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Aliases for KDM5B Gene

Aliases for KDM5B Gene

  • Lysine Demethylase 5B 2 3 5
  • Cancer/Testis Antigen 31 2 3 4
  • Protein Phosphatase 1, Regulatory Subunit 98 2 3
  • Retinoblastoma-Binding Protein 2 Homolog 1 3 4
  • Jumonji/ARID Domain-Containing Protein 1B 3 4
  • Jumonji, AT Rich Interactive Domain 1B 2 3
  • Lysine (K)-Specific Demethylase 5B 2 3
  • Histone Demethylase JARID1B 3 4
  • JARID1B 3 4
  • RBP2-H1 3 4
  • PLU-1 3 4
  • CT31 3 4
  • PLU1 3 4
  • Jumonji, AT Rich Interactive Domain 1B (RBP2-Like) 2
  • Retinoblastoma-Binding Protein 2, Homolog 1A 3
  • Putative DNA/Chromatin Binding Motif 3
  • Lysine-Specific Demethylase 5B 3
  • EC 1.14.11.- 4
  • EC 1.14.11 61
  • RBBP2H1A 3
  • PPP1R98 3
  • RBBP2H1 4
  • PUT1 3

External Ids for KDM5B Gene

Previous HGNC Symbols for KDM5B Gene

  • JARID1B

Previous GeneCards Identifiers for KDM5B Gene

  • GC01M200965
  • GC01M173862

Summaries for KDM5B Gene

Entrez Gene Summary for KDM5B Gene

  • This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

GeneCards Summary for KDM5B Gene

KDM5B (Lysine Demethylase 5B) is a Protein Coding gene. Diseases associated with KDM5B include Ascending Colon Cancer and Breast Cancer. Among its related pathways are Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors and Gene Expression. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors. An important paralog of this gene is KDM5A.

UniProtKB/Swiss-Prot for KDM5B Gene

  • 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. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).

Gene Wiki entry for KDM5B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM5B Gene

Genomics for KDM5B Gene

Regulatory Elements for KDM5B Gene

Enhancers for KDM5B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G202809 1.4 ENCODE dbSUPER 25.3 -2.2 -2167 3.6 PKNOX1 FOXA2 MLX CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B KDM5B PCAT6 IPO9-AS1 MGAT4EP
GH01G202835 1 ENCODE 32 -27.2 -27222 3.0 ATF1 PKNOX1 SIN3A ZBTB7B YY1 GLIS2 ZNF766 CAVIN1 YY2 KAT8 KDM5B PCAT6 PRELP RABIF CYB5R1 CHIT1 MGAT4EP LOC730222
GH01G202856 1.3 Ensembl ENCODE 12 -50.0 -50030 5.6 FOXA2 ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 FOS ZNF263 SP3 LOC730222 ADIPOR1 RABIF PCAT6 KDM5B ZBED6 ELF3-AS1 LOC100506672 RNPEP ENSG00000273478
GH01G202963 1.7 FANTOM5 ENCODE dbSUPER 9 -157.2 -157185 6.6 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A YBX1 ZBTB7B ZNF766 ZNF143 CYB5R1 BTG2 KLHL12 LOC100506747 ADIPOR1 KDM5B PCAT6 LOC148709 LOC730222 RABIF
GH01G202956 1.4 ENCODE dbSUPER 9.5 -150.2 -150213 6.8 CREB3L1 MLX AGO1 ZFP64 DMAP1 FEZF1 YBX1 YY1 SLC30A9 ZNF143 SNRPE ADIPOR1 RNPEP PRELP CYB5R1 LOC100506747 LOC100506672 PTPRVP ENSG00000273478 ZBED6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM5B on UCSC Golden Path with GeneCards custom track

Promoters for KDM5B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000256221 -1430 1401 PKNOX1 FOXA2 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1
ENSR00000018345 1870 2801 HDGF MLX CREB3L1 ZFP64 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for KDM5B Gene

Chromosome:
1
Start:
202,724,491 bp from pter
End:
202,809,470 bp from pter
Size:
84,980 bases
Orientation:
Minus strand

Genomic View for KDM5B Gene

Genes around KDM5B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM5B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM5B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM5B Gene

Proteins for KDM5B Gene

  • Protein details for KDM5B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UGL1-KDM5B_HUMAN
    Recommended name:
    Lysine-specific demethylase 5B
    Protein Accession:
    Q9UGL1
    Secondary Accessions:
    • O95811
    • Q15752
    • Q9Y3Q5

    Protein attributes for KDM5B Gene

    Size:
    1544 amino acids
    Molecular mass:
    175658 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7.
    SequenceCaution:
    • Sequence=CAB63108.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM5B Gene

    Alternative splice isoforms for KDM5B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM5B Gene

Selected DME Specific Peptides for KDM5B Gene

Q9UGL1:
  • EAFGFEQA
  • NFAEAVNF
  • QRLNELEA
  • DKEYKPH
  • DYFNMPVHMVPTE
  • LLEVLCP
  • FELLPDDERQC
  • MNPNTLM
  • RTNQCAGEFV
  • VMKKLAPELF
  • FLPPPECPVFEP
  • EKEFWRLV
  • TGICKVRPPPDWQPPFACDVD
  • SVAQQLLNGKRQTRYR
  • SQPDLLHQLVTIMNPN
  • MGFAPGKAVGSH
  • SLQRIRVRLPEGDALRYMIER
  • EQSVLAHI
  • LLCDGCDDSYHTFCL
  • VERKILDL
  • RYCVFSH
  • GEPKTWY
  • LRYRYTLD
  • KCKTTCF
  • EDVTVEYGAD
  • YSINYLH
  • PPPECPVFEPSW
  • PWLYVGM

Post-translational modifications for KDM5B Gene

  • Ubiquitination at isoforms=2355, posLast=363363, isoforms=2821, isoforms=2832, posLast=956956, isoforms=21011, isoforms=21136, posLast=11661166, and isoforms=21276
  • Modification sites at PhosphoSitePlus

Domains & Families for KDM5B Gene

Graphical View of Domain Structure for InterPro Entry

Q9UGL1

UniProtKB/Swiss-Prot:

KDM5B_HUMAN :
  • Both the JmjC domain and the JmjN domain are required for enzymatic activity.
  • Belongs to the JARID1 histone demethylase family.
Domain:
  • Both the JmjC domain and the JmjN domain are required for enzymatic activity.
  • The 2 first PHD-type zinc finger domains are required for transcription repression activity.
Family:
  • Belongs to the JARID1 histone demethylase family.
genes like me logo Genes that share domains with KDM5B: view

Function for KDM5B Gene

Molecular function for KDM5B Gene

UniProtKB/Swiss-Prot 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. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).

Enzyme Numbers (IUBMB) for KDM5B Gene

Gene Ontology (GO) - Molecular Function for KDM5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IDA 15640446
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 10336460
GO:0003714 transcription corepressor activity IDA 12657635
GO:0005515 protein binding IPI 12657635
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with KDM5B: view
genes like me logo Genes that share phenotypes with KDM5B: view

Animal Models for KDM5B Gene

MGI Knock Outs for KDM5B:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM5B

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM5B Gene

Localization for KDM5B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM5B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM5B gene
Compartment Confidence
nucleus 5
cytosol 5

Gene Ontology (GO) - Cellular Components for KDM5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 20403335
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with KDM5B: view

Pathways & Interactions for KDM5B Gene

genes like me logo Genes that share pathways with KDM5B: view

Pathways by source for KDM5B Gene

1 GeneTex pathway for KDM5B Gene
1 Cell Signaling Technology pathway for KDM5B Gene

Gene Ontology (GO) - Biological Process for KDM5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter TAS --
GO:0007338 single fertilization IEA --
GO:0009791 post-embryonic development IEA --
genes like me logo Genes that share ontologies with KDM5B: view

No data available for SIGNOR curated interactions for KDM5B Gene

Drugs & Compounds for KDM5B Gene

(1) Drugs for KDM5B Gene - From: DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
PBIT Pharma 0
genes like me logo Genes that share compounds with KDM5B: view

Transcripts for KDM5B Gene

Unigene Clusters for KDM5B Gene

Lysine (K)-specific demethylase 5B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM5B

Alternative Splicing Database (ASD) splice patterns (SP) for KDM5B Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a ·
SP1: - - - - - -
SP2: - - - -
SP3:
SP4:
SP5:
SP6: - - - -
SP7:
SP8:

ExUns: 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28a · 28b ^ 29 ^ 30a · 30b ^ 31
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for KDM5B Gene

GeneLoc Exon Structure for
KDM5B
ECgene alternative splicing isoforms for
KDM5B

Expression for KDM5B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM5B Gene

mRNA differential expression in normal tissues according to GTEx for KDM5B Gene

This gene is overexpressed in Testis (x6.0).

Protein differential expression in normal tissues from HIPED for KDM5B Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (47.7) and Cerebrospinal fluid (14.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for KDM5B Gene



NURSA nuclear receptor signaling pathways regulating expression of KDM5B Gene:

KDM5B

SOURCE GeneReport for Unigene cluster for KDM5B Gene:

Hs.443650

mRNA Expression by UniProt/SwissProt for KDM5B Gene:

Q9UGL1-KDM5B_HUMAN
Tissue specificity: Ubiquitously expressed, with highest levels in testis. Down-regulated in melanoma and glioblastoma. Up-regulated in breast cancer (at protein level).

Evidence on tissue expression from TISSUES for KDM5B Gene

  • Nervous system(4.4)
  • Lung(2.6)
genes like me logo Genes that share expression patterns with KDM5B: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM5B Gene

Orthologs for KDM5B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for KDM5B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM5B 34 35
  • 99.05 (n)
dog
(Canis familiaris)
Mammalia KDM5B 34 35
  • 93.08 (n)
oppossum
(Monodelphis domestica)
Mammalia KDM5B 35
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM5B 35
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm5b 34 16 35
  • 88.97 (n)
rat
(Rattus norvegicus)
Mammalia Kdm5b 34
  • 88.56 (n)
cow
(Bos Taurus)
Mammalia KDM5B 34 35
  • 87.29 (n)
chicken
(Gallus gallus)
Aves KDM5B 34 35
  • 76.07 (n)
lizard
(Anolis carolinensis)
Reptilia KDM5B 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm5b 34
  • 68.47 (n)
Str.10255 34
zebrafish
(Danio rerio)
Actinopterygii kdm5bb 34 35
  • 63.2 (n)
kdm5ba 35
  • 63 (a)
OneToMany
idibd5050 34
fruit fly
(Drosophila melanogaster)
Insecta lid 35
  • 36 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rbr-2 34 35
  • 45.94 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD2 35
  • 29 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.10868 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 40 (a)
OneToMany
Species where no ortholog for KDM5B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM5B Gene

ENSEMBL:
Gene Tree for KDM5B (if available)
TreeFam:
Gene Tree for KDM5B (if available)

Paralogs for KDM5B Gene

Variants for KDM5B Gene

Sequence variations from dbSNP and Humsavar for KDM5B Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs869312703 Uncertain significance 202,733,583(-) GTATC(C/T)GAGTT reference, stop-gained
rs367537995 untested 202,752,904(-) TGCCT(A/G)TATGT splice-donor-variant
rs1000008229 -- 202,766,739(+) TATTC(A/G)ATTCC intron-variant
rs1000018840 -- 202,766,866(+) TGCCA(C/G)ACAGC intron-variant
rs1000030971 -- 202,790,858(+) GACAT(C/T)AAACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM5B Gene

Variant ID Type Subtype PubMed ID
dgv562n100 CNV gain 25217958
esv1740431 CNV deletion 17803354
esv2490406 CNV insertion 19546169
esv2758992 CNV loss 17122850
esv3588586 CNV loss 21293372
nsv1068807 CNV deletion 25765185
nsv1145395 CNV deletion 24896259
nsv4110 CNV insertion 18451855
nsv832348 CNV loss 17160897
nsv832359 CNV loss 17160897
nsv946587 CNV duplication 23825009

Variation tolerance for KDM5B Gene

Residual Variation Intolerance Score: 1.34% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.38; 54.07% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM5B Gene

Human Gene Mutation Database (HGMD)
KDM5B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM5B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM5B Gene

Disorders for KDM5B Gene

MalaCards: The human disease database

(2) MalaCards diseases for KDM5B Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
ascending colon cancer
  • ca ascending colon
breast cancer
  • breast cancer, invasive ductal
- elite association - COSMIC cancer census association via MalaCards
Search KDM5B in MalaCards View complete list of genes associated with diseases

Relevant External Links for KDM5B

Human Genome Epidemiology (HuGE) Navigator
KDM5B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM5B
genes like me logo Genes that share disorders with KDM5B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KDM5B Gene

Publications for KDM5B Gene

  1. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. (PMID: 17363312) Yamane K. … Zhang Y. (Mol. Cell 2007) 3 4 64
  2. Breast cancer associated transcriptional repressor PLU-1/JARID1B interacts directly with histone deacetylases. (PMID: 17373667) Barrett A. … Taylor-Papadimitriou J. (Int. J. Cancer 2007) 3 4 64
  3. Re-expression of the retinoblastoma-binding protein 2-homolog 1 reveals tumor-suppressive functions in highly metastatic melanoma cells. (PMID: 16645588) Roesch A. … Vogt T. (J. Invest. Dermatol. 2006) 3 4 64
  4. Retinoblastoma-binding protein 2-homolog 1: a retinoblastoma-binding protein downregulated in malignant melanomas. (PMID: 15803180) Roesch A. … Vogt T. (Mod. Pathol. 2005) 3 4 64
  5. Human PLU-1 has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9. (PMID: 12657635) Tan K. … Freemont P.S. (J. Biol. Chem. 2003) 3 4 64

Products for KDM5B Gene

  • Addgene plasmids for KDM5B

Sources for KDM5B Gene

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