protein N(6),N(6)-dimethyl-L-lysine + 2- oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2).
CATALYTIC ACTIVITY: Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate + formaldehyde + CO(2).
COFACTOR: Binds 1 Fe(2+) ion per subunit.
SUBUNIT: Part of a SCF (SKP1-cullin-F-box) protein ligase complex (By similarity). Interacts with CBX5/HP1A; the interaction promotes CBX5 localization to chromatin.
SUBCELLULAR LOCATION: Nucleus, nucleoplasm. Note=Punctate expression throughout the nucleoplasm and enriched in the perinucleolar region. Specifically nucleates at CpG islands where it's presence results in chromatin depleted in H3K36me2.
TISSUE SPECIFICITY: Widely expressed, with highest levels in brain, testis and ovary, followed by lung.
DOMAIN: The JmjC domain mediates demethylation activity and is required for satellite silencing.
DOMAIN: The CXXC zinc finger preferentially recognizes nonmethylated CpG DNA, and binding is blocked when the CpG DNA is methylated.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the JHDM1 histone demethylase family.
SIMILARITY: Contains 1 CXXC-type zinc finger.
SIMILARITY: Contains 1 F-box domain.
SIMILARITY: Contains 1 JmjC domain.
SIMILARITY: Contains 6 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAD56012.1; Type=Erroneous initiation; Sequence=BAA76848.2; Type=Erroneous initiation; Sequence=BAB15795.1; Type=Frameshift; Positions=410;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.12 RPKM in Testis
Total median expression: 767.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -458.00864-0.530 Picture PostScript Text
3' UTR -1077.103024-0.356 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001810 - F-box_dom_cyclin-like
IPR003347 - JmjC_dom
IPR019786 - Zinc_finger_PHD-type_CS
IPR002857 - Znf_CXXC
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00646 - F-box domain
PF02008 - CXXC zinc finger domain
PF02373 - JmjC domain, hydroxylase
PF12937 - F-box-like
PF16866 - PHD-finger

SCOP Domains:
81383 - F-box domain
51182 - RmlC-like cupins
51197 - Clavaminate synthase-like
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2YU1
- X-ray MuPIT

2YU2
- X-ray MuPIT

4BBQ
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y2K7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0032452 histone demethylase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0051864 histone demethylase activity (H3-K36 specific)

Biological Process:
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0055114 oxidation-reduction process
GO:0070544 histone H3-K36 demethylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC047486 - Homo sapiens F-box and leucine-rich repeat protein 11, mRNA (cDNA clone MGC:51265 IMAGE:5296445), complete cds.
BC064360 - Homo sapiens F-box and leucine-rich repeat protein 11, mRNA (cDNA clone MGC:74784 IMAGE:5534384), complete cds.
AB023221 - Homo sapiens KIAA1004 mRNA for KIAA1004 protein.
AK024505 - Homo sapiens mRNA for FLJ00115 protein, partial cds.
JQ710741 - Homo sapiens lysine-specific demethylase 2A (KDM2A) mRNA, complete cds, alternatively spliced.
JQ710742 - Homo sapiens N-terminus deleted lysine-specific demethylase 2A (KDM2A) mRNA, complete cds, alternatively spliced.
JQ710743 - Homo sapiens N-terminal-782AA lysine-specific demethylase 2A (KDM2A) mRNA, complete cds, alternatively spliced.
JQ710744 - Homo sapiens C-terminal-620AA lysine-specific demethylase 2A (KDM2A) mRNA, complete cds, alternatively spliced.
AB384080 - Synthetic construct DNA, clone: pF1KSDA1004, Homo sapiens FBXL11 gene for jmjC domain-containing histone demethylation protein 1A, complete cds, without stop codon, in Flexi system.
BC047371 - Homo sapiens F-box and leucine-rich repeat protein 11, mRNA (cDNA clone MGC:48461 IMAGE:5270744), complete cds.
JD520927 - Sequence 501951 from Patent EP1572962.
JD410721 - Sequence 391745 from Patent EP1572962.
JD468543 - Sequence 449567 from Patent EP1572962.
JD393119 - Sequence 374143 from Patent EP1572962.
JD504122 - Sequence 485146 from Patent EP1572962.
DQ587173 - Homo sapiens piRNA piR-54285, complete sequence.
AB490246 - Homo sapiens kdm2a mRNA for SF-KDM2A, complete cds.
AK299725 - Homo sapiens cDNA FLJ51294 complete cds, highly similar to JmjC domain-containing histone demethylation protein 1A (EC 1.14.11.-).
DQ583103 - Homo sapiens piRNA piR-50215, complete sequence.
BC056905 - Homo sapiens F-box and leucine-rich repeat protein 11, mRNA (cDNA clone IMAGE:6171996), partial cds.
AF179221 - Homo sapiens F-box protein Lilina (LILINA) mRNA, complete cds.
AK128293 - Homo sapiens cDNA FLJ46431 fis, clone THYMU3014620, highly similar to Homo sapiens F-box protein Lilina (LILINA) mRNA.
AK022684 - Homo sapiens cDNA FLJ12622 fis, clone NT2RM4001731, highly similar to Homo sapiens F-box protein Lilina (LILINA) mRNA.
BC001203 - Homo sapiens, Similar to f-box and leucine-rich repeat protein 11, clone IMAGE:3357072, mRNA, partial cds.
BC027467 - Homo sapiens F-box and leucine-rich repeat protein 11, mRNA (cDNA clone IMAGE:4478268), with apparent retained intron.
AL117517 - Homo sapiens mRNA; cDNA DKFZp434M1735 (from clone DKFZp434M1735).
JD514369 - Sequence 495393 from Patent EP1572962.
JD306612 - Sequence 287636 from Patent EP1572962.
JD421621 - Sequence 402645 from Patent EP1572962.
JD143003 - Sequence 124027 from Patent EP1572962.
JD519509 - Sequence 500533 from Patent EP1572962.
JD417490 - Sequence 398514 from Patent EP1572962.
JD483133 - Sequence 464157 from Patent EP1572962.
JD510609 - Sequence 491633 from Patent EP1572962.
JD261062 - Sequence 242086 from Patent EP1572962.
JD260419 - Sequence 241443 from Patent EP1572962.
JD434827 - Sequence 415851 from Patent EP1572962.
JD544654 - Sequence 525678 from Patent EP1572962.
JD233821 - Sequence 214845 from Patent EP1572962.
JD095410 - Sequence 76434 from Patent EP1572962.
JD162395 - Sequence 143419 from Patent EP1572962.
JD487544 - Sequence 468568 from Patent EP1572962.
JD108248 - Sequence 89272 from Patent EP1572962.
JD316179 - Sequence 297203 from Patent EP1572962.
JD340371 - Sequence 321395 from Patent EP1572962.
JD068333 - Sequence 49357 from Patent EP1572962.
JD037000 - Sequence 18024 from Patent EP1572962.
JD131544 - Sequence 112568 from Patent EP1572962.
JD271894 - Sequence 252918 from Patent EP1572962.
JD290741 - Sequence 271765 from Patent EP1572962.
JD386193 - Sequence 367217 from Patent EP1572962.
JD259996 - Sequence 241020 from Patent EP1572962.
JD059264 - Sequence 40288 from Patent EP1572962.
JD449331 - Sequence 430355 from Patent EP1572962.
JD177024 - Sequence 158048 from Patent EP1572962.
JD105020 - Sequence 86044 from Patent EP1572962.
JD415884 - Sequence 396908 from Patent EP1572962.
JD107796 - Sequence 88820 from Patent EP1572962.
JD310066 - Sequence 291090 from Patent EP1572962.
JD455687 - Sequence 436711 from Patent EP1572962.
JD233421 - Sequence 214445 from Patent EP1572962.
JD283932 - Sequence 264956 from Patent EP1572962.
JD496709 - Sequence 477733 from Patent EP1572962.
JD540954 - Sequence 521978 from Patent EP1572962.
JD259334 - Sequence 240358 from Patent EP1572962.
JD450104 - Sequence 431128 from Patent EP1572962.
JD393643 - Sequence 374667 from Patent EP1572962.
JD161337 - Sequence 142361 from Patent EP1572962.
JD280649 - Sequence 261673 from Patent EP1572962.
JD451666 - Sequence 432690 from Patent EP1572962.
JD227989 - Sequence 209013 from Patent EP1572962.
JD328349 - Sequence 309373 from Patent EP1572962.
JD370732 - Sequence 351756 from Patent EP1572962.
JD392210 - Sequence 373234 from Patent EP1572962.
JD455738 - Sequence 436762 from Patent EP1572962.
JD265499 - Sequence 246523 from Patent EP1572962.
JD468940 - Sequence 449964 from Patent EP1572962.
JD082222 - Sequence 63246 from Patent EP1572962.
JD540298 - Sequence 521322 from Patent EP1572962.
JD300987 - Sequence 282011 from Patent EP1572962.
JD205729 - Sequence 186753 from Patent EP1572962.
JD186793 - Sequence 167817 from Patent EP1572962.
JD048264 - Sequence 29288 from Patent EP1572962.
JD204996 - Sequence 186020 from Patent EP1572962.
JD399603 - Sequence 380627 from Patent EP1572962.
JD535696 - Sequence 516720 from Patent EP1572962.
JD470343 - Sequence 451367 from Patent EP1572962.
JD422594 - Sequence 403618 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y2K7 (Reactome details) participates in the following event(s):

R-HSA-4722133 KDM2A, KDM2B, KDM4A demethylate MeK37-histone H3
R-HSA-5661114 KDM2A, KDM2B, KDM4A, KDM8 demethylate Me2K37-histone H3
R-HSA-3214842 HDMs demethylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: CXXC8, FBL7, FBXL11, JHDM1A, KDM2A_HUMAN, KIAA1004, NM_012308, NP_036440, Q49A21, Q4G0M3, Q69YY8, Q9BVH5, Q9H7H5, Q9UK66, Q9Y2K7
UCSC ID: uc001ojw.3
RefSeq Accession: NM_012308
Protein: Q9Y2K7 (aka KDM2A_HUMAN)
CCDS: CCDS44657.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012308.2
exon count: 21CDS single in 3' UTR: no RNA size: 7393
ORF size: 3489CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7142.00frame shift in genome: no % Coverage: 99.78
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.