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SETDB2 Gene

protein-coding   GIFtS: 57
GCID: GC13P050018

SET Domain, Bifurcated 2

(Previous name: chromosome 13 open reading frame 4)
(Previous symbol: C13orf4)
  See SETDB2-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SET Domain, Bifurcated 21 2     Chromosome 13 Open Reading Frame 41
C13orf41 2 3     CLLL82
CLLD82 3 5     Chronic Lymphocytic Leukemia Deletion Region 82
Chronic Lymphocytic Leukemia Deletion Region Gene 8 Protein2 3     Histone-Lysine N-Methyltransferase SETDB22
Lysine N-Methyltransferase 1F2 3     EC 2.1.1.433
KMT1F2 3     SET Domain Bifurcated 23

External Ids:    HGNC: 202631   Entrez Gene: 838522   Ensembl: ENSG000001361697   OMIM: 6078655   UniProtKB: Q96T683   

Export aliases for SETDB2 gene to outside databases

Previous GC identifers: GC13P048954 GC13P047816 GC13P048916 GC13P030812


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SETDB2 Gene:
Proteins that contain a SET domain, such as SETDB2, modulate gene expression epigenetically through histone H3
(see MIM 601128) methylation. SETDB2 is likely a histone H3 methyltransferase, as it contains both the active
site and flanking cysteine residues required for catalytic activity (Zhang et al., 2003 (PubMed
12754510)).(supplied by OMIM, Mar 2008)

GeneCards Summary for SETDB2 Gene:
SETDB2 (SET domain, bifurcated 2) is a protein-coding gene. Diseases associated with SETDB2 include chronic lymphocytic leukemia, and leukemia. GO annotations related to this gene include histone methyltransferase activity (H3-K9 specific). An important paralog of this gene is NSD1.

UniProtKB/Swiss-Prot: SETB2_HUMAN, Q96T68
Function: Histone methyltransferase involved in left-right axis specification in early development and mitosis.
Specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). H3K9me3 is a specific tag for epigenetic
transcriptional repression that recruits HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones.
Contributes to H3K9me3 in both the interspersed repetitive elements and centromere-associated repeats. Plays a
role in chromosome condensation and segregation during mitosis




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000013.10  NT_024524.15  NC_018924.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SETDB2 gene promoter:
         E2F-4   E2F-3a   E2F-5   E2F-2   E2F   E2F-1   POU2F1   POU2F1a   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSETDB2 promoter sequence
   Search Chromatin IP Primers for SETDB2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SETDB2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q14   Ensembl cytogenetic band:  13q14.2   HGNC cytogenetic band: 13q14

SETDB2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SETDB2 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P050018:  view genomic region     (about GC identifiers)

Start:
50,018,429 bp from pter      End:
50,069,139 bp from pter
Size:
50,711 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SETB2_HUMAN, Q96T68 (See protein sequence)
Recommended Name: Histone-lysine N-methyltransferase SETDB2  
Size: 719 amino acids; 81894 Da
Sequence caution: Sequence=CAH56265.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential
poly-A sequence; Sequence=CAI10818.2; Type=Erroneous gene model prediction;
Secondary accessions: Q5TC65 Q5TC66 Q5W0A7 Q659A7 Q86UD6 Q96AI6
Alternative splicing: 3 isoforms:  Q96T68-1   Q96T68-2   Q96T68-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SETDB2: NX_Q96T68

Explore proteomics data for SETDB2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SETDB2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001153780.1  NP_114121.2  

    ENSEMBL proteins: 
     ENSP00000326477   ENSP00000258672   ENSP00000346175  

    SETDB2 Human Recombinant Protein Products:

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    Novus Biologicals SETDB2 Proteins
    Novus Biologicals SETDB2 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SETDB2

     
    Search eBioscience for Proteins for SETDB2 

     
    antibodies-online proteins for SETDB2 (5 products) 

     
    antibodies-online peptides for SETDB2

    SETDB2 Antibody Products:

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    antibodies-online antibodies for SETDB2 (41 products) 

    SETDB2 Assay Products:

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    Cloud-Clone Corp. ELISAs for SETDB2
    Cloud-Clone Corp. CLIAs for SETDB2
    Search eBioscience for ELISAs for SETDB2 
    antibodies-online kits for SETDB2 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    KMT: Chromatin-modifying enzymes / K-methyltransferases

    4 InterPro protein domains:
     IPR001214 SET_dom
     IPR001739 Methyl_CpG_DNA-bd
     IPR016177 DNA-bd_dom
     IPR007728 Pre-SET_dom

    Graphical View of Domain Structure for InterPro Entry Q96T68

    ProtoNet protein and cluster: Q96T68

    1 Blocks protein domain: IPB001214 Nuclear protein SET

    UniProtKB/Swiss-Prot: SETB2_HUMAN, Q96T68
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 1 MBD (methyl-CpG-binding) domain
    Similarity: Contains 1 pre-SET domain
    Similarity: Contains 1 SET domain


    Find genes that share domains with SETDB2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SETB2_HUMAN, Q96T68
    Function: Histone methyltransferase involved in left-right axis specification in early development and mitosis.
    Specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). H3K9me3 is a specific tag for epigenetic
    transcriptional repression that recruits HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones.
    Contributes to H3K9me3 in both the interspersed repetitive elements and centromere-associated repeats. Plays a
    role in chromosome condensation and segregation during mitosis
    Catalytic activity: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine +
    N(6)-methyl-L-lysine-[histone]

         Enzyme Number (IUBMB): EC 2.1.1.431

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0018024histone-lysine N-methyltransferase activity ----
    GO:0046974histone methyltransferase activity (H3-K9 specific) IDA--
         
    Find genes that share ontologies with SETDB2           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SETDB2

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SETDB2 (see all 20):
    hsa-miR-3938 hsa-miR-642a hsa-miR-300 hsa-miR-29a hsa-miR-29c hsa-miR-767-5p hsa-let-7a-2* hsa-miR-410
    SwitchGear 3'UTR luciferase reporter plasmidSETDB2 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for SETDB2
    Predesigned siRNA for gene silencing in human, mouse, rat SETDB2

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    GenScript: all cDNA clones in your preferred vector (see all 2): SETDB2 (NM_031915)
    Sino Biological Human cDNA Clone for SETDB2
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SETDB2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SETDB2

    Cell Line
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETDB2


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SETB2_HUMAN, Q96T68: Nucleus. Chromosome (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    plasma membrane3
    cytosol2
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005694chromosome IEA--

    Find genes that share ontologies with SETDB2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SETDB2 About    
    See pathways by source

    SuperPathContained pathways About
    1Lysine degradation
    Lysine degradation


    Find genes that share SuperPaths with SETDB2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    1 Kegg Pathway  (Kegg details for SETDB2):
        Lysine degradation

        Pathway & Disease-focused RT2 Profiler PCR Array including SETDB2: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for SETDB2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SETDB2 (Q96T683 ENSP000003264774) via UniProtKB, MINT, STRING, and/or I2D (see all 26)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    IGHG1P018573, ENSP000003749904I2D: score=1 STRING: ENSP00000374990
    TATP177353I2D: score=1 
    PLOD1ENSP000001960614STRING: ENSP00000196061
    PLOD2ENSP000002829034STRING: ENSP00000282903
    PLOD3ENSP000002231274STRING: ENSP00000223127
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001947heart looping ISS--
    GO:0007059chromosome segregation IMP--
    GO:0007067mitosis IMP--
    GO:0034968histone lysine methylation ----
    GO:0045892negative regulation of transcription, DNA-templated ISS--

    Find genes that share ontologies with SETDB2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SETDB2 (SETB2)

    2 HMDB Compounds for SETDB2    About this table
    CompoundSynonyms CAS #PubMed Ids
    S-Adenosylhomocysteine(S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine (see all 19)979-92-0--
    S-Adenosylmethionine(3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine (see all 16)29908-03-0--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SETDB2 gene (2 alternative transcripts): 
    NM_001160308.1  NM_031915.2  

    Unigene Cluster for SETDB2:

    SET domain, bifurcated 2
    Hs.631789  [show with all ESTs]
    Unigene Representative Sequence: NM_031915
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000317257 ENST00000481439 ENST00000258672(uc021rjn.1) ENST00000354234(uc010adg.2 uc010adh.2 uc001vcz.3 uc001vda.3)

    miRNA
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    Block miRNA regulation of human, mouse, rat SETDB2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SETDB2 (see all 20):
    hsa-miR-3938 hsa-miR-642a hsa-miR-300 hsa-miR-29a hsa-miR-29c hsa-miR-767-5p hsa-let-7a-2* hsa-miR-410
    SwitchGear 3'UTR luciferase reporter plasmidSETDB2 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SETDB2
    Clone
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    OriGene ORF clones in mouse, rat for SETDB2
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): SETDB2 (NM_031915)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SETDB2
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SETDB2
      QuantiTect SYBR Green Assays in human, mouse, rat SETDB2
      QuantiFast Probe-based Assays in human, mouse, rat SETDB2

    Additional mRNA sequence: 

    AF086317.1 AF277186.1 AF334407.1 AK307593.1 AK308220.1 AK308354.1 AK311602.1 AL831937.1 
    BC017078.1 BC028202.1 BC047434.2 

    14 DOTS entries:

    DT.451703  DT.100754350  DT.100021760  DT.99941016  DT.107354  DT.100754352  DT.120771099  DT.112490 
    DT.40114015  DT.91682494  DT.91819713  DT.120771066  DT.92416347  DT.95368814 

    Selected AceView cDNA sequences (see all 88):

    CR597159 AV709114 AA648818 CA771828 AI374660 AA281080 BC017078 AA252557 
    AF334407 AA761971 AL833957 BX281643 AA831594 AV709444 AI804313 AI075941 
    AI697183 AA262434 CK905119 AF086317 BM272746 NM_031915 CR608721 BI093360 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SETDB2 (see all 9)    About this scheme

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

    ExUns: 17a · 17b
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for SETDB2

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SETDB2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SETDB2 Expression
    About this image


    SETDB2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Brain (Nervous System)    fully expand to see all 5 entries
             Epithalamus
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    SETDB2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SETDB2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631789

    UniProtKB/Swiss-Prot: SETB2_HUMAN, Q96T68
    Tissue specificity: Ubiquitous. Highest expression in heart, testis and ovary

        Pathway & Disease-focused RT2 Profiler PCR Array including SETDB2: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat SETDB2
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETDB2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SETDB2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Setdb21 , 5 SET domain, bifurcated 21, 5 78.95(n)1
    68.22(a)1
      14 (31.48 cM)5
    2391221  NM_001081024.11  NP_001074493.11 
     594020095 
    chicken
    (Gallus gallus)
    Aves SETDB21 SET domain, bifurcated 2 59.64(n)
    50(a)
      418866  XM_417061.3  XP_417061.2 
    lizard
    (Anolis carolinensis)
    Reptilia SETDB26
    SET domain, bifurcated 2
    43(a)
    1 ↔ 1
    1(137440405-137460787)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3987112 putative histone methylatransferase CLLD8 77.52(n)    AY145835.1 
    zebrafish
    (Danio rerio)
    Actinopterygii SETDB26
    SET domain, bifurcated 2
    29(a)
    1 ↔ 1
    1(769342-772993) ENSDARG00000090668
    fruit fly
    (Drosophila melanogaster)
    Insecta Set26
    Set2
    4(a)
    many ↔ many
    X(13307275-13315057)
    worm
    (Caenorhabditis elegans)
    Secernentea set-116
    met-26
    Protein MET-2 (met-2) mRNA, complete cds
    24(a)
    12(a)
    many ↔ many
    many ↔ many
    II(2690472-2694311) WBGene00018023
    III(8375298-8380849) WBGene00019883
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SET26
    Histone methyltransferase with a role in transcrip...
    9(a)
    1 → many
    X(102227-104428) YJL168C


    ENSEMBL Gene Tree for SETDB2 (if available)
    TreeFam Gene Tree for SETDB2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SETDB2 gene
    NSD12  ASH1L2  WHSC12  WHSC1L12  SUV39H22  SETBP12  SUV39H12  SETD22  
    EHMT12  EHMT22  SETMAR2  SETDB12  
    2 SIMAP similar genes for SETDB2 using alignment to 1 protein entry:     SETB2_HUMAN:
    DKFZp586I0123    FP13812

    Find genes that share paralogs with SETDB2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SETDB2 (see all 916)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs619599921,2
    C,F--50020280(+) ATATGG/CTATAA 1 -- int111Minor allele frequency- C:0.46NA WA CSA EA 373
    rs1497855151,2
    C--50020355(+) CTTTT-/ACATTC 1 -- int10--------
    rs1391740001,2
    --50020372(+) AGAATA/TGGTAC 1 -- int10--------
    rs1499851521,2
    --50020402(+) ATCCAC/GATTTT 1 -- int10--------
    rs1451593871,2
    C--50020416(+) CTTGAA/GTTTTT 1 -- int10--------
    rs1921702771,2
    C--50020546(+) TCCCTC/TACTCC 1 -- int11Minor allele frequency- T:0.00EU 591
    rs1491701731,2
    --50020646(+) TATAGA/GTGAAT 1 -- int10--------
    rs1844843561,2
    --50020829(+) TTAATA/GTAAAA 1 -- int10--------
    rs1893583071,2
    --50020919(+) ATTCTC/TTGAGA 1 -- int10--------
    rs1928971741,2
    --50021010(+) TCTAGG/TATATA 1 -- int10--------

    HapMap Linkage Disequilibrium report for SETDB2 (50018429 - 50069139 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for SETDB2:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv3404CNV Deletion18987735
    esv2747395CNV Deletion23290073
    esv2747394CNV Deletion23290073
    esv272759CNV Insertion20981092
    esv267803CNV Insertion20981092
    nsv900070CNV Loss21882294
    nsv523648CNV Gain19592680

    Human Gene Mutation Database (HGMD): SETDB2
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SETDB2
    DNA2.0 Custom Variant and Variant Library Synthesis for SETDB2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607865    OMIM disorders: --

    2 diseases for SETDB2:    
    About MalaCards
    chronic lymphocytic leukemia    leukemia


    Find genes that share disorders with SETDB2           About GenesLikeMe

    Genetic Association Database (GAD): SETDB2
    Human Genome Epidemiology (HuGE) Navigator: SETDB2 (3 documents)

    Export disorders for SETDB2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SETDB2 gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with SETDB2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of CLLD6, CLLD7, and CLLD8, novel candidate genes for leukemogenesis at chromosome 13q14, a region commonly deleted in B-cell chronic lymphocytic leukemia. (PubMed id 11306461)1, 2, 3 Mabuchi H.... Croce C.M. (Cancer Res. 2001)
    2. CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation. (PubMed id 20404330)1, 2 Falandry C.... Magdinier F. (J. Biol. Chem. 2010)
    3. A multi-centre study of candidate genes for wheeze and allergy: the International Study of Asthma and Allergies in Childhood Phase 2. (PubMed id 20085599)1, 4 Genuneit J....Moffatt M.F. (Clin. Exp. Allergy 2009)
    4. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)1, 2 Dunham A.... Ross M.T. (Nature 2004)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. (PubMed id 12754510)1, 2 Zhang Y.... Cookson W.O.C.M. (Nat. Genet. 2003)
    7. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    8. Lysine methylation of HIV-1 Tat regulates transcriptional activity of the viral LTR. (PubMed id 18498648)1 Van Duyne R....Kashanchi F. (Retrovirology 2008)
    9. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 83852 HGNC: 20263 AceView: SETDB2 Ensembl:ENSG00000136169 euGenes: HUgn83852
    ECgene: SETDB2 Kegg: 83852 H-InvDB: SETDB2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SETDB2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SETDB2 gene:
    Search GeneIP for patents involving SETDB2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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