KDM5B Gene
protein-coding GIFtS: 46
GC01M200965
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lysine (K)-specific demethylase 5B (Previous names: Jumonji, AT rich interactive domain 1B (RBP2-like), jumonji, AT rich interactive domain 1B ) Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database (Previous symbol: JARID1B)
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Aliases & Descriptions for KDM5B
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
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| Aliases |
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| CT31 1, 2, 3 | | EC 1.14.11.- 3 | | FLJ10538 2 | | FLJ12459 2 | | FLJ12491 2 | | FLJ16281 2 | | FLJ23670 2 | | JARID1B 2, 3 | | OTTHUMP00000038815 2 | | PLU-1 1, 2, 3 | | PLU1 3 | | PUT1 2 | | RBBP2H1 3 | | RBBP2H1A 1, 2 | | RBP2-H1 3 | | RBP2-like 2 |
| | | Descriptions |
|---|
| Cancer/testis antigen 31 2, 3 | | Histone demethylase JARID1B 3 | | Jumonji, AT rich interactive domain 1B (RBP2-like) 1 | | Jumonji/ARID domain-containing protein 1B 3 | | Retinoblastoma-binding protein 2 homolog 1 3 | | jumonji, AT rich interactive domain 1B 1, 2 | | lysine (K)-specific demethylase 5B 2 | | lysine-specific demethylase 5B 1 | | putative DNA/chromatin binding motif 2 | | retinoblastoma-binding protein 2, homolog 1A 2 |
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| | Search outside databases for aliases for KDM5B gene |
Summaries for KDM5B(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1Function: 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 melanomaGene Wiki entry for KDM5B (JARID1B) |
Genomic Location for KDM5B
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to
UCSC and
Ensembl,
Transcription factor binding sites according to
SABiosciences) About This Section
| Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 1q32.1 HGNC cytogenetic band: 1q32.1KDM5B Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different)
 GeneLoc gene densities for chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01M200965:
(about GC identifiers)
Start:
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200,963,155 bp from pter |
End:
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201,044,172 bp from pter |
Size:
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81,018 bases |
Orientation:
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minus strand |
RefSeq DNA sequence:- NC_000001.9 NT_004487.18
| Proteins for KDM5B
(According to
1UniProtKB,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Enzo Life Sciences,
Abnova,
OriGene and/or,
Abcam,
Biochemical Assays by
Invitrogen,
Millipore,
R&D Systems,
Cell Signaling Technology, and/or
Enzo Life Sciences,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene,
Antibodies by Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Cell Signaling Technology,
Abcam,
Abnova, and/or
Novus Biologicals)
About This Section
| UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1 (See
protein sequence)Recommended Name: Lysine-specific demethylase 5B Size: 1544 amino acids; 175645 Da
Cofactor: Fe(2+) (By similarity)
Subunit: Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7 (By similarity)
Subcellular location: Nucleus
Secondary accessions: O95811 Q15752 Q9Y3Q5Alternative splicing: 2 isoforms: Q9UGL1-1 Q9UGL1-2 Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins: NP_006609.3 Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
2 Gene Ontology (GO) cellular component terms (links to tree view): About this table
Antibodies for KDM5B: Assays for KDM5B: | Protein
Domains/ Families for KDM5B(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry Q9UGL1
ProtoNet protein and cluster: Q9UGL1 5 Blocks protein families: IPB001606 ARID (AT-rich interaction domain) protein IPB003347 Transcription factor jumonji IPB003349 Transcription factor jumonji IPB004198 Zn-finger IPB013637 PLU-1-like
UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1Domain: Both the JmjC domain and the JmjN domain are required for enzymatic activityDomain: The 2 first PHD-type zinc finger domains are required for transcription repression activitySimilarity: Belongs to the JARID1 histone demethylase familySimilarity: Contains 1 ARID domainSimilarity: Contains 1 JmjC domainSimilarity: Contains 1 JmjN domainSimilarity: Contains 3 PHD-type zinc fingers | Gene Function for KDM5B
(According to MGI Jun 06 2009, UniProtKB,
IUBMB,and/or Genatlas,
shRNA from
OriGene,
Sigma-Aldrich, RNAi from
Sigma-Aldrich,
RNAi Products,
Clones, and
Q-PCR Products
from Invitrogen,
Millipore,
OriGene, and/or
Abnova,
siRNAs from
Applied Biosystems,
SYBR primers from OriGene,
Cell-based Assays from Millipore,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006618
Applied Biosystems Silencer® siRNAs for KDM5B
Sigma-Aldrich siRNA and siRNA Panels for KDM5B  Sigma-Aldrich shRNA for KDM5B  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_006618                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_006618                                  untagged cDNA clone in CMV expression vector: NM_006618 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_006618
UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1Function: 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 melanomaEnzyme Number (IUBMB): EC 1.14.11.- 5/8 Gene Ontology (GO) molecular function terms (links to tree view) (see all 8
): About this table | Pathways & Interactions for KDM5B
(Pathways according to Invitrogen
(maps by GeneGo),
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Proteins Network according to
SABiosciences,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
| 1 Sigma-Aldrich "Your Favorite Gene" Pathway for KDM5B (Your Favorite Gene powered by Ingenuity) 
Gene Network CentralTM Interacting Genes and Proteins Network for KDM5B 
--4 Gene Ontology (GO) biological process terms (links to tree view): About this table
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Drugs & Compounds for KDM5B(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
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Browse Tocris compounds for KDM5B
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Transcripts for KDM5B(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank, RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from Invitrogen,
Millipore, and/or
Abnova,
siRNAs from Applied Biosystems,
Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
Tagged/untagged cDNA clones from
OriGene, Expression Assays from Applied Biosystems) About This Section
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006618
Sigma-Aldrich siRNA and siRNA Panels for KDM5B  Sigma-Aldrich shRNA for KDM5B  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_006618 REFSEQ mRNAs for KDM5B gene: NM_006618.3
Applied Biosystems TaqMan ® Gene Expression Assays: NM_006618               OriGene GFP tagged cDNA clone in CMV expression vector: NM_006618                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_006618                                  untagged cDNA clone in CMV expression vector: NM_006618  Additional cDNA sequence: AB015348.1 AF087481.1 AJ132440.1 AJ243706.1 AK001400.1 AK022521.1 AK022553.1 AK074250.1 AK122752.1 AK125746.1 AL133040.1 AL133048.1 AL133072.1 AL137622.1 AL833515.1 CR610637.1 18 DOTS entries: DT.97857065 DT.449384 DT.101963351 DT.97770938 DT.121434552 DT.101967997 DT.97810559 DT.91804138 DT.121434559 DT.121434585 DT.92008652 DT.120304 DT.121434525 DT.121434554 DT.121434565 DT.121434582 DT.92384997 DT.95200889 24/359 AceView cDNA sequences (see all 359
):BM702957 BQ637269 AI026894 AL704530 W72258 BX104183 BF000575 BM985272 AU149588 AU132575 BM998212 AI352104 AW151255 Z39493 BF901260 AI005463 AA948108 AA630339 CB133686 CA450574 AI751550 BF594529 BQ222747 BE550346 Unigene Cluster for KDM5B: Lysine (K)-specific demethylase 5B Hs.443650 [show with all ESTs]Unigene Representative Sequence: AJ243706
GeneLoc Exon Structure
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Expression for KDM5B
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Expression Assays from
Applied Biosystems
)
About This Section
| KDM5B expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for KDM5B
1 / 2 9 probe-sets matching KDM5B gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: TACAGCATTA
SOURCE GeneReport for Unigene cluster: Hs.443650 UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1Tissue specificity: Ubiquitously expressed, with highest levels in testis. Down-regulated in melanoma and gllioblastoma. Up-regulated in breast cancer (at protein level) |
Orthologs for KDM5B
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
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Orthologs for KDM5B gene from 5/11 species (see all 11
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About this table Species with no ortholog for KDM5B | Paralogs for KDM5B(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
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SNPs/Variants for KDM5B(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
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HapMap Linkage Disequilibrium images for KDM5B (up to first 250kb)
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Disorders & Mutations for KDM5B
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
HGMD, GAD,
HuGE Navigator,
BCGD,
and/or TGDB.)
About This Section
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OMIM: 605393
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Medical News for KDM5B(Possibly Related Articles in
Doctor's Guide)
About This Section
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Publications for KDM5B (in
PubMed.
Associations of this gene to articles via
1Novoseek,
2HGNC,
3Entrez Gene,
4UniProtKB/Swiss-Prot,
5UniProtKB/TrEMBL,
6GAD, and/or
7PharmGKB)
About This Section
| 10/23 PubMed articles for KDM5B gene (see all 23
):- PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. (PubMed id 17363312)3, 4 Yamane K.... Zhang Y. (2007)
- Breast cancer associated transcriptional repressor PLU-1/JARID1B interacts directly with histone deacetylases. (PubMed id 17373667)3, 4 Barrett A.... Taylor-Papadimitriou J. (2007)
- Human PLU-1 has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9. (PubMed id 12657635)3, 4 Tan K....Freemont P.S. (2003)
- PLU-1 nuclear protein, which is upregulated in breast cancer, shows restricted expression in normal human adult tissues: a new cancer/testis antigen? (PubMed id 12237901)3, 4 Barrett A.... Taylor-Papadimitriou J. (2002)
- Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs. (PubMed id 11483573)2, 3 Lahoud M.H....Kola I. (2001)
- Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA. (PubMed id 11478881)2, 3 Zhu L....Chen Y. (2001)
- Isolation and chromosomal localization of a new human retinoblastoma binding protein 2 homologue 1a (RBBP2H1A). (PubMed id 10878660)3, 4 Kashuba V.... Zabarovsky E. (2000)
- A novel gene (PLU-1) containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer. (PubMed id 10336460)3, 4 Lu P.J....Taylor-Papadimitriou J. (1999)
- RBP2-H1/JARID1B is a transcriptional regulator with a tumor suppressive potential in melanoma cells. (PubMed id 17973255)3 Roesch A....Vogt T. (2008)
- A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)4 Dephoure N.... Gygi S.P. (2008)
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Search for KDM5B
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
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Genome Databases showing KDM5B
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing KDM5B
(According to HUGE)
About This Section
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Specialized Databases showing KDM5B(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL, Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot) About This Section
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| Services for KDM5B(Reagents available from Applied Biosystems, Antibodies and assays by Cell
Signaling Technology, Abcam, Novus Biologicals, Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich, Enzo Life Sciences, and/or Tocris Bioscience) About This Section
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 Products for KDM5B:

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| Antibodies & Assays for KDM5B  (JARID1B) |
| | | | Search Tocris compounds for KDM5B |
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GeneCards Homepage - Last full update: 2 Jul 2009
Incremental update: 13 Oct 2009
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