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Aliases for KDM5B Gene

Aliases for KDM5B Gene

  • Lysine Demethylase 5B 2 3
  • Lysine (K)-Specific Demethylase 5B 2 3 5
  • Cancer/Testis Antigen 31 2 3 4
  • Retinoblastoma-Binding Protein 2 Homolog 1 3 4
  • Jumonji/ARID Domain-Containing Protein 1B 3 4
  • Jumonji, AT Rich Interactive Domain 1B 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
  • Protein Phosphatase 1, Regulatory Subunit 98 3
  • Putative DNA/Chromatin Binding Motif 3
  • Protein Phosphatase 1 2
  • Regulatory Subunit 98 2
  • EC 1.14.11.- 4
  • EC 1.14.11 63
  • 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 resultsi n multiple transcript variants. [provided by RefSeq, Sep 2015]

GeneCards Summary for KDM5B Gene

KDM5B (Lysine Demethylase 5B) is a Protein Coding gene. Diseases associated with KDM5B include breast cancer. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. 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 KDM5D.

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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM5B Gene

Genomics for KDM5B Gene

Regulatory Elements for KDM5B Gene

Promoters for KDM5B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around KDM5B on UCSC Golden Path with GeneCards custom track

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

Proteomics data for KDM5B Gene at MOPED

Post-translational modifications for KDM5B Gene

  • Ubiquitination at Lys 355, Lys 363, Lys 821, Lys 832, Lys 956, Lys 1011, Lys 1136, Lys 1166, and Lys 1276
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM5B Gene

Antibody Products

  • R&D Systems Antibodies for KDM5B (Lysine (K)-specific Demethylase 5B/KDM5B)
  • Cell Signaling Technology (CST) Antibodies for KDM5B (JARID1B)

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.
  • Contains 3 PHD-type zinc fingers.
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.
  • Contains 1 ARID domain.
  • Contains 1 JmjC domain.
  • Contains 1 JmjN domain.
Family:
  • Belongs to the JARID1 histone demethylase family.
Similarity:
  • Contains 3 PHD-type zinc fingers.
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 IEA --
GO:0005515 protein binding IEA,IPI 12657635
GO:0032452 histone demethylase activity TAS --
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

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
Jensen Localization Image for KDM5B Gene COMPARTMENTS Subcellular localization image for KDM5B gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for KDM5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm 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

Gene Ontology (GO) - Biological Process for KDM5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0009791 post-embryonic development IEA --
GO:0033601 positive regulation of mammary gland epithelial cell proliferation IEA --
GO:0034720 histone H3-K4 demethylation IDA 20228790
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:

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 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, MOPED, and MaxQB for KDM5B Gene



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).
genes like me logo Genes that share expression patterns with KDM5B: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners 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
cow
(Bos Taurus)
Mammalia KDM5B 35
  • 87.29 (n)
  • 91.94 (a)
KDM5B 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM5B 35
  • 93.08 (n)
  • 96.56 (a)
KDM5B 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm5b 35
  • 88.97 (n)
  • 94.24 (a)
Kdm5b 16
Kdm5b 36
  • 94 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia KDM5B 35
  • 99.05 (n)
  • 99.29 (a)
KDM5B 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm5b 35
  • 88.56 (n)
  • 93.98 (a)
oppossum
(Monodelphis domestica)
Mammalia KDM5B 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM5B 36
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM5B 35
  • 76.07 (n)
  • 84.11 (a)
KDM5B 36
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM5B 36
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm5b 35
  • 68.47 (n)
  • 73.55 (a)
Str.10255 35
zebrafish
(Danio rerio)
Actinopterygii idibd5050 35
kdm5bb 35
  • 63.2 (n)
  • 65.05 (a)
kdm5ba 36
  • 63 (a)
OneToMany
kdm5bb 36
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta lid 36
  • 36 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rbr-2 35
  • 45.94 (n)
  • 33.74 (a)
rbr-2 36
  • 29 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD2 36
  • 29 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.10868 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 40 (a)
OneToMany
Species with no ortholog for KDM5B:
  • 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

Paralogs for KDM5B Gene

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

Variants for KDM5B Gene

Sequence variations from dbSNP and Humsavar for KDM5B Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs12967 -- 202,728,675(+) GTGAG(C/T)TGGAC utr-variant-3-prime
rs1141108 -- 202,746,156(-) CCTTA(C/T)AAATA reference, synonymous-codon
rs1141109 -- 202,736,327(-) ATCCC(A/C/G)GTACA reference, synonymous-codon
rs1892163 -- 202,748,900(+) ACTAA(A/G)TAATA intron-variant
rs1892164 -- 202,749,074(+) TCATC(A/G)TGGGA reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
dgv173e1 CNV Complex 17122850
nsv832348 CNV Loss 17160897
nsv832359 CNV Loss 17160897
esv1740431 CNV Deletion 17803354
nsv4110 CNV Insertion 18451855
esv2490406 CNV Insertion 19546169

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

HapMap Linkage Disequilibrium report
KDM5B
Human Gene Mutation Database (HGMD)
KDM5B

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

Disorders for KDM5B Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
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 67
  2. Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA. (PMID: 11478881) Zhu L. … Chen Y. (Biochemistry 2001) 2 3
  3. Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs. (PMID: 11483573) Lahoud M.H. … Kola I. (Genome Res. 2001) 2 3
  4. Substrate trapping proteomics reveals targets of the I^TrCP2/FBXW11 ubiquitin ligase. (PMID: 25332235) Kim T.Y. … Major M.B. (Mol. Cell. Biol. 2015) 3
  5. Overexpression of JARID1B is associated with poor prognosis and chemotherapy resistance in epithelial ovarian cancer. (PMID: 25663457) Wang L. … Han S. (Tumour Biol. 2015) 3

Products for KDM5B Gene

Sources for KDM5B Gene

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