Human Gene KDM2B (ENST00000377071.9_9) from GENCODE V47lift37
  Description: lysine demethylase 2B, transcript variant 1 (from RefSeq NM_032590.5)
Gencode Transcript: ENST00000377071.9_9
Gencode Gene: ENSG00000089094.21_14
Transcript (Including UTRs)
   Position: hg19 chr12:121,866,899-122,018,928 Size: 152,030 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg19 chr12:121,868,091-122,018,816 Size: 150,726 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:121,866,899-122,018,928)mRNA (may differ from genome)Protein (1336 aa)
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-  Comments and Description Text from UniProtKB
  ID: KDM2B_HUMAN
DESCRIPTION: RecName: Full=Lysine-specific demethylase 2B; EC=1.14.11.27; AltName: Full=CXXC-type zinc finger protein 2; AltName: Full=F-box and leucine-rich repeat protein 10; AltName: Full=F-box protein FBL10; AltName: Full=F-box/LRR-repeat protein 10; AltName: Full=JmjC domain-containing histone demethylation protein 1B; AltName: Full=Jumonji domain-containing EMSY-interactor methyltransferase motif protein; Short=Protein JEMMA; AltName: Full=Protein-containing CXXC domain 2; AltName: Full=[Histone-H3]-lysine-36 demethylase 1B;
FUNCTION: Histone demethylase that demethylates 'Lys-4' and 'Lys- 36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.
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 (By similarity).
SUBUNIT: Directly interacts with SKP1 and CUL1 (By similarity).
INTERACTION: Q6W2J9:BCOR; NbExp=2; IntAct=EBI-3955564, EBI-950027;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
DOMAIN: The JmjC domain mediates demethylation activity (By similarity). It is also required for repression of ribosomal RNA genes.
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 7 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAH08735.2; Type=Erroneous initiation; Sequence=BAB55112.1; Type=Erroneous initiation; Sequence=BAB55301.1; Type=Erroneous initiation; Sequence=BAC11159.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: KDM2B
Diseases sorted by gene-association score: exencephaly (9), syndromic intellectual disability (6), plexiform neurofibroma (6)

-  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: 13.85 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 171.63 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -22.00112-0.196 Picture PostScript Text
3' UTR -324.301192-0.272 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
IPR002857 - Znf_CXXC
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00646 - F-box domain
PF02008 - CXXC zinc finger domain
PF12937 - F-box-like
PF16866 - PHD-finger
PF17811 - Jumonji helical domain

SCOP Domains:
81383 - F-box domain
88633 - Positive stranded ssRNA viruses
51182 - RmlC-like cupins
51197 - Clavaminate synthase-like
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
57802 - Rubredoxin-like
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q8NHM5
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0019843 rRNA binding
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:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007283 spermatogenesis
GO:0021555 midbrain-hindbrain boundary morphogenesis
GO:0021592 fourth ventricle development
GO:0021670 lateral ventricle development
GO:0021678 third ventricle development
GO:0021993 initiation of neural tube closure
GO:0030307 positive regulation of cell growth
GO:0030900 forebrain development
GO:0030901 midbrain development
GO:0030902 hindbrain development
GO:0035518 histone H2A monoubiquitination
GO:0043524 negative regulation of neuron apoptotic process
GO:0048596 embryonic camera-type eye morphogenesis
GO:0055114 oxidation-reduction process
GO:0070544 histone H3-K36 demethylation
GO:1902459 positive regulation of stem cell population maintenance
GO:2000178 negative regulation of neural precursor cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0031519 PcG protein complex


-  Descriptions from all associated GenBank mRNAs
  AB031230 - Homo sapiens PCCX2 mRNA for protein containing CXXC domain 2, partial cds.
AL133572 - Homo sapiens mRNA; cDNA DKFZp434I0535 (from clone DKFZp434I0535).
AK027440 - Homo sapiens cDNA FLJ14534 fis, clone NT2RM2000599, weakly similar to Homo sapiens F-box protein Lilina (LILINA) mRNA.
BC028612 - Homo sapiens cDNA clone IMAGE:4812413, containing frame-shift errors.
AK127328 - Homo sapiens cDNA FLJ45399 fis, clone BRHIP3028246, highly similar to JmjC domain-containing histone demethylation protein 1B (EC 1.14.11.-).
BC115379 - Homo sapiens F-box and leucine-rich repeat protein 10, mRNA (cDNA clone IMAGE:40029130), complete cds.
BC115380 - Homo sapiens F-box and leucine-rich repeat protein 10, mRNA (cDNA clone MGC:134812 IMAGE:40029132), complete cds.
AK299827 - Homo sapiens cDNA FLJ55590 complete cds, highly similar to JmjC domain-containing histone demethylation protein 1B (EC 1.14.11.-).
AK316470 - Homo sapiens cDNA, FLJ79369 complete cds, highly similar to JmjC domain-containing histone demethylation protein 1B (EC 1.14.11.-).
AJ459424 - Homo sapiens mRNA for JEMMA protein (PCCX2 gene).
BC008735 - Homo sapiens F-box and leucine-rich repeat protein 10, mRNA (cDNA clone IMAGE:3163445), partial cds.
AK027692 - Homo sapiens cDNA FLJ14786 fis, clone NT2RP4000737, moderately similar to Mus musculus F-box protein FBL10 mRNA.
JD111776 - Sequence 92800 from Patent EP1572962.
JD565339 - Sequence 546363 from Patent EP1572962.
JD423557 - Sequence 404581 from Patent EP1572962.
JD147521 - Sequence 128545 from Patent EP1572962.
JD491001 - Sequence 472025 from Patent EP1572962.
JD096283 - Sequence 77307 from Patent EP1572962.
JD176448 - Sequence 157472 from Patent EP1572962.
LF379360 - JP 2014500723-A/186863: Polycomb-Associated Non-Coding RNAs.
AK074718 - Homo sapiens cDNA FLJ90237 fis, clone NT2RM2000622.
JD502899 - Sequence 483923 from Patent EP1572962.
JD565383 - Sequence 546407 from Patent EP1572962.
JD206482 - Sequence 187506 from Patent EP1572962.
JD256143 - Sequence 237167 from Patent EP1572962.
JD048033 - Sequence 29057 from Patent EP1572962.
JD236133 - Sequence 217157 from Patent EP1572962.
MA614937 - JP 2018138019-A/186863: Polycomb-Associated Non-Coding RNAs.
BX648928 - Homo sapiens mRNA; cDNA DKFZp686A1784 (from clone DKFZp686A1784).
KY966266 - Homo sapiens cell line 95T1000 KDM2B/CELF2 fusion mRNA, partial sequence.
AK097933 - Homo sapiens cDNA FLJ40614 fis, clone THYMU2012826.

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

Protein Q8NHM5 (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: A8MRS1, CXXC2, ENST00000377071.1, ENST00000377071.2, ENST00000377071.3, ENST00000377071.4, ENST00000377071.5, ENST00000377071.6, ENST00000377071.7, ENST00000377071.8, FBL10, FBXL10, JHDM1B, KDM2B_HUMAN, NDY1 , NM_032590, PCCX2, Q1RLM7, Q8NCI2, Q8NHM5, Q96HC7, Q96SL0, Q96T03, Q9NS96, Q9UF75, uc318nji.1, uc318nji.2
UCSC ID: ENST00000377071.9_9
RefSeq Accession: NM_032590.5
Protein: Q8NHM5 (aka KDM2B_HUMAN)

-  Gene Model Information
  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.