Human Gene KDM5B (ENST00000367265.9_10) from GENCODE V47lift37
  Description: lysine demethylase 5B, transcript variant 2 (from RefSeq NM_006618.5)
Gencode Transcript: ENST00000367265.9_10
Gencode Gene: ENSG00000117139.18_21
Transcript (Including UTRs)
   Position: hg19 chr1:202,693,623-202,777,549 Size: 83,927 Total Exon Count: 27 Strand: -
Coding Region
   Position: hg19 chr1:202,698,164-202,777,433 Size: 79,270 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:202,693,623-202,777,549)mRNA (may differ from genome)Protein (1544 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KDM5B_HUMAN
DESCRIPTION: RecName: Full=Lysine-specific demethylase 5B; EC=1.14.11.-; AltName: Full=Cancer/testis antigen 31; Short=CT31; AltName: Full=Histone demethylase JARID1B; AltName: Full=Jumonji/ARID domain-containing protein 1B; AltName: Full=PLU-1; AltName: Full=Retinoblastoma-binding protein 2 homolog 1; Short=RBP2-H1;
FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma.
COFACTOR: Binds 1 Fe(2+) ion per subunit (By similarity).
SUBUNIT: Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7 (By similarity).
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitously expressed, with highest levels in testis. Down-regulated in melanoma and glioblastoma. Up-regulated in breast cancer (at protein level).
DOMAIN: Both the JmjC domain and the JmjN domain are required for enzymatic activity.
DOMAIN: The 2 first PHD-type zinc finger domains are required for transcription repression activity.
SIMILARITY: Belongs to the JARID1 histone demethylase family.
SIMILARITY: Contains 1 ARID domain.
SIMILARITY: Contains 1 JmjC domain.
SIMILARITY: Contains 1 JmjN domain.
SIMILARITY: Contains 3 PHD-type zinc fingers.
SEQUENCE CAUTION: Sequence=CAB63108.1; 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


-  MalaCards Disease Associations
  MalaCards Gene Search: KDM5B
Diseases sorted by gene-association score: ascending colon cancer (11), autosomal dominant non-syndromic intellectual disability* (6), melanoma (3), breast cancer (2)
* = Manually curated disease association

-  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: 65.25 RPKM in Testis
Total median expression: 389.36 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 -37.80116-0.326 Picture PostScript Text
3' UTR -1241.804541-0.273 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
IPR001606 - ARID/BRIGHT_DNA-bd
IPR003347 - JmjC_dom
IPR013637 - Lys_sp_deMease_like_dom
IPR003349 - TF_JmjN
IPR019786 - Zinc_finger_PHD-type_CS
IPR004198 - Znf_C5HC2
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF01388 - ARID/BRIGHT DNA binding domain
PF02373 - JmjC domain, hydroxylase
PF02375 - jmjN domain
PF02928 - C5HC2 zinc finger
PF08429 - PLU-1-like protein

SCOP Domains:
46774 - ARID-like
51197 - Clavaminate synthase-like
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9UGL1
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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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0032452 histone demethylase activity
GO:0032453 histone demethylase activity (H3-K4 specific)
GO:0034647 histone demethylase activity (H3-trimethyl-K4 specific)
GO:0034648 histone demethylase activity (H3-dimethyl-K4 specific)
GO:0042393 histone binding
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:1990837 sequence-specific double-stranded DNA binding

Biological Process:
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:0007338 single fertilization
GO:0009791 post-embryonic development
GO:0010628 positive regulation of gene expression
GO:0033601 positive regulation of mammary gland epithelial cell proliferation
GO:0034720 histone H3-K4 demethylation
GO:0034721 histone H3-K4 demethylation, trimethyl-H3-K4-specific
GO:0044344 cellular response to fibroblast growth factor stimulus
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048511 rhythmic process
GO:0055114 oxidation-reduction process
GO:0060444 branching involved in mammary gland duct morphogenesis
GO:0060763 mammary duct terminal end bud growth
GO:0060992 response to fungicide
GO:0061038 uterus morphogenesis
GO:0070306 lens fiber cell differentiation
GO:1990830 cellular response to leukemia inhibitory factor
GO:2000864 regulation of estradiol secretion

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LP895185 - Sequence 49 from Patent EP3253886.
AJ132440 - Homo sapiens mRNA for PLU-1 protein.
LF383641 - JP 2014500723-A/191144: Polycomb-Associated Non-Coding RNAs.
AJ243706 - Homo sapiens mRNA for RB-binding protein (rbbp2h1a gene).
AF087481 - Homo sapiens retinoblastoma binding protein 2 homolog 1 (RBBP2H1) mRNA, complete cds.
BC157031 - Synthetic construct Homo sapiens clone IMAGE:100063314, MGC:190738 jumonji, AT rich interactive domain 1B (JARID1B) mRNA, encodes complete protein.
BC156049 - Synthetic construct Homo sapiens clone IMAGE:100062365, MGC:190485 jumonji, AT rich interactive domain 1B (JARID1B) mRNA, encodes complete protein.
AK122752 - Homo sapiens cDNA FLJ16281 fis, clone NT2RI3003104, highly similar to Homo sapiens Jumonji, AT rich interactive domain 1B (RBP2-like) (JARID1B), mRNA.
MA619218 - JP 2018138019-A/191144: Polycomb-Associated Non-Coding RNAs.
LF319667 - JP 2014500723-A/127170: Polycomb-Associated Non-Coding RNAs.
AL133048 - Homo sapiens mRNA; cDNA DKFZp434D0815 (from clone DKFZp434D0815); partial cds.
AL833515 - Homo sapiens mRNA; cDNA DKFZp686F1537 (from clone DKFZp686F1537).
AK074250 - Homo sapiens cDNA FLJ23670 fis, clone HEP04649, highly similar to Homo sapiens mRNA for PLU-1 protein.
AL133040 - Homo sapiens mRNA; cDNA DKFZp434N0335 (from clone DKFZp434N0335); partial cds.
AK022521 - Homo sapiens cDNA FLJ12459 fis, clone NT2RM1000691, highly similar to Homo sapiens Jumonji, AT rich interactive domain 1B (RBP2-like) (JARID1B), mRNA.
JD089823 - Sequence 70847 from Patent EP1572962.
JD053191 - Sequence 34215 from Patent EP1572962.
JD501384 - Sequence 482408 from Patent EP1572962.
JD298137 - Sequence 279161 from Patent EP1572962.
JD103448 - Sequence 84472 from Patent EP1572962.
JD554566 - Sequence 535590 from Patent EP1572962.
LF319666 - JP 2014500723-A/127169: Polycomb-Associated Non-Coding RNAs.
JD304820 - Sequence 285844 from Patent EP1572962.
JD561722 - Sequence 542746 from Patent EP1572962.
JD260863 - Sequence 241887 from Patent EP1572962.
JD293805 - Sequence 274829 from Patent EP1572962.
JD202440 - Sequence 183464 from Patent EP1572962.
JD559796 - Sequence 540820 from Patent EP1572962.
JD201661 - Sequence 182685 from Patent EP1572962.
JD485128 - Sequence 466152 from Patent EP1572962.
JD157358 - Sequence 138382 from Patent EP1572962.
JD183450 - Sequence 164474 from Patent EP1572962.
JD101141 - Sequence 82165 from Patent EP1572962.
AL133072 - Homo sapiens mRNA; cDNA DKFZp434I0617 (from clone DKFZp434I0617); partial cds.
JD290110 - Sequence 271134 from Patent EP1572962.
JD202139 - Sequence 183163 from Patent EP1572962.
JD300926 - Sequence 281950 from Patent EP1572962.
JD359585 - Sequence 340609 from Patent EP1572962.
JD315220 - Sequence 296244 from Patent EP1572962.
JD292102 - Sequence 273126 from Patent EP1572962.
JD549260 - Sequence 530284 from Patent EP1572962.
AL137622 - Homo sapiens mRNA; cDNA DKFZp434I2412 (from clone DKFZp434I2412); partial cds.
LF319665 - JP 2014500723-A/127168: Polycomb-Associated Non-Coding RNAs.
JD431449 - Sequence 412473 from Patent EP1572962.
JD065232 - Sequence 46256 from Patent EP1572962.
JD324132 - Sequence 305156 from Patent EP1572962.
JD240714 - Sequence 221738 from Patent EP1572962.
JD248490 - Sequence 229514 from Patent EP1572962.
JD429059 - Sequence 410083 from Patent EP1572962.
DQ597891 - Homo sapiens piRNA piR-35957, complete sequence.
AB015348 - Homo sapiens HRIHFB2060 mRNA, partial cds.
LF319664 - JP 2014500723-A/127167: Polycomb-Associated Non-Coding RNAs.
AK001400 - Homo sapiens cDNA FLJ10538 fis, clone NT2RP2001127, highly similar to Homo sapiens Jumonji, AT rich interactive domain 1B (RBP2-like) (JARID1B), mRNA.
AK022553 - Homo sapiens cDNA FLJ12491 fis, clone NT2RM2001605, highly similar to Homo sapiens Jumonji, AT rich interactive domain 1B (RBP2-like) (JARID1B), mRNA.
LF319661 - JP 2014500723-A/127164: Polycomb-Associated Non-Coding RNAs.
LF319658 - JP 2014500723-A/127161: Polycomb-Associated Non-Coding RNAs.
LF319656 - JP 2014500723-A/127159: Polycomb-Associated Non-Coding RNAs.
LF319655 - JP 2014500723-A/127158: Polycomb-Associated Non-Coding RNAs.
LF319653 - JP 2014500723-A/127156: Polycomb-Associated Non-Coding RNAs.
LF319652 - JP 2014500723-A/127155: Polycomb-Associated Non-Coding RNAs.
LF319651 - JP 2014500723-A/127154: Polycomb-Associated Non-Coding RNAs.
LF319650 - JP 2014500723-A/127153: Polycomb-Associated Non-Coding RNAs.
LF319648 - JP 2014500723-A/127151: Polycomb-Associated Non-Coding RNAs.
LF319647 - JP 2014500723-A/127150: Polycomb-Associated Non-Coding RNAs.
LF319645 - JP 2014500723-A/127148: Polycomb-Associated Non-Coding RNAs.
LF319644 - JP 2014500723-A/127147: Polycomb-Associated Non-Coding RNAs.
LF319643 - JP 2014500723-A/127146: Polycomb-Associated Non-Coding RNAs.
LF319641 - JP 2014500723-A/127144: Polycomb-Associated Non-Coding RNAs.
LF319640 - JP 2014500723-A/127143: Polycomb-Associated Non-Coding RNAs.
LF319639 - JP 2014500723-A/127142: Polycomb-Associated Non-Coding RNAs.
LF319637 - JP 2014500723-A/127140: Polycomb-Associated Non-Coding RNAs.
LF319635 - JP 2014500723-A/127138: Polycomb-Associated Non-Coding RNAs.
LF319632 - JP 2014500723-A/127135: Polycomb-Associated Non-Coding RNAs.
LF319631 - JP 2014500723-A/127134: Polycomb-Associated Non-Coding RNAs.
LF319630 - JP 2014500723-A/127133: Polycomb-Associated Non-Coding RNAs.
LF319629 - JP 2014500723-A/127132: Polycomb-Associated Non-Coding RNAs.
MA555244 - JP 2018138019-A/127170: Polycomb-Associated Non-Coding RNAs.
MA555243 - JP 2018138019-A/127169: Polycomb-Associated Non-Coding RNAs.
MA555242 - JP 2018138019-A/127168: Polycomb-Associated Non-Coding RNAs.
MA555241 - JP 2018138019-A/127167: Polycomb-Associated Non-Coding RNAs.
MA555238 - JP 2018138019-A/127164: Polycomb-Associated Non-Coding RNAs.
MA555235 - JP 2018138019-A/127161: Polycomb-Associated Non-Coding RNAs.
MA555233 - JP 2018138019-A/127159: Polycomb-Associated Non-Coding RNAs.
MA555232 - JP 2018138019-A/127158: Polycomb-Associated Non-Coding RNAs.
MA555230 - JP 2018138019-A/127156: Polycomb-Associated Non-Coding RNAs.
MA555229 - JP 2018138019-A/127155: Polycomb-Associated Non-Coding RNAs.
MA555228 - JP 2018138019-A/127154: Polycomb-Associated Non-Coding RNAs.
MA555227 - JP 2018138019-A/127153: Polycomb-Associated Non-Coding RNAs.
MA555225 - JP 2018138019-A/127151: Polycomb-Associated Non-Coding RNAs.
MA555224 - JP 2018138019-A/127150: Polycomb-Associated Non-Coding RNAs.
MA555222 - JP 2018138019-A/127148: Polycomb-Associated Non-Coding RNAs.
MA555221 - JP 2018138019-A/127147: Polycomb-Associated Non-Coding RNAs.
MA555220 - JP 2018138019-A/127146: Polycomb-Associated Non-Coding RNAs.
MA555218 - JP 2018138019-A/127144: Polycomb-Associated Non-Coding RNAs.
MA555217 - JP 2018138019-A/127143: Polycomb-Associated Non-Coding RNAs.
MA555216 - JP 2018138019-A/127142: Polycomb-Associated Non-Coding RNAs.
MA555214 - JP 2018138019-A/127140: Polycomb-Associated Non-Coding RNAs.
MA555212 - JP 2018138019-A/127138: Polycomb-Associated Non-Coding RNAs.
MA555209 - JP 2018138019-A/127135: Polycomb-Associated Non-Coding RNAs.
MA555208 - JP 2018138019-A/127134: Polycomb-Associated Non-Coding RNAs.
MA555207 - JP 2018138019-A/127133: Polycomb-Associated Non-Coding RNAs.
MA555206 - JP 2018138019-A/127132: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9UGL1 (Reactome details) participates in the following event(s):

R-HSA-8865265 TFAP2C homodimer binds MYC and KDM5B
R-HSA-8865280 TFAP2C homodimer binds the CDKN1A (p21) gene promoter
R-HSA-4754181 KDM5A-D demethylate Me2K5-histone H3
R-HSA-5661116 KDM5A-D demethylate Me3K5-histone H3
R-HSA-8866911 TFAP2 (AP-2) family regulates transcription of cell cycle factors
R-HSA-8864260 Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
R-HSA-3214842 HDMs demethylate histones
R-HSA-212436 Generic Transcription Pathway
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-4839726 Chromatin organization
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000367265.1, ENST00000367265.2, ENST00000367265.3, ENST00000367265.4, ENST00000367265.5, ENST00000367265.6, ENST00000367265.7, ENST00000367265.8, JARID1B, KDM5B_HUMAN, NM_006618, O95811, PLU1, Q15752, Q9UGL1, Q9Y3Q5, RBBP2H1, uc318ftz.1, uc318ftz.2
UCSC ID: ENST00000367265.9_10
RefSeq Accession: NM_006618.5
Protein: Q9UGL1 (aka KDM5B_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.