KDM3B Gene
protein-coding GIFtS: 51
GC05P137717
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lysine (K)-specific demethylase 3B (Previous names: chromosome 5 open reading frame 7, jumonji domain containing 1B ) Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database (Previous symbols: C5orf7, JMJD1B)
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Aliases & Descriptions for KDM3B
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
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| Aliases |
|---|
| 5qNCA 2 | | C5orf7 2, 3 | | EC 1.14.11.- 3 | | JHDM2B 3 | | JMJD1B 2, 3 | | KIAA1082 1, 2, 3 |
| | | Descriptions |
|---|
| JmjC domain-containing histone demethylation protein 2B 3 | | Jumonji domain-containing protein 1B 3 | | Nuclear protein 5qNCA 2, 3 | | chromosome 5 open reading frame 7 1 | | jumonji domain containing 1B 1, 2 | | lysine (K)-specific demethylase 3B 2 | | lysine-specific demethylase 3B 1 |
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| | Search outside databases for aliases for KDM3B gene |
Summaries for KDM3B(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activityGene Wiki entry for KDM3B (JMJD1B) |
Genomic Location for KDM3B
(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: 5q31 Ensembl cytogenetic band: 5q31.2 HGNC cytogenetic band: 5q31KDM3B 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 5 GeneLoc Exon Structure GeneLoc location for GC05P137717:
(about GC identifiers)
Start:
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137,716,184 bp from pter |
End:
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137,800,615 bp from pter |
Size:
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84,432 bases |
Orientation:
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plus strand |
RefSeq DNA sequence:- NC_000005.8 NT_034772.5
| Proteins for KDM3B
(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: KDM3B_HUMAN, Q7LBC6 (See
protein sequence)Recommended Name: Lysine-specific demethylase 3B Size: 1761 amino acids; 191611 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Nucleus (By similarity)
Miscellaneous: Its gene is located in the 5q region of the genome which is deleted in del(5q) interstitial deletion, a frequent deletion found in myeloid leukemias and myelodysplasias, suggesting that it may be a good candidate for the del(5q) tumor suppressor gene
Secondary accessions: Q9BVH6 Q9BW93 Q9BZ52 Q9NYF4 Q9UPS0Alternative splicing: 3 isoforms: Q7LBC6-1 Q7LBC6-2 Q7LBC6-3 Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins: NP_057688.2
ENSEMBL proteins: ENSP00000326563 ENSP00000378335
Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
1 Gene Ontology (GO) cellular component term (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- | About this table
Antibodies for KDM3B: Assays for KDM3B: | Protein
Domains/ Families for KDM3B(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 Q7LBC6
ProtoNet protein and cluster: Q7LBC6 1 Blocks protein family: IPB003347 Transcription factor jumonji
UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6Domain: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors (By similarity)Similarity: Belongs to the JHDM2 histone demethylase familySimilarity: Contains 1 JmjC domain | Gene Function for KDM3B
(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_016604
Applied Biosystems Silencer® siRNAs for KDM3B
Sigma-Aldrich siRNA for KDM3B  Sigma-Aldrich shRNA for KDM3B  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_016604                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_016604                                  untagged cDNA clone in CMV expression vector: NM_016604 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_016604
UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activityEnzyme Number (IUBMB): EC 1.14.11.- 5 Gene Ontology (GO) molecular function terms (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
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| GO:0005506 | iron ion binding |
IEA | -- | | GO:0008270 | zinc ion binding |
IEA | -- | | GO:0016491 | oxidoreductase activity |
IEA | -- | | GO:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
IEA | -- | | GO:0046872 | metal ion binding |
IEA | -- | About this table | Pathways & Interactions for KDM3B
(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
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1 Interacting protein for KDM3B (Q7LBC62) via UniProtKB, MINT, and/or STRINGAbout this table
4 Gene Ontology (GO) biological process terms (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006350 | transcription |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
IEA | -- | | GO:0016568 | chromatin modification |
IEA | -- | | GO:0055114 | oxidation reduction |
IEA | -- | About this table
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Drugs & Compounds for KDM3B(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 KDM3B 2 Novoseek chemical compound relationships for KDM3B gene
About this table
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Transcripts for KDM3B(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_016604
Sigma-Aldrich siRNA for KDM3B  Sigma-Aldrich shRNA for KDM3B  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_016604 REFSEQ mRNAs for KDM3B gene: NM_016604.3
Applied Biosystems TaqMan ® Gene Expression Assays: NM_016604               OriGene GFP tagged cDNA clone in CMV expression vector: NM_016604                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_016604                                  untagged cDNA clone in CMV expression vector: NM_016604  Additional cDNA sequence: AB029005.2 AF251039.1 AF338242.1 AK025755.1 AK304371.1 BC000539.2 BC001202.1 BC073869.1 BC117692.1 BC117693.1 BC146788.1 CR596928.1 CR615541.1 12 DOTS entries: DT.87009767 DT.95190557 DT.92447513 DT.95352632 DT.100795486 DT.40245180 DT.440580 DT.100795487 DT.100795492 DT.40191866 DT.92447515 DT.75125761 24/262 AceView cDNA sequences (see all 262
):BF445534 BI917674 AI439064 AA337372 BC000539 H03250 BI768210 AL561650 CD671660 BE082546 CR615541 BQ023995 F03931 BM802414 BM457347 CR596928 AF338242 BE265035 BE048898 AL698902 BX477892 BQ311965 AI560465 AI219862 Unigene Cluster for KDM3B: Lysine (K)-specific demethylase 3B Hs.714832 [show with all ESTs]Unigene Representative Sequence: NM_016604
GeneLoc Exon Structure
5/7 Alternative Splicing Database (ASD) splice patterns (SP) for KDM3B (see all 7
)
| ExUns: | 1 | ^ | 2a | · | 2b | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6a | · | 6b | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14a | · | 14b | ^ | 15 | ^ | 16a | · | 16b | ^ | 17a | · | 17b | ^ | 18a | · | 18b | ^ | 19a | · | 19b | ^ | |
| SP1: | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | - |   | |
| SP2: | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | - |   | |
| SP3: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP4: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | - |   | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP5: | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   | |   |
| ExUns: | 20a | · | 20b | ^ | 21 | ^ | 22 | ^ | 23 | ^ | 24 | ^ | 25 | ^ | 26 | |
| SP1: | - |   | |   | |   | |   | |   | |   | |   | |   | |
| SP2: | - |   | |   | |   | |   | |   | |   | |   | |   | |
| SP3: | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP4: | |   | |   | |   | |   | |   | |   | |   | |   | |
| SP5: | |   | |   | |   | |   | |   | |   | |   | |   |
About this scheme
ECgene alternative splicing isoforms for KDM3B
2 Ensembl transcripts including schematic representations: ENST00000314358
ENST00000394866
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Expression for KDM3B
(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
| KDM3B expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for KDM3B
1 / 2 6 probe-sets matching KDM3B gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: TTCTTATTAA
SOURCE GeneReport for Unigene cluster: Hs.714832 UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6Tissue specificity: Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and liver |
Orthologs for KDM3B
(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 KDM3B gene from 5/8 species (see all 8
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About this table Species with no ortholog for KDM3B
ENSEMBL Gene Tree for KDM3B | Paralogs for KDM3B(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| Paralogs for KDM3B gene
- JMJD1C2 KDM3A2 HR2
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SNPs/Variants for KDM3B(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 KDM3B (up to first 250kb)
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Disorders & Mutations for KDM3B
(in which this Gene is Involved, According to
OMIM, UniProtKB,
Novoseek, 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: 609373
1 Novoseek disease relationship for KDM3B gene
| Disease |
Score |
Articles |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| tumors |
0.00 |
2 |
11687974 (2) |
About this table
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Medical News for KDM3B(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for KDM3B (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
| 10/35 PubMed articles for KDM3B gene (see all 35
):- A novel nuclear protein, 5qNCA (LOC51780) is a candidate for the myeloid leukemia tumor suppressor gene on chromosome 5 band q31. (PubMed id 11687974)1, 3, 4 Hu Z.... Westbrook C.A. (2001)
- Identification and characterization of JMJD2 family genes in silico. (PubMed id 15138608)1, 2, 3 Katoh M. and Katoh M. (2004)
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)3, 4 Olsen J.V....Mann M. (2006)
- JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. (PubMed id 16603237)3, 4 Yamane K.... Zhang Y. (2006)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)3, 4 Gerhard D.S....Malek J. (2004)
- Large-scale characterization of HeLa cell nuclear phosphoproteins. (PubMed id 15302935)3, 4 Beausoleil S.A....Gygi S.P. (2004)
- Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PubMed id 12168954)3, 4 Nakajima D.... Nagase T. (2002)
- cDNA cloning and genomic structure of three genes localized to human chromosome band 5q31 encoding potential nuclear proteins. (PubMed id 11087669)3, 4 Lai F....Le Beau M.M. (2000)
- Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10470851)3, 4 Kikuno R....Ohara O. (1999)
- A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)4 Dephoure N.... Gygi S.P. (2008)
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Search for KDM3B
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
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Genome Databases showing KDM3B
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
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| Other Databases showing KDM3B
(According to HUGE)
About This Section
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Specialized Databases showing KDM3B(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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| About This Section
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| Services for KDM3B(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 KDM3B:

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GeneCards Homepage - Last full update: 2 Jul 2009
Incremental update: 13 Oct 2009
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