DNMT3B Gene
protein-coding GIFtS : 72
GCID: GC20 P031350
DNA (cytosine-5-)-methyltransferase 3 beta
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Aliasesfor DNMT3B gene
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc ,
7 Ensembl ,
8 DME ,
9 miRBase ,
and/or 10 fRNAdb )About This Section Aliases DNA (Cytosine-5-)-Methyltransferase 3 Beta 1 2 ICF2 5 M.HsaIIIB2 3 ICF12 DNA Methyltransferase HsaIIIB2 3 DNA (Cytosine-5)-Methyltransferase 3B2 DNA MTase HsaIIIB2 3 Dnmt3b3 EC 2.1.1.373 8
Export aliases for DNMT3B gene to outside databases Previous GC identifers: GC20P031108 GC20P032018 GC20P032065 GC20P030813 GC20P028137
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Summariesfor DNMT3B gene (According to Entrez Gene ,
Tocris Bioscience ,
Wikipedia's
Gene Wiki ,
PharmGKB ,
UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
About This Section Entrez Gene summary for DNMT3B : CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase which is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is developmentally regulated. Mutations in this gene cause the immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined. (provided by RefSeq, May 2011) UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3 Function : Required for genome-wide de novo methylation and is essential for the establishment of DNA methylationpatterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1 summary
for DNMT3B : DNA methyltransferase (DNMT) add methyl groups to DNA to effect gene expression. There are three types ofDNMTs. DNMT1 is predominately responsible for hemimethylated CpG island methylation, DNMT2 in fact transfersmethyl groups to RNA not DNA, hence has been renamed to tRNA aspartic acid methyltransferase 1 (TRDMT1) andDNMT3 is responsible for unmethylated CpG island methylation. Gene Wiki entry for DNMT3B
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Genomic Viewsfor DNMT3B gene
(According to
GeneLoc and/or
HGNC , and/or
Entrez Gene (NCBI build 37) ,
and/or miRBase ,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69) ,
Regulatory elements and Epigenetics data according to
QIAGEN ,
SABiosciences , and/or
SwitchGear Genomics )About This Section RefSeq DNA sequence: NC_000020.10 NC_018931.1 NT_011362.10 Regulatory elements: SABiosciences Regulatory transcription factor binding sites in the DNMT3B gene promoter: Lmo2 Olf-1 MyoD Other transcription factors Search SABiosciences Chromatin IP Primers for DNMT3B Epigenetics: QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human , mouse , rat DNMT3B
Genomic Location: Genomic View : UCSC Golden Path with GeneCards custom track Entrez Gene cytogenetic band: 20q11.2 Ensembl cytogenetic band: 20q11.21 HGNC cytogenetic band: 20q11.2 DNMT3B Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different) GeneLoc information about chromosome 20 GeneLoc Exon Structure
GeneLoc location for GC20P031350: view genomic region
(about GC identifiers )
Start:
31,350,191 bp from pter
End:
31,397,162 bp from pter
Size:
46,972 bases
Orientation:
plus strand
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Proteinsfor DNMT3B gene
(According to
1 UniProtKB ,
HORDE ,
neXtProt ,
Ensembl ,
and/or Reactome ,
Modification sites according to 2 PhosphoSitePlus ,
Specific Peptides from DME ,
Protein expression images according to data from SPIRE MOPED and PaxDb ,
RefSeq according to NCBI ,
PDB rendering according to OCA and/or Proteopedia ,
Recombinant Proteins
from
EMD Millipore ,
R&D Systems ,
GenScript ,
Enzo Life Sciences ,
OriGene ,
Novus Biologicals ,
Sino Biological ,
ProSpec , and/or
Uscn ,
Biochemical Assays by
EMD Millipore ,
R&D Systems ,
OriGene ,
GenScript ,
Cell Signaling Technology ,
Enzo Life Sciences , and/or
Uscn ,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene ,
Antibodies by
EMD Millipore ,
R&D Systems ,
GenScript ,
Cell Signaling Technology ,
OriGene ,
Novus Biologicals ,
Thermo Fisher Scientific ,
Abcam , and/or
Uscn )
About This Section UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3 (See
protein sequence )Recommended Name: DNA (cytosine-5)-methyltransferase 3B Size : 853 amino acids; 95751 Da
Subunit : Interacts with BAZ2A/TIP5, SUV39H1 and CBX4. Interacts with UHRF1 (By similarity). Interacts with DNMT1 andDNMT3A, SETDB1, UBL1, UBE2I9 and ZHX1. Interacts with the PRC2/EED-EZH2 complex
Subcellular location : Nucleus
2 PDB 3D structures from and Proteopedia for DNMT3B :3FLG (3D)
  3QKJ (3D)
 
Secondary accessions : A2A2E2 B4DSM8 B4DSU1 E1P5M6 E1P5M7 E7EN63 E9PBF2 Q9UBD4 Q9UJQ5 Q9UKA6 Q9UNE5Q9Y5R9 Q9Y5S0 Alternative splicing : 8 isoforms : Q9UBC3-1 Q9UBC3-2 Q9UBC3-3 Q9UBC3-4 Q9UBC3-5 Q9UBC3-6 Q9UBC3-7 Q9UBC3-8 (No experimental confirmation available) Explore the universe of human proteins at neXtProt for DNMT3B: NX_Q9UBC3 Post-translational modifications:
Sumoylated1
View modification sites using PhosphoSitePlus 2 View neXtProt modification sites for NX_Q9UBC3 4/13 DME Specific Peptides for DNMT3B (Q9UBC3 ) (see all 13 )DNMT3B Protein expression data from MOPED and PaxDb : About this image
REFSEQ proteins (6 alternative transcripts):
NP_001193984.1 NP_001193985.1 NP_008823.1 NP_787044.1 NP_787045.1 NP_787046.1 ENSEMBL proteins: ENSP00000328547 ENSP00000313397 ENSP00000337764 ENSP00000201963 ENSP00000403169 ENSP00000412305 ENSP00000345105 ENSP00000364774 Human Recombinant Protein Products: Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7 ): About this table
DNMT3B for ontologies About GeneDecksing DNMT3B Antibody Products: Assay Products for DNMT3B:
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Protein
Domains / Familiesfor DNMT3B gene (According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
About This Section
DNMT3B for domains About GeneDecksing 5/6 InterPro domains/families (see all 6 ):
Graphical View of Domain Structure for InterPro Entry Q9UBC3 ProtoNet protein and cluster: Q9UBC3
2 Blocks protein families : IPB000313 PWWP domain IPB001525 C-5 cytosine-specific DNA methylase UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3 Domain : The PWWP domain is essential for targeting to pericentric heterochromatinSimilarity : Belongs to the C5-methyltransferase familySimilarity : Contains 1 ADD domainSimilarity : Contains 1 GATA-type zinc fingerSimilarity : Contains 1 PHD-type zinc fingerSimilarity : Contains 1 PWWP domain
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Functionfor DNMT3B gene
(According to 1 UniProtKB ,
Genatlas ,
LifeMap Discovery™ ,
IUBMB , and/or
2 DME ,
Human phenotypes from GenomeRNAi ,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences ,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene ,
RNAi from
EMD Millipore ,
siRNAs from
OriGene ,
QIAGEN ,
microRNA from QIAGEN ,
Gene Editing from DNA2.0 ,
Clones from EMD Millipore ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
Sino Biological ,
DNA2.0 ,
and Vector BioLabs ,
Cell Lines from GenScript ,
LifeMap BioReagents ,
In Situ Hybridization Assays from Advanced Cell Diagnostics ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene .)
About This Section Function Summary: UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3 Function : Required for genome-wide de novo methylation and is essential for the establishment of DNA methylationpatterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1 Catalytic activity : S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosineEnzyme regulation : Activated by binding to the regulatory factor DNMT3L (By similarity)
Genatlas biochemistry entry for DNMT3B : DNA (cytosine -5)-methyltransferase 3 beta ,abundantly expressed in ES cells in testis and thymus but barely detectable in differentiated cells and adult tissues,with at least two alternatively spliced isoforms essential for de novo DNA methylation and development (at least in mouse) Enzyme Number (IUBMB): EC 2.1.1.37 1 2 Clone Products: Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human , mouse , rat for DNMT3B (see all 10 ) OriGene untagged cDNA clones in CMV expression vector in human , mouse , rat for DNMT3B (see all 4 )OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling GenScript: all cDNA clones in your preferred vector (see all 4 ): DNMT3B (NM_006892 ) Browse Sino Biological Human cDNA Clones DNA2.0 Custom Codon Optimized Gene
Synthesis Service for DNMT3B Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat DNMT3B
In Situ Assay Products: Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DNMT3B
Gene Ontology (GO): 5/9 molecular function terms (GO ID links to tree view) (see all 9 ): About this table
DNMT3B for ontologies About GeneDecksing 3 GenomeRNAi human phenotypes for DNMT3B :Animal Models: Mouse knock-outs for DNMT3B: Dnmt3b tm5.2Enl Dnmt3b tm2Enl 15 MGI mutant phenotypes (inferred from 9 alleles ) (MGI details for Dnmt3b) :
DNMT3B for phenotypes About GeneDecksing
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Pathways & Interactionsfor DNMT3B gene
(Pathways according to
EMD Millipore ,
R&D Systems ,
Cell Signaling Technology ,
KEGG ,
PharmGKB ,
BioSystems ,
Reactome ,
Tocris Bioscience ,
GeneGo (Thomson Reuters) ,
QIAGEN ,
and/or UniProtKB ,
Sets of similar genes according to GeneDecks ,
Interaction Networks according to
SABiosciences ,
and/or STRING ,
Interactions according to 1 UniProtKB ,
2 MINT ,
3 I2D , and/or
4 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene) .
About This Section Unified GeneCards pathways  - 5/6 super-pathways (see all 6 ) About this table See pathways by source Super-pathway contained gene-specific pathways 1 Methionine metabolism 2 Selected targets of Oct-3/4 3 One Carbon Metabolism 4 DNA Methylation and Transcriptional Repression 5 Metabolism
Pathway sources See GeneCards unified pathways Show all pathways 2 EMD Millipore Pathways for DNMT3B 1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for DNMT3B 1 GeneGo (Thomson Reuters) Pathway for DNMT3B 1 BioSystems Pathway for DNMT3B 2
Kegg Pathways (Kegg details for DNMT3B) :
DNMT3B for pathways About GeneDecksing Interactions: SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for DNMT3B STRING Interaction
Network Preview (showing 5 interactants - click image to see 25)5/75 Interacting proteins for DNMT3B (Q9UBC3 1 , 2 , 3 ENSP00000328547 4 ) via UniProtKB, MINT, STRING , and/or I2D (see all 75 )Interactant Interaction Details GeneCard External ID(s) UHRF1 Q96T88 2 , 3 MINT-7296336 MINT-7296510 MINT-7296314 MINT-7296421 MINT-7296305 MINT-7296379 MINT-7296468 I2D:
score=2 DNMT3A Q9Y6K1 2 , 3 , ENSP00000264709 4 MINT-7296314 MINT-6178415 MINT-6178447 MINT-7296379 MINT-6178404 I2D:
score=2 STRING: ENSP00000264709 UBE2I P63279 1 , 3 , ENSP00000324897 4 EBI-80125,EBI-80168 I2D:
score=4 STRING: ENSP00000324897 EED O75530 1 , 3 , ENSP00000263360 4 EBI-80125,EBI-1177693 I2D:
score=3 STRING: ENSP00000263360 EZH2 Q15910 1 , 3 , ENSP00000320147 4 EBI-80125,EBI-746496 I2D:
score=3 STRING: ENSP00000320147
About this table Gene Ontology (GO): 5/20 biological process terms (GO ID links to tree view) (see all 20 ): About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0000122 negative regulation of transcription from RNA polymerase II promoter
IDA 17303076 GO:0006306 DNA methylation
TAS 10433969 GO:0006346 methylation-dependent chromatin silencing
IEA -- GO:0006349 regulation of gene expression by genetic imprinting
IEA -- GO:0010212 response to ionizing radiation
-- --
DNMT3B for ontologies About GeneDecksing
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Drugs & Compoundsfor DNMT3B gene (Chemical Compounds according to UniProtKB , Enzo Life Sciences ,
EMD Millipore , Tocris Bioscience
HMDB ,
BitterDB , and/or
Novoseek , and Drugs according to
DrugBank ,
Enzo Life Sciences , and/or
PharmGKB , with drugs/clinical trials/news
search links to CenterWatch )
About This Section
DNMT3B for compounds About GeneDecksing Compounds for DNMT3B available from Tocris Bioscience About this table Compound Action
CAS
# RG 108 Non-nucleoside DNA methyltransferase inhibitor [48208-26-0] Zebularine DNA methyltransferase and cytidine deaminase inhibitor [3690-10-6] Decitabine DNA methyltransferase inhibitor [2353-33-5] 5-Azacytidine DNA methyltransferase inhibitor [320-67-2]
3 HMDB Compounds for DNMT3B About this table 10/11 Novoseek chemical compound relationships for DNMT3B gene (see all 11 ) About this table
Search CenterWatch for drugs/clinical trials and news about DNMT3B / DNM3B
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Transcriptsfor DNMT3B gene (Secondary structures according to
fRNAdb ,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank , RefSeq according to Entrez Gene ,
DOTS (version 10), and/or
AceView ,
transcript ids from Ensembl
with links to UCSC ,
exon structure from GeneLoc ,
alternative splicing isoforms according to ASD and/or
ECgene ,
RNAi Products from
EMD Millipore ,
siRNAs from
OriGene ,
QIAGEN ,
shRNA from
OriGene ,
microRNA from QIAGEN ,
Tagged/untagged cDNA clones from
OriGene ,
SwitchGear Genomics ,
GenScript ,
DNA2.0 ,
Vector BioLabs ,
Primers from
OriGene ,
SABiosciences , and/or
QIAGEN
)About This Section REFSEQ mRNAs for DNMT3B gene (6 alternative transcripts): NM_001207055.1 NM_001207056.1 NM_006892.3 NM_175848.1 NM_175849.1 NM_175850.2 Unigene Clusters for DNMT3B:
DNA (cytosine-5-)-methyltransferase 3 beta Hs.643024 [show with all ESTs ] , Hs.713611 [show with all ESTs ] Unigene Representative Sequences: BQ222535 , DQ321787 8 Ensembl transcripts including schematic representations, and UCSC links where relevant : ENST00000328111 (uc010ztx.1 uc010zty.1 uc002wyc.3 uc002wyd.3 uc002wye.3 uc010ztz.2 uc010zua.2 uc010gee.3 uc010gef.3 uc002wyg.3 )ENST00000353855 (uc010geg.3 uc010geh.3 ) ENST00000348286 ENST00000201963 (uc002wyf.3 )ENST00000443239 ENST00000456297 ENST00000344505 ENST00000375623 Clone Products: OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human , mouse , rat for DNMT3B (see all 10 ) OriGene untagged cDNA clones in CMV expression vector in human , mouse , rat for DNMT3B (see all 4 )OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling GenScript: all cDNA clones in your preferred vector (see all 4 ): DNMT3B (NM_006892 ) DNA2.0 Custom Codon Optimized Gene
Synthesis Service for DNMT3B Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat DNMT3B
Additional cDNA sequence: AB208880.1 AF129267.1 AF129268.1 AF129269.1 AF156487.1 AF156488.1 AF176228.1 AF331857.1 AK001191.1 AK295176.1 AK299776.1 AK299821.1 AK299915.1 AK300857.1 DQ321787.1
14 DOTS entries : DT.113253 DT.113255
DT.100781518 DT.120812129 DT.100781515 DT.100781514 DT.40118740 DT.100730319 DT.102842807 DT.97812649 DT.100730272 DT.102842808 DT.91846915 DT.102842804 24/103 AceView cDNA sequences (see all 103 ):
AF176228 CK825649 BE046956 BQ277772 AF129268 AA565566 NM_006892 AF129269 AF331857 NM_175849 BU850032 BU854958 CD654323 AA206264 CR609754 AL120820 AI114879 AF129267 AI954642 NM_175850 NM_175848 BM834719 AI332472 BM677321 GeneLoc Exon Structure 5/17 Alternative Splicing Database (ASD) splice patterns (SP) for DNMT3B (see all 17 ) About this scheme ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · SP1 :                           -       -       -               SP2 :                                 -       -               SP3 :                                                     SP4 :                                                     SP5 :                           -       -     -   -              
ExUns: 16b · 16c ^ 17 ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b · 24c SP1 :                                   SP2 :                                   SP3 :                                   SP4 :                         -           SP5 :                                  
ECgene alternative splicing isoforms for DNMT3B
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Expression for DNMT3B gene
(RNA expression data according to
H-InvDB ,
NONCODE ,
miRBase , and
RNAdb ,
Expression images according to data from
BioGPS ,
Illumina Human BodyMap , and
CGAP
SAGE ,
Sets of similar genes according to GeneDecks ,
in vivo and in vitro expression data from LifeMap Discovery™ ,
plus additional links to
Genevestigator , and/or
SOURCE , and/or
BioGPS , and/or
UniProtKB ,
PCR Arrays from
SABiosciences ,
Primers from
OriGene ,
SABiosciences , and/or
QIAGEN ,
In Situ Hybridization Assays from Advanced Cell Diagnostics )
About This Section DNMT3B expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this image BioGPS CGAP TAG: TAGCTACAGG
About this image DNMT3B expression in embryonic tissues and stem cells Expression by the Database of Embryonic development, Stem cell research, and
Regenerative medicine About this table 1 LifeMap In Vivo Development Anatomical Compartment/Cell Tissue Anatomical Compartment
Cell Category (developmental path) Neural Tube Mesencephalic Ventricular Zone Neural Tube Expression: Positive Negative
Selective markerExperimental details:
Curated
Microarrays
In-situ hybridization
Stem Cell Differentiation: 10/18 LifeMap Cells (see all 18 ) Name Category Induced pluripotent stem cell line 201B6 (Induced Pluripotent Stem Cell)Early Embryo, Fibroblast BG01V (Embryonic Stem Cell)Early Embryo, Inner Cell Mass CA1 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass CA2 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass VUB02 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass VUB03_DM1 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass VUB04_CF (Embryonic Stem Cell)Early Embryo, Inner Cell Mass VUB07 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass VUB09_FSHD (Embryonic Stem Cell)Early Embryo, Inner Cell Mass FES22 (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
See DNMT3B Protein Expression from SPIRE MOPED and PaxDB Genevestigator expression for DNMT3B SOURCE GeneReport for Unigene clusters: Hs.643024 Hs.713611 UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3 Tissue specificity : Ubiquitous; highly expressed in fetal liver, heart, kidney, placenta, and at lower levels inspleen, colon, brain, liver, small intestine, lung, peripheral blood mononuclear cells, and skeletal muscle. Isoform 1 is expressed in all tissues except brain, skeletal muscle and PBMC, 3 is ubiquitous, 4 is expressed in all tissues except brain, skeletal muscle, lung and prostate and 5 is detectable only in testis and at very low level in brain and prostate SABiosciences Expression via Pathway-Focused PCR Arrays including DNMT3B : Primer Products: OriGene genome-wide validated SYBR primer pairs in human , mouse , rat for DNMT3BBrowse OriGene validated miRNA SYBR primer pairs SABiosciences RT2 qPCR Primer Assay in human , mouse , rat DNMT3B QIAGEN QuantiTect SYBR Green Assays in human , mouse , rat DNMT3B QIAGEN QuantiFast Probe-based Assays in human , mouse , rat DNMT3B In Situ Assay Products: Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DNMT3B
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Orthologsfor DNMT3B gene
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
,
5 MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase ,
and/or
6 Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam )
About This Section
This gene was present in the common ancestor of animals.
Orthologs for DNMT3B gene from 5/16 species (see all 16 ) About this table
ENSEMBL Gene Tree for DNMT3B (if available)TreeFam Gene Tree for DNMT3B (if available)
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Paralogsfor DNMT3B gene (Paralogs according to
1 HomoloGene , 2 Ensembl , and 3 SIMAP , Pseudogenes according to 4 Pseudogene.org Build 68)About This Section Paralogs for DNMT3B gene DNMT3A 2 DNMT3L 2 1 SIMAP similar gene for DNMT3B using alignment to 3 protein entries: DNM3B_HUMAN (see all proteins ):DNMT3A
DNMT3B for paralogs About GeneDecksing 1 Pseudogenes.org Pseudogene for DNMT3B PGOHUM00000240078
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Genomic Variantsfor DNMT3B gene (SNPs/Variants according to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE ,
UniProtKB , and
DNA2.0 ,
Linkage Disequilibrium by HapMap ,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants , Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB) , Blood group antigen gene mutations by BGMUT ,
Resequencing Primers from QIAGEN ,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences )
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Genomic Data Transcription Related Data Allele Frequencies SNP ID Valid Clinical significance Chr 20 pos Sequence # AA Chg Type More # Allele freq Pop Total sample More
HapMap Linkage Disequilibrium report for DNMT3B (31350191 - 31397162 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions) Database of Genomic Variants (DGV): 1 variation for DNMT3B 1 CNV : 5133 Human Gene Mutation Database (HGMD) : DNMT3B Locus Specific Mutation Databases (LSDB): DNMT3B SABiosciences Cancer Mutation PCR Assays
2 SABiosciences qBiomarker Copy Number PCR Arrays containing DNMT3B :
QIAGEN SeqTarget long-range PCR primers in human , mouse , rat for resequencing DNMT3B
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Disorders
/ Diseasesfor DNMT3B gene
(in which this Gene is Involved, According to MalaCards ,
OMIM, UniProtKB ,
the University of Copenhagen DISEASES
database , Novoseek ,
Genatlas , GeneTests ,
GAD ,
HuGE Navigator ,
and/or TGDB .)
About This Section
DNMT3B for disorders About GeneDecksing OMIM gene information: 602900 OMIM disorders : 242860 UniProtKB/Swiss-Prot: DNM3B_HUMAN, Q9UBC3
Defects in DNMT3B are a cause of immunodeficiency-centromeric instability-facial anomalies syndrome type 1 (ICF1) [MIM:242860]. A rare disorder characterized by a variable immunodeficiency, facial anomalies, and branching of chromosomes 1, 9, and 16. Other variable symptoms include growth retardation, failure to thrive, and psychomotor retardation. Laboratory studies show limited hypomethylation of DNA in a small fraction of the genome in some, but not all, patients 20/74 diseases for DNMT3B (see all 74 ): About MalaCards immunodeficiency diffuse large b-cell lymphoma b-cell lymphomas mutagen sensitivity testicular germ cell tumor malignant pleural mesothelioma germ cell tumor x inactivation adenoid cystic carcinoma squamous cell carcinoma of the head and neck systemic lupus erythematosus squamous cell carcinoma lupus erythematosus myelodysplastic syndrome transitional cell carcinoma acute lymphoblastic leukemia chronic lymphocytic leukemia lymphoblastic leukemia acute myeloid leukemia carcinoma 1 disease from the University of Copenhagen DISEASES database for DNMT3B :Cancer 10/35 Novoseek disease relationships for DNMT3B gene (see all 35 ) About this table
Disease
-log (P-Val)
Hits
PubMed IDs for Articles with Shared Sentences (# sentences)
icf syndrome
95.5
37
18762900 (3), 18029387 (3), 15326630 (2), 10588719 (2) (see all 21 )
cancer
58.1
58
15721400 (4), 15661247 (4), 12015329 (3), 18455294 (2) (see all 27 )
tumors
49.5
54
17067458 (2), 18097598 (2), 18563322 (2), 15661247 (2) (see all 31 )
immunodeficiency
45.6
31
20211012 (2), 10588719 (2), 18432406 (2), 11087891 (1) (see all 21 )
colon cancer
39.3
8
19723660 (2), 15547111 (1), 19156137 (1), 12496760 (1) (see all 6 )
purpura thrombocytopenic idiopathic
38.2
2
18437543 (2)
colorectal cancer
35.7
19
19470733 (4), 16702365 (3), 18662374 (2), 18089774 (1) (see all 8 )
hepatocellular carcinoma
31.9
19
16318277 (5), 19567080 (3), 19465161 (2), 18023104 (2) (see all 7 )
gastric cancer
31.3
22
16211278 (5), 20127025 (3), 19517237 (3), 11146446 (2) (see all 5 )
endometrial cancer
29.5
11
15661247 (4), 19306077 (2), 19107573 (1)
Genetic Association Database (GAD): DNMT3B Human Genome Epidemiology (HuGE) Navigator: DNMT3B (50 documents) Export disorders for DNMT3B gene to outside databases
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Publicationsfor DNMT3B gene (in
PubMed .
Associations of this gene to articles via
1 Entrez Gene ,
2 UniProtKB/Swiss-Prot ,
3 HGNC ,
4 GAD ,
5 PharmGKB ,
6 HMDB ,
7 DrugBank ,
8 UniProtKB/TrEMBL ,
9 Novoseek , and/or
10 fRNAdb )
About This Section PubMed articles for DNMT3B gene, integrated from 9 sources (see all 369 ): (articles sorted by number of sources associating them with DNMT3B) Utopia : connect your pdf to the dynamic world of online information
Cloning, expression and chromosome locations of the human DNMT3 gene family. (PubMed id 10433969) 1 , 2 , 3, 9 Xie S....Li E. (1999) DNMT3B polymorphisms and risk of primary lung cancer. (PubMed id 15528220) 1 , 4, 9 Lee S.J....Park J.Y. (2005) No evidence of correlation between the single nucleotide polymorphism of DNMT3B promoter and gastric cancer risk in a Japanese population. (PubMed id 16211278) 1 , 4, 9 Aung P.P....Yasui W. (2005) The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. (PubMed id 10588719) 1 , 2 , 9 Hansen R.S.... Gartler S.M. (1999) Genetic variation in ICF syndrome: evidence for genetic heterogeneity. (PubMed id 11102980) 1 , 2 , 9 Wijmenga C.... Pearson P.L. (2000) Polymorphisms in the DNA methyltransferase 3b gene and prostate cancer risk. (PubMed id 16012746) 1 , 4, 9 Singal R....Schlesselman J.J. (2005) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. (PubMed id 10555141) 1 , 2 , 9 Okano M.... Li E. (1999) DNA methyltransferase 3B acts as a co-repressor of the human polycomb protein hPc2 to repress fibroblast growth factor receptor 3 transcription. (PubMed id 18567530) 1 , 2 , 9 Kim S.-H.... Kim T.-Y. (2008) Single nucleotide polymorphism in DNA methyltransferase 3B promoter and its association with gastric cardiac adenocarcinoma in North China. (PubMed id 15962389) 1 , 4, 9 Wang Y.M....Zhang J.H. (2005) DNMT3B mutations and DNA methylation defect define two types of ICF syndrome. (PubMed id 15580563) 1 , 2 , 9 Jiang Y.L.... Viegas-Pequignot E. (2005)
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External Searches for DNMT3B gene
(in PubMed ,
OMIM , and NCBI Bookshelf ) About This Section
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Genome Databases showing DNMT3B gene
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
Kegg ,
and/or
H-InvDB )
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Other Databases showing DNMT3B gene
(According to HUGE )
About This Section --
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Specialized Databases showing DNMT3B gene (According to PharmGKB ,
ATLAS , HORDE , IMGT , 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 Patent Information for DNMT3B gene: Search GeneIP for patents involving DNMT3B GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Productsfor DNMT3B gene (Antibodies, recombinant proteins, and assays from EMD Millipore , R&D Systems , OriGene , QIAGEN , GenScript , Cell Signaling Technology , SABiosciences , Novus Biologicals , Sino Biological , Enzo Life Sciences , Abcam , ProSpec , Uscn , Thermo Fisher Scientific , Gene Editing from DNA2.0 , Clones from EMD Millipore , OriGene , GenScript , Sino Biological , DNA2.0 , SwitchGear Genomics , Vector BioLabs , Cell lines from GenScript and LifeMap BioReagents , PCR Arrays from SABiosciences , Drugs and/or compounds from EMD Millipore , Tocris Bioscience , and/or
Enzo Life Sciences ), In Situ Hybridization Assays from Advanced Cell Diagnostics About This Section
OriGene Antibodies for DNMT3B OriGene shRNA RFP for DNMT3B OriGene 29mer shRNA kits in GFP-retroviral vector in human , mouse , rat for DNMT3B OriGene genome-wide validated SYBR primer pairs in human , mouse , rat for DNMT3B OriGene Protein Over-expression Lysate for DNMT3B Browse OriGene Fluorogenic Cell Assay Kits OriGene siRNA for DNMT3B OriGene 3'-UTR Clone for DNMT3B OriGene untagged cDNA clones in CMV expression vector in human , mouse , rat for DNMT3B OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human , mouse , rat for DNMT3B Browse OriGene GFP tagged cDNA clones in CMV expression vector Browse OriGene MicroRNA Expression Plasmids Browse OriGene basic RS shRNAs Browse OriGene validated miRNA SYBR primer pairs OriGene Purified Protein for DNMT3B OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling OriGene Custom Antibody Services for DNMT3B OriGene Custom Protein Services for DNMT3B OriGene Custom Immunoassay Development
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat DNMT3B QIAGEN SeqTarget long-range PCR primers in human , mouse , rat for resequencing DNMT3B QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human , mouse , rat DNMT3B QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human , mouse , rat DNMT3B QIAGEN QuantiFast Probe-based Assays in human , mouse , rat DNMT3B QIAGEN QuantiTect SYBR Green Assays in human , mouse , rat DNMT3B
DNMT3B Proteins, Antibodies, CLIAs, and ELISAs
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DNMT3B
ThermoFisher Antibody for DNMT3B
Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat DNMT3B
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