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SETDB1 Gene

protein-coding   GIFtS: 65
GCID: GC01P150898

SET Domain, Bifurcated 1

  See 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 11 2     H3-K9-HMTase42
Tudor Domain Containing 211 2     KG1T2
Histone H3-K9 Methyltransferase 42 3     TDRD212
Lysine N-Methyltransferase 1E2 3     ERG-Associated Protein With A SET Domain, ESET2
ESET2 3     Histone-Lysine N-Methyltransferase SETDB12
KMT1E2 3     Histone-Lysine N-Methyltransferase, H3lysine-9 Specific 42
ERG-Associated Protein With SET Domain2 3     KIAA00673
H3-K9-HMTase 42 3     SET Domain Bifurcated 13
EC 2.1.1.433 8     

External Ids:    HGNC: 107611   Entrez Gene: 98692   Ensembl: ENSG000001433797   OMIM: 6043965   UniProtKB: Q150473   

Export aliases for SETDB1 gene to outside databases

Previous GC identifers: GC01P148740 GC01P146646 GC01P147673 GC01P148115 GC01P147711 GC01P149165 GC01P122275


(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 SETDB1 Gene:
This gene encodes a histone methyltransferase which regulates histone methylation, gene silencing, and
transcriptional repression. This gene has been identified as a target for treatment in Huntington Disease, given
that gene silencing and transcription dysfunction likely play a role in the disease pathogenesis. Alternatively
spliced transcript variants of this gene have been described.(provided by RefSeq, Jun 2011)

GeneCards Summary for SETDB1 Gene:
SETDB1 (SET domain, bifurcated 1) is a protein-coding gene. Diseases associated with SETDB1 include yaws, and huntington's disease. GO annotations related to this gene include histone-lysine N-methyltransferase activity. An important paralog of this gene is NSD1.

UniProtKB/Swiss-Prot: SETB1_HUMAN, Q15047
Function: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9'
trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3
and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central
role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation.
Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and
histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA
replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by
KRAB zinc-finger proteins

Gene Wiki entry for SETDB1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NT_004487.20  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SETDB1 gene promoter:
         Sp1   Lmo2   Cdc5   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSETDB1 promoter sequence
   Search Chromatin IP Primers for SETDB1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SETDB1


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

Entrez Gene cytogenetic band: 1q21   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21

SETDB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SETDB1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P150898:  view genomic region     (about GC identifiers)

Start:
150,898,739 bp from pter      End:
150,937,220 bp from pter
Size:
38,482 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SETB1_HUMAN, Q15047 (See protein sequence)
Recommended Name: Histone-lysine N-methyltransferase SETDB1  
Size: 1291 amino acids; 143157 Da
Subunit: Interacts with MBD1; interaction is abolished when MBD1 is sumoylated. Interacts with ATF7IP and ATF7IP2;
the interaction with ATF7IP is required to stimulate histone methyltransferase activity and facilitate the
conversion of dimethylated to trimethylated H3 'Lys-9'. During DNA replication, it is recruited by SETDB1 to form
a S phase-specific complex that facilitates methylation of H3 'Lys-9' during replication-coupled chromatin
assembly and is at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1. Interacts with ERG, TRIM28/TIF1B,
CBX1, CBX5, CHD7, DNMT3A, HDAC1, HDAC2, NLK, PPARG, SIN3A, SIN3B, DNMT3B and SUMO2. Interacts with MPHOSPH8. Part
of a complex containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2
Miscellaneous: Highly up-regulated in Huntington disease patients, suggesting that participates in the altered
chromatin modulation and transcription dysfunction observed in Huntington disease. Its down-regulation has
salubrious effects on patients, suggesting that it may be a promising treatment in Huntington disease patients
Sequence caution: Sequence=BAA06689.2; Type=Erroneous initiation; Sequence=CAI13325.1; Type=Erroneous gene model
prediction; Sequence=CAI13326.1; Type=Erroneous gene model prediction;
1 PDB 3D structure from and Proteopedia for SETDB1:
3DLM (3D)    
Secondary accessions: A6NEW2 Q5SZD8 Q5SZD9 Q5SZE0 Q5SZE7 Q96GM9
Alternative splicing: 3 isoforms:  Q15047-1   Q15047-2   Q15047-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SETDB1: NX_Q15047

Explore proteomics data for SETDB1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys59, Lys182, Lys597
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for SETDB1 (Q15047) (see all 13)
     DKSKCAC  NHSCSPN  EWIYRGS  LSCVNEID 


    See SETDB1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001138887.1  NP_001230420.1  NP_036564.3  

    ENSEMBL proteins: 
     ENSP00000435922   ENSP00000271640   ENSP00000409379   ENSP00000357958   ENSP00000436148  
     ENSP00000357965   ENSP00000357959   ENSP00000432348   ENSP00000357960   ENSP00000407831  

    SETDB1 Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for SETDB1
    OriGene Protein Over-expression Lysate for SETDB1
    OriGene MassSpec for SETDB1
    OriGene Custom Protein Services for SETDB1
    GenScript Custom Purified and Recombinant Proteins Services for SETDB1
    Novus Biologicals SETDB1 Proteins
    Novus Biologicals SETDB1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SETDB1

    SETDB1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of SETDB1
    Browse R&D Systems for Antibodies
    Cell Signaling Technology (CST) Antibodies for SETDB1 
    OriGene Antibodies for SETDB1
    OriGene Custom Antibody Services for SETDB1
    Novus Biologicals SETDB1 Antibodies
    Abcam antibodies for SETDB1
    Cloud-Clone Corp. Antibodies for SETDB1
    ThermoFisher Antibodies for SETDB1
    LSBio Antibodies in human, mouse, rat for SETDB1

    SETDB1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for SETDB1
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for SETDB1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SETDB1
    Cloud-Clone Corp. CLIAs for SETDB1


    (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
    TDRD: Tudor domain containing

    Selected InterPro protein domains (see all 8):
     IPR001214 SET_dom
     IPR003616 Post-SET_dom
     IPR003606 Pre-SET_Zn-bd_sub
     IPR001739 Methyl_CpG_DNA-bd
     IPR025796 Hist-Lys_N-MeTrfase_SETDB1

    Graphical View of Domain Structure for InterPro Entry Q15047

    ProtoNet protein and cluster: Q15047

    5 Blocks protein domains:
    IPB001214 Nuclear protein SET
    IPB001739 Methyl-CpG binding
    IPB002999 Tudor domain
    IPB003606 Nuclear protein Zn2+-binding
    IPB003616 SET-related region


    UniProtKB/Swiss-Prot: SETB1_HUMAN, Q15047
    Domain: The pre-SET, SET and post-SET domains are all required for methyltransferase activity. The 347-amino-acid
    insertion in the SET domain has no effect on the catalytic activity
    Domain: Isoform 2 lacks all domains required for histone methyltransferase activity
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine
    methyltransferase family. Suvar3-9 subfamily
    Similarity: Contains 1 MBD (methyl-CpG-binding) domain
    Similarity: Contains 1 post-SET domain
    Similarity: Contains 1 pre-SET domain
    Similarity: Contains 1 SET domain
    Similarity: Contains 2 Tudor domains


    SETDB1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SETB1_HUMAN, Q15047
    Function: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9'
    trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3
    and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central
    role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation.
    Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and
    histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA
    replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by
    KRAB zinc-finger proteins
    Catalytic activity: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine +
    N(6)-methyl-L-lysine-[histone]

         Genatlas biochemistry entry for SETDB1:
    protein with an unusual bifurcated SET domain protein 1

         Enzyme Number (IUBMB): EC 2.1.1.431 2

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding IPI16682412
    GO:0008270zinc ion binding IEA--
    GO:0018024histone-lysine N-methyltransferase activity IEA--
         
    SETDB1 for ontologies           About GeneDecksing


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Setdb1):
     cellular  embryogenesis  hematopoietic system  immune system  mortality/aging 
     nervous system  normal  skeleton 

    SETDB1 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SETDB1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SETDB1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SETDB1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SETDB1

    miRNA
    Products:
        
    miRTarBase miRNAs that target SETDB1:
    hsa-mir-1260b (MIRT052718), hsa-mir-92a-3p (MIRT048947), hsa-mir-296-3p (MIRT038516), hsa-mir-152-3p (MIRT045818), hsa-mir-324-3p (MIRT043011)

    Block miRNA regulation of human, mouse, rat SETDB1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SETDB1 (see all 13):
    hsa-miR-498 hsa-miR-3130-5p hsa-miR-4324 hsa-miR-29a hsa-miR-29c hsa-miR-621 hsa-miR-3139 hsa-miR-708
    SwitchGear 3'UTR luciferase reporter plasmidSETDB1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SETDB1
    Predesigned siRNA for gene silencing in human, mouse, rat SETDB1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for SETDB1

    Clone
    Products:
         
    OriGene clones in human, mouse for SETDB1 (see all 15)
    OriGene ORF clones in mouse, rat for SETDB1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): SETDB1 (NM_001145415)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SETDB1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SETDB1

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for SETDB1
    Browse ESI BIO Cell Lines and PureStem Progenitors for SETDB1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETDB1


    (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
    SETB1_HUMAN, Q15047: Nucleus. Chromosome. Note=Associated with non-pericentromeric regions of chromatin. Excluded
    from nucleoli and islands of condensed chromatin
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    golgi apparatus4
    plasma membrane4
    cytosol3

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005694chromosome IEA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0005794Golgi apparatus IDA--

    SETDB1 for ontologies           About GeneDecksing


    (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 SETDB1 About    
    See pathways by source

    SuperPathContained pathways About
    1Packaging Of Telomere Ends
    Histone modification0.31
    2Noncanonical Wnt signaling pathway
    Noncanonical Wnt signaling pathway
    3Lysine degradation
    Lysine degradation
    4Chromatin Regulation / Acetylation
    Chromatin Regulation / Acetylation

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for SETDB1
        Chromatin Regulation / Acetylation

    1 BioSystems Pathway for SETDB1
        Noncanonical Wnt signaling pathway


    1 Kegg Pathway  (Kegg details for SETDB1):
        Lysine degradation


    SETDB1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including SETDB1: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SETDB1

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

    Selected Interacting proteins for SETDB1 (Q150471, 2, 3 ENSP000003579654) via UniProtKB, MINT, STRING, and/or I2D (see all 233)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H3BP684312, 3MINT-7221095 I2D: score=2 
    HIST1H3CP684312, 3MINT-7221095 I2D: score=2 
    HIST1H3DP684312, 3MINT-7221095 I2D: score=2 
    HIST1H3EP684312, 3MINT-7221095 I2D: score=2 
    HIST1H3FP684312, 3MINT-7221095 I2D: score=2 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001833inner cell mass cell proliferation IEA--
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0034968histone lysine methylation ----
    GO:0060348bone development IEA--

    SETDB1 for ontologies           About GeneDecksing



    (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 SETDB1 (SETB1)

    3 HMDB Compounds for SETDB1    About this table
    CompoundSynonyms CAS #PubMed Ids
    L-Lysine(+)-S-Lysine (see all 25)56-87-1--
    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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SETDB1 gene (3 alternative transcripts): 
    NM_001145415.1  NM_001243491.1  NM_012432.3  

    Unigene Cluster for SETDB1:

    SET domain, bifurcated 1
    Hs.643565  [show with all ESTs]
    Unigene Representative Sequence: NM_001145415
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000525956 ENST00000487584 ENST00000463774 ENST00000271640(uc009wmf.2 uc001evv.2 uc001evu.2)
    ENST00000448029 ENST00000368962(uc001evw.4) ENST00000534805 ENST00000368969
    ENST00000368963 ENST00000459773 ENST00000498193(uc009wmg.2) ENST00000368964
    ENST00000423081 ENST00000481219 ENST00000497314 ENST00000528749 ENST00000533529

    miRNA
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    Block miRNA regulation of human, mouse, rat SETDB1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SETDB1 (see all 13):
    hsa-miR-498 hsa-miR-3130-5p hsa-miR-4324 hsa-miR-29a hsa-miR-29c hsa-miR-621 hsa-miR-3139 hsa-miR-708
    SwitchGear 3'UTR luciferase reporter plasmidSETDB1 3' UTR sequence
    Inhib. RNA
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): SETDB1 (NM_001145415)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SETDB1
    Primer
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    OriGene qPCR primer pairs and template standards for SETDB1
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SETDB1
      QuantiTect SYBR Green Assays in human, mouse, rat SETDB1
      QuantiFast Probe-based Assays in human, mouse, rat SETDB1

    Additional mRNA sequence: 

    AK308335.1 BC009362.2 BC028671.2 D31891.1 

    22 DOTS entries:

    DT.313478  DT.100792734  DT.91752091  DT.99972291  DT.100792736  DT.97859023  DT.100792735  DT.121452959 
    DT.100792739  DT.313480  DT.91659902  DT.97780296  DT.121453028  DT.91844257  DT.102841839  DT.121452951 
    DT.91686941  DT.95181462  DT.95206841  DT.97859022  DT.87002754  DT.95085160 

    Selected AceView cDNA sequences (see all 176):

    AL704885 BQ055551 CN481814 D31891 AA744245 BU624516 CB270416 NM_012432 
    AI886301 CB149707 N54657 AW023901 BC009362 BC028671 AL039272 CB268330 
    CD559066 AI337052 BE727991 BQ935376 BM827499 BG057891 BM785063 BM464383 

    GeneLoc Exon Structure


    (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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    SETDB1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATCTTCGCTT
    SETDB1 Expression
    About this image

    SETDB1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SETDB1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.643565

    UniProtKB/Swiss-Prot: SETB1_HUMAN, Q15047
    Tissue specificity: Widely expressed. High expression in testis

        Pathway & Disease-focused RT2 Profiler PCR Array including SETDB1: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Primer
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    OriGene qPCR primer pairs and template standards for SETDB1
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    QuantiFast Probe-based Assays in human, mouse, rat SETDB1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETDB1

    (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 SETDB1 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Setdb11 , 5 SET domain, bifurcated 11, 5 88.98(n)1
    91.93(a)1
      3 (40.74 cM)5
    845051  NM_018877.31  NP_061365.31 
     953235255 
    chicken
    (Gallus gallus)
    Aves LOC1017511501 histone-lysine N-methyltransferase SETDB1-like 70.92(n)
    78.05(a)
      101751150  XM_004948341.1  XP_004948398.1 
    lizard
    (Anolis carolinensis)
    Reptilia SETDB16
    SET domain, bifurcated 1
    62(a)
    1 ↔ 1
    GL343893.1(58321-124103)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.168482 Xenopus laevis transcribed sequence with weak similarity more 76.95(n)    48054231 
    zebrafish
    (Danio rerio)
    Actinopterygii wufa04a122 wufa04a12 82.65(n)   334802  AA495195.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG304263   -- 44(a)
    (best of 2)
      60E1   --
    worm
    (Caenorhabditis elegans)
    Secernentea set-116
    met-26
    Protein MET-2 (met-2) mRNA, complete cds
    26(a)
    20(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...
    10(a)
    1 → many
    X(102227-104428) YJL168C


    ENSEMBL Gene Tree for SETDB1 (if available)
    TreeFam Gene Tree for SETDB1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SETDB1 gene
    NSD12  ASH1L2  WHSC12  WHSC1L12  SUV39H22  SETBP12  SETDB22  SUV39H12  
    SETD22  EHMT12  EHMT22  SETMAR2  

    SETDB1 for paralogs           About GeneDecksing



    (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 SETDB1 (see all 911)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1414585811,2
    --150896926(+) CTCACG/TCCTGT 3 -- us2k10--------
    rs1885225211,2
    --150896973(+) ATCACC/TTGAGG 3 -- us2k10--------
    rs115898861,2
    C,F,A,H--150897025(+) gtctcC/Taccaa 3 -- us2k15Minor allele frequency- T:0.50NA CSA 10
    rs1398372191,2
    C--150897159(+) GCACTA/CCAGCT 3 -- us2k10--------
    rs360397001,2
    C--150897173(+) GTGAC-/AAGAGCG 3 -- us2k11Minor allele frequency- AA:0.00NA 2
    rs1931048371,2
    --150897271(+) GGAGGC/TCGAGG 3 -- us2k10--------
    rs727046791,2
    C--150897477(+) CGAAAT/CGCCTT 3 -- us2k17Minor allele frequency- C:0.49WA NA CSA EA 365
    rs1857347931,2
    --150897658(+) GCCTCC/TGCCAC 3 -- us2k10--------
    rs727046821,2
    C--150897677(+) AAGCGA/TTCCTC 3 -- us2k15Minor allele frequency- T:0.39NA CSA WA EA 361
    rs727046851,2
    C--150897687(+) CCCCCC/GGCCTC 3 -- us2k15Minor allele frequency- G:0.38NA CSA WA EA 362

    HapMap Linkage Disequilibrium report for SETDB1 (150898739 - 150937220 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SETDB1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2661989CNV Deletion23128226
    nsv522317CNV Loss19592680
    nsv522840CNV Gain19592680

    Human Gene Mutation Database (HGMD): SETDB1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SETDB1
    DNA2.0 Custom Variant and Variant Library Synthesis for SETDB1

    (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: 604396    OMIM disorders: --

    8 diseases for SETDB1:    
    About MalaCards
    yaws    huntington's disease    kidney disease    ataxia
    melanoma    hiv-1    breast cancer    leukemia


    SETDB1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SETDB1
    Human Genome Epidemiology (HuGE) Navigator: SETDB1 (1 document)

    Export disorders for SETDB1 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 SETDB1 gene, integrated from 10 sources (see all 72):
    (articles sorted by number of sources associating them with SETDB1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. (PubMed id 16682412)1, 2, 9 Li H.... Pfeifer G.P. (J. Biol. Chem. 2006)
    2. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. (PubMed id 11959841)1, 2, 9 Schultz D.C.... Rauscher F.J. III (Genes Dev. 2002)
    3. ESET/SETDB1 gene expression and histone H3 (K9) trimethylation in Huntington's disease. (PubMed id 17142323)1, 2, 9 Ryu H.... Ferrante R.J. (Proc. Natl. Acad. Sci. U.S.A. 2006)
    4. Transcriptional repression and heterochromatin formation by MBD1 and MCAF/AM family proteins. (PubMed id 15691849)1, 2, 9 Ichimura T.... Nakao M. (J. Biol. Chem. 2005)
    5. A histone lysine methyltransferase activated by non-canonical Wnt signalling suppresses PPAR-gamma transactivation. (PubMed id 17952062)1, 2, 9 Takada I.... Kato S. (Nat. Cell Biol. 2007)
    6. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. (PubMed id 12869583)1, 2, 9 Ayyanathan K.... Rauscher F.J. III (Genes Dev. 2003)
    7. Common genetic variation in candidate genes and susceptibility to subtypes of breast cancer. (PubMed id 19124506)1, 4 Mavaddat N....Pharoah P.D. (amp 2009)
    8. CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation. (PubMed id 19061646)1, 2 Mulligan P....Shi Y. (Mol. Cell 2008)
    9. Regulation of MBD1-mediated transcriptional repression by SUMO and PIAS proteins. (PubMed id 17066076)1, 2 Lyst M.J.... Stancheva I. (EMBO J. 2006)
    10. NXP-2 association with SUMO-2 depends on lysines required for transcriptional repression. (PubMed id 16567619)1, 2 Rosendorff A.... Gill G. (Proc. Natl. Acad. Sci. U.S.A. 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: 9869 HGNC: 10761 AceView: SETDB1 Ensembl:ENSG00000143379 euGenes: HUgn9869
    ECgene: SETDB1 Kegg: 9869 H-InvDB: SETDB1

    (According to HUGE)
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    HUGE: KIAA0067

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SETDB1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SETDB1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SETDB1 gene:
    Search GeneIP for patents involving SETDB1

    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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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