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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SETD6 Gene

protein-coding   GIFtS: 41
GCID: GC16P058549

SET domain containing 6

  Search for SETD6
in our new
 Human Malady Compendium 
Biological research products
for SETD6
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
SET Domain Containing 61 2
SET Domain-Containing Protein 62 3
FLJ211481
N-Lysine Methyltransferase SETD62
EC 2.1.1.-3

External Ids:    HGNC: 261161   Entrez Gene: 799182   Ensembl: ENSG000001030377   UniProtKB: Q8TBK23   

Export aliases for SETD6 gene to outside databases

Previous GC identifers: GC16P057107 GC16P044417


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: SETD6_HUMAN, Q8TBK2
Function: Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of
NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity




(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_000016.9  NC_018927.1  NT_010498.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SETD6 gene promoter:
         GATA-3   AP-4   C/EBPalpha   YY1   Roaz   NF-AT4   PPAR-gamma1   NF-AT3   PPAR-gamma2   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSETD6 promoter sequence
   Search SABiosciences Chromatin IP Primers for SETD6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SETD6


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

Entrez Gene cytogenetic band: 16q21   Ensembl cytogenetic band:  16q21   HGNC cytogenetic band: 16q21

SETD6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SETD6 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P058549:  view genomic region     (about GC identifiers)

Start:
58,549,383 bp from pter      End:
58,554,431 bp from pter
Size:
5,049 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, 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: SETD6_HUMAN, Q8TBK2 (See protein sequence)
Recommended Name: N-lysine methyltransferase SETD6  
Size: 473 amino acids; 53189 Da
Subcellular location: Nucleus
2 PDB 3D structures from and Proteopedia for SETD6:
3QXY (3D)        3RC0 (3D)    
Secondary accessions: A8K380 B5ME38 Q9H787
Alternative splicing: 2 isoforms:  Q8TBK2-1   Q8TBK2-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SETD6: NX_Q8TBK2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8TBK2

  • SETD6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001153777.1  NP_079136.2  

    ENSEMBL proteins: 
     ENSP00000310082   ENSP00000377809   ENSP00000219315   ENSP00000398033   ENSP00000396437  
     ENSP00000412858  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for SETD6

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--


    SETD6 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    SETD6 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR011383 RuBisCo-cyt_methylase
     IPR001214 SET_dom
     IPR015353 Rubisco_LSMT_subst-bd

    Graphical View of Domain Structure for InterPro Entry Q8TBK2

    ProtoNet protein and cluster: Q8TBK2

    UniProtKB/Swiss-Prot: SETD6_HUMAN, Q8TBK2
    Similarity: Belongs to the SETD6 family
    Similarity: Contains 1 SET domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, 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: SETD6_HUMAN, Q8TBK2
    Function: Protein-lysine N-methyltransferase that specifically monomethylates 'Lys-310' of the RELA subunit of
    NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity

    Enzyme Number (IUBMB): EC 2.1.1.-1

    miRNA
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    hsa-miR-411* hsa-miR-2052 hsa-miR-4307 hsa-miR-379* hsa-miR-199a-3p hsa-miR-15a hsa-miR-503 hsa-miR-578
    SwitchGear 3'UTR luciferase reporter plasmidSETD6 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:0016279protein-lysine N-methyltransferase activity IDA--
    GO:0051059NF-kappaB binding IPI--


    SETD6 for ontologies           About GeneDecksing


    Animal Models:
         1 MGI phenotypic allele for Setd6 (no phenotypes)

    SETD6 for phenotypes           About GeneDecksing


    (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 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SETD6

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    3 Interacting proteins for SETD6 (Q8TBK21, 3 ENSP000003100824) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RELAQ042063, ENSP000003842734I2D: score=1 STRING: ENSP00000384273
    UBCENSP000003448184STRING: ENSP00000344818
    RelaQ042071EBI-3863032,EBI-644400
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0018026peptidyl-lysine monomethylation IDA--
    GO:0032088negative regulation of NF-kappaB transcription factor activity IMP--
    GO:0050727regulation of inflammatory response IMP--


    SETD6 for ontologies           About GeneDecksing



    (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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SETD6
    Search CenterWatch for drugs/clinical trials and news about SETD6 

    (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 SETD6 gene (2 alternative transcripts): 
    NM_001160305.1  NM_024860.2  

    Unigene Cluster for SETD6:

    SET domain containing 6
    Hs.731691  [show with all ESTs]
    Unigene Representative Sequence: NM_001160305
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000310682 ENST00000394266(uc002enr.3 uc002ens.3 uc010cdm.3)
    ENST00000219315(uc010vij.1 uc010cdl.2) ENST00000427443(uc021tjh.1)
    ENST00000470003 ENST00000492050 ENST00000447443 ENST00000468223 ENST00000418480
    ENST00000422445 ENST00000467320 ENST00000463954 ENST00000491587

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SETD6
    8/49 QIAGEN miScript miRNA Assays for microRNAs that regulate SETD6 (see all 49):
    hsa-miR-411* hsa-miR-2052 hsa-miR-4307 hsa-miR-379* hsa-miR-199a-3p hsa-miR-15a hsa-miR-503 hsa-miR-578
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    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SETD6
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    Additional cDNA sequence: 

    AK024801.1 AK290495.1 AK297288.1 AK309468.1 BC022451.1 BC110433.1 

    13 DOTS entries:

    DT.119935  DT.100878056  DT.97860255  DT.120655337  DT.91741987  DT.95365752  DT.100652566  DT.120655350 
    DT.75145539  DT.91979260  DT.95337611  DT.120655381  DT.120655399 

    24/119 AceView cDNA sequences (see all 119):

    BU677517 BF981196 AW294517 BM968443 BQ776520 BM353722 BG150157 BQ428163 
    BM053078 BM353451 AI683799 CR616142 BM792634 BX112654 AI022677 BM052780 
    BQ185125 BM690278 BP338820 BU633510 AW439917 BQ057751 CA947083 CA946809 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for SETD6 (see all 8)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b · 10c · 10d · 10e
    SP1:                    -                             -                       -     -                                                   
    SP2:                                                  -                       -     -                                                   
    SP3:                          -                                                                                                         
    SP4:                    -                                                                                                               
    SP5:                                                  -     -     -     -     -     -     -     -                                       


    ECgene alternative splicing isoforms for SETD6

    (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

    SETD6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See SETD6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SETD6

    SOURCE GeneReport for Unigene cluster: Hs.731691
        SABiosciences Expression via Pathway-Focused PCR Array including SETD6: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETD6

    (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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SETD6 gene from 7/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Setd61 , 5 SET domain containing 61, 5 83.93(n)1
    82.37(a)1
      8 (47.17 cM)5
    660831  NM_001035123.31  NP_001030295.11 
     957159155 
    chicken
    (Gallus gallus)
    Aves SETD61 SET domain containing 6 71.57(n)
    69.46(a)
      415675  NM_001030563.2  NP_001025734.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    63(a)
    60(a)
    many → 1
    many → 1
    AAWZ02039808(1955-5005)
    AAWZ02038141(1691-12879)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.13972 Xenopus laevis transcribed sequence with weak similarity more 74.73(n)    CD098703.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb58f112 wufb58f11 71.89(n)   322348  BC044440.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G565706
    SET domain-containing protein
    17(a)
    1 ↔ 1
    3(20958660-20961137)
    rice
    (Oryza sativa)
    Liliopsida --
    SET domain containing protein, expressed
    20(a)
    1 ↔ 1
    1(38156276-38158742)


    ENSEMBL Gene Tree for SETD6 (if available)
    TreeFam Gene Tree for SETD6 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SETD6 gene
    SETD32  

    SETD6 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SETD6
    PGOHUM00000240242


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 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)
    About This Section

    10/147 NCBI SNPs in SETD6 are shown (see all 147    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1378801051,2
    --58548152(+) CCTCAC/TAAGAT 2 -- us2k10--------
    rs1423114911,2
    --58548169(+) TGGGCC/TACAGG 2 -- us2k10--------
    rs1138534121,2
    --58548203(+) GGCTTC/TTAAAT 2 -- us2k11Minor allele frequency- T:0.50CSA 2
    rs777599181,2
    C,--58548362(+) CAGGC-/CGCGCG
            
    CGGTG
    2 -- us2k10--------
    rs1916604831,2
    --58548387(+) TGTAAA/TCCTAG 2 -- us2k10--------
    rs355563131,2
    C,F,--58548415(+) GCGGGG/AGGATT 2 -- us2k12Minor allele frequency- A:0.50NA 4
    rs671687251,2
    C--58548650(+) GCGCC-/AAAAAAAA 2 -- us2k10--------
    rs740231141,2
    C,--58548847(+) TCCCTA/TCTATG 2 -- us2k12Minor allele frequency- T:0.09WA 120
    rs1837933231,2
    --58548913(+) GGCAAA/GTAAGG 2 -- us2k10--------
    rs38095961,2
    C,F,H,--58549014(-) GGAACT/CCTTTT 2 -- us2k124Minor allele frequency- C:0.41EA NS NA WA CSA 3844

    HapMap Linkage Disequilibrium report for SETD6 (58549383 - 58554431 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SETD6: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SETD6
    DNA2.0 Custom Variant and Variant Library Synthesis for SETD6

    (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.)
    About This Section
      --

    (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)
    About This Section

    PubMed articles for SETD6 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with SETD6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Lysine methylation of the NF-kappaB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-kappaB signaling. (PubMed id 21131967)1, 2 Levy D.... Gozani O. (2011)
    2. 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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    5. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    6. Structural basis of SETD6-mediated regulation of the N F-kB network via methyl-lysine signaling. (PubMed id 21515635)1 Chang Y....Cheng X. (2011)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. The transcriptome of human CD34+ hematopoietic stem-p rogenitor cells. (PubMed id 19416867)1 Kim Y.C....Wang S.M. (2009)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79918 HGNC: 26116 AceView: FLJ21148 Ensembl:ENSG00000103037 euGenes: HUgn79918
    ECgene: SETD6 H-InvDB: SETD6

    (According to HUGE)
    About This Section
      --

    (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
    NameDescription
    PharmGKB entry for SETD6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SETD6 gene:
    Search GeneIP for patents involving SETD6

    GeneCards and IP:
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