Human Gene KDM6B (ENST00000448097.7_8) from GENCODE V47lift37
  Description: lysine demethylase 6B, transcript variant 2 (from RefSeq NM_001348716.2)
Gencode Transcript: ENST00000448097.7_8
Gencode Gene: ENSG00000132510.11_15
Transcript (Including UTRs)
   Position: hg19 chr17:7,737,535-7,758,114 Size: 20,580 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr17:7,748,873-7,756,839 Size: 7,967 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray 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 (chr17:7,737,535-7,758,114)mRNA (may differ from genome)Protein (1643 aa)
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-  Comments and Description Text from UniProtKB
  ID: KDM6B_HUMAN
DESCRIPTION: RecName: Full=Lysine-specific demethylase 6B; EC=1.14.11.-; AltName: Full=JmjC domain-containing protein 3; AltName: Full=Jumonji domain-containing protein 3; AltName: Full=Lysine demethylase 6B;
FUNCTION: Histone demethylase that specifically demethylates 'Lys- 27' of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated H3 'Lys-27'. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation.
COFACTOR: Ascorbate (By similarity).
COFACTOR: Fe(2+).
SUBUNIT: Interacts with TLE1 (By similarity). Component of the MLL4 complex, at least composed of MLL4, ASH2L, RBBP5, WDR5, and KDM6B.
SUBCELLULAR LOCATION: Nucleus (Probable).
INDUCTION: By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells.
SIMILARITY: Belongs to the UTX family.
SIMILARITY: Contains 1 JmjC domain.
SEQUENCE CAUTION: Sequence=BAA21572.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 31.49 RPKM in Whole Blood
Total median expression: 490.52 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 -245.50521-0.471 Picture PostScript Text
3' UTR -447.041275-0.351 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
IPR003347 - JmjC_dom
IPR011990 - TPR-like_helical

Pfam Domains:
PF02373 - JmjC domain, hydroxylase

SCOP Domains:
48452 - TPR-like
101447 - Formin homology 2 domain (FH2 domain)
51182 - RmlC-like cupins
51197 - Clavaminate synthase-like
51215 - Regulatory protein AraC

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2XUE - X-ray MuPIT 2XXZ - X-ray MuPIT 4ASK - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O15054
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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:0003682 chromatin binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0016491 oxidoreductase activity
GO:0032452 histone demethylase activity
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0071558 histone demethylase activity (H3-K27 specific)

Biological Process:
GO:0002437 inflammatory response to antigenic stimulus
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006954 inflammatory response
GO:0010468 regulation of gene expression
GO:0014823 response to activity
GO:0016577 histone demethylation
GO:0021766 hippocampus development
GO:0045165 cell fate commitment
GO:0045446 endothelial cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048333 mesodermal cell differentiation
GO:0055007 cardiac muscle cell differentiation
GO:0055114 oxidation-reduction process
GO:0060992 response to fungicide
GO:0070301 cellular response to hydrogen peroxide
GO:0071557 histone H3-K27 demethylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC067879 - Homo sapiens cDNA clone IMAGE:30343109.
AB002344 - Homo sapiens mRNA for KIAA0346 gene.
JD335845 - Sequence 316869 from Patent EP1572962.
JD126093 - Sequence 107117 from Patent EP1572962.
JD270318 - Sequence 251342 from Patent EP1572962.
JD220681 - Sequence 201705 from Patent EP1572962.
JD051402 - Sequence 32426 from Patent EP1572962.
JD543906 - Sequence 524930 from Patent EP1572962.
JD467191 - Sequence 448215 from Patent EP1572962.
JD135137 - Sequence 116161 from Patent EP1572962.
JD426198 - Sequence 407222 from Patent EP1572962.
AB383855 - Synthetic construct DNA, clone: pF1KSDA0346, Homo sapiens JMJD3 gene for jmjC domain-containing protein 3, complete cds, without stop codon, in Flexi system.
LF209132 - JP 2014500723-A/16635: Polycomb-Associated Non-Coding RNAs.
LF326338 - JP 2014500723-A/133841: Polycomb-Associated Non-Coding RNAs.
LF326336 - JP 2014500723-A/133839: Polycomb-Associated Non-Coding RNAs.
BC009994 - Homo sapiens jumonji domain containing 3, histone lysine demethylase, mRNA (cDNA clone IMAGE:4129810), partial cds.
LF326334 - JP 2014500723-A/133837: Polycomb-Associated Non-Coding RNAs.
LF326331 - JP 2014500723-A/133834: Polycomb-Associated Non-Coding RNAs.
BC035897 - Homo sapiens jumonji domain containing 3, histone lysine demethylase, mRNA (cDNA clone IMAGE:5240292), with apparent retained intron.
JD408816 - Sequence 389840 from Patent EP1572962.
JD257125 - Sequence 238149 from Patent EP1572962.
JD117413 - Sequence 98437 from Patent EP1572962.
JD106369 - Sequence 87393 from Patent EP1572962.
JD055734 - Sequence 36758 from Patent EP1572962.
JD458151 - Sequence 439175 from Patent EP1572962.
JD299444 - Sequence 280468 from Patent EP1572962.
JD280487 - Sequence 261511 from Patent EP1572962.
MA561915 - JP 2018138019-A/133841: Polycomb-Associated Non-Coding RNAs.
MA561913 - JP 2018138019-A/133839: Polycomb-Associated Non-Coding RNAs.
MA561911 - JP 2018138019-A/133837: Polycomb-Associated Non-Coding RNAs.
MA561908 - JP 2018138019-A/133834: Polycomb-Associated Non-Coding RNAs.
MA444709 - JP 2018138019-A/16635: Polycomb-Associated Non-Coding RNAs.

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

Protein O15054 (Reactome details) participates in the following event(s):

R-HSA-8979071 KDM6B binds iron
R-HSA-3222593 KDM6B demethylates H3K27me3 on p16-INK4A promoter
R-HSA-4754187 KDM6A, KDM6B, KDM7A demethylate Me2K28-histone H3
R-HSA-5661121 KDM6A, KDM6B, KDM7A demethylate Me3K28-histone H3
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2559583 Cellular Senescence
R-HSA-3214842 HDMs demethylate histones
R-HSA-2262752 Cellular responses to stress
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: C9IZ40, ENST00000448097.1, ENST00000448097.2, ENST00000448097.3, ENST00000448097.4, ENST00000448097.5, ENST00000448097.6, JMJD3, KDM6B_HUMAN, KIAA0346, NM_001348716, O15054, Q96G33, uc320prx.1, uc320prx.2
UCSC ID: ENST00000448097.7_8
RefSeq Accession: NM_001348716.2
Protein: O15054 (aka KDM6B_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.