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

SETD9 Gene

protein-coding   GIFtS: 39
GCID: GC05P056206

SET Domain Containing 9

(Previous name: chromosome 5 open reading frame 35)
(Previous symbol: C5orf35)
  Search for SETD9
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
SET Domain Containing 91 2
C5orf351 2 3
Chromosome 5 Open Reading Frame 351
SET Domain-Containing Protein 92
EC 2.1.1.-3

External Ids:    HGNC: 285081   Entrez Gene: 1333832   Ensembl: ENSG000001555427   UniProtKB: Q8NE223   

Export aliases for SETD9 gene to outside databases


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

GeneCards Summary for SETD9 Gene: 
SETD9 (SET domain containing 9) is a protein-coding 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NT_006713.15  NC_018916.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SETD9
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SETD9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SETD9


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

Entrez Gene cytogenetic band: 5q11.2   Ensembl cytogenetic band:  5q11.2   HGNC cytogenetic band: 5q11.2

SETD9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SETD9 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P056206:  view genomic region     (about GC identifiers)

Start:
56,205,087 bp from pter      End:
56,221,359 bp from pter
Size:
16,273 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SETD9_HUMAN, Q8NE22 (See protein sequence)
Recommended Name: SET domain-containing protein 9  
Size: 299 amino acids; 34095 Da
Secondary accessions: F5H713
Alternative splicing: 2 isoforms:  Q8NE22-1   Q8NE22-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SETD9: NX_Q8NE22

Explore proteomics data for SETD9 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8NE22

  • SETD9 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SETD9 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001165461.1  NP_714917.2  

    ENSEMBL proteins: 
     ENSP00000285947   ENSP00000398449   ENSP00000406183   ENSP00000442886  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR001214 SET_dom

    Graphical View of Domain Structure for InterPro Entry Q8NE22

    ProtoNet protein and cluster: Q8NE22

    UniProtKB/Swiss-Prot: SETD9_HUMAN, Q8NE22
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 1 SET domain


    SETD9 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Enzyme Number (IUBMB): EC 2.1.1.-1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008168methyltransferase activity IEA--
         
    SETD9 for ontologies           About GeneDecksing


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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SETD9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/6 Interacting proteins for SETD9 (ENSP000002859474) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RORCENSP000003270254STRING: ENSP00000327025
    SIKE1ENSP000003585414STRING: ENSP00000358541
    SNRKENSP000002960884STRING: ENSP00000296088
    TAS1R1ENSP000003318674STRING: ENSP00000331867
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SETD9

    Search CenterWatch for drugs/clinical trials and news about SETD9

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SETD9 gene (2 alternative transcripts): 
    NM_001171990.1  NM_153706.3  

    Unigene Cluster for SETD9:

    SET domain containing 9
    Hs.85950  [show with all ESTs]
    Unigene Representative Sequence: AK093147
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000475908 ENST00000285947(uc003jqx.3) ENST00000498322 ENST00000418299
    ENST00000480414 ENST00000463805 ENST00000472636 ENST00000423328 ENST00000477359
    ENST00000541720(uc021xyu.1)
    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AK093147.1 AK309152.1 BC036528.1 

    5 DOTS entries:

    DT.105460  DT.70103748  DT.99942003  DT.206555  DT.97861281 

    24/45 AceView cDNA sequences (see all 45):

    AK093147 AA621479 AA758553 CR625068 AI989350 BP342016 AF114126 BP336535 
    BG719045 BC036528 NM_153706 BX094293 AA194646 BG721885 AI685269 AI239728 
    BG703195 BX394558 AA404649 BG574944 AA314907 BQ429063 BI093176 AI082667 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for SETD9 (see all 7)    About this scheme

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


    ECgene alternative splicing isoforms for SETD9

    (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

    SETD9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATAAAAGCTA
    SETD9 Expression
    About this image


    See SETD9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SETD9

    SOURCE GeneReport for Unigene cluster: Hs.85950
        SABiosciences Custom PCR Arrays for SETD9
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    In Situ
    Assay Products:
     

     
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    (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 chordates.

    Orthologs for SETD9 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia SETD91 SET domain containing 9 93.31(n)
    92.64(a)
      608050  XM_844651.2  XP_849744.1 
    chicken
    (Gallus gallus)
    Aves SETD91 SET domain containing 9 67.12(n)
    66.33(a)
      770222  XM_001233555.2  XP_001233556.2 
    lizard
    (Anolis carolinensis)
    Reptilia SETD96
    Uncharacterized protein
    67(a)
    1 ↔ 1
    2(1876665-1885644)
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.166432 Transcribed sequences 73.03(n)    BI979940.1 


    ENSEMBL Gene Tree for SETD9 (if available)
    TreeFam Gene Tree for SETD9 (if available)

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

    (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) 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

    10/263 SNPs in SETD9 are shown (see all 263)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1999487951,2
    --56203211(+) ACAAT-/ACTC  
            
    ACACA
    2 -- us2k10--------
    rs1448521101,2
    --56203250(+) CATACA/GCGGGT 2 -- us2k10--------
    rs1841707611,2
    --56203388(+) TACCAC/TGTTTC 2 -- us2k10--------
    rs1479358401,2
    --56203441(+) GATTAA/CAATTA 2 -- us2k10--------
    rs1455250961,2
    C--56203480(+) AGAAA-/AAGAAGGT 2 -- us2k10--------
    rs2014026461,2
    C--56203537(+) AATAT-/AAAAAA 2 -- us2k10--------
    rs560222291,2
    C--56203677(+) CCACTC/TATTAA 2 -- us2k10--------
    rs2529251,2
    C,F,H--56203773(-) AGAGGC/TTTTCT 2 -- us2k121Minor allele frequency- T:0.34NS EA NA CSA WA 2319
    rs1932211051,2
    --56203844(+) TCTTTA/CTTTCT 2 -- us2k10--------
    rs786008151,2
    C,F--56203871(+) TTAGTC/TCCGCA 2 -- us2k11Minor allele frequency- T:0.03NA 120

    HapMap Linkage Disequilibrium report for SETD9 (56205087 - 56221359 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SETD9: --
    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for SETD9

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, 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 SETD9 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SETD9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Uncovering the human methyltransferasome. (PubMed id 20930037)1, 3 Petrossian T.C. and Clarke S.G. (2011)
    2. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    3. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 133383 HGNC: 28508 AceView: MGC33648 Ensembl:ENSG00000155542 euGenes: HUgn133383
    ECgene: SETD9 H-InvDB: SETD9

    (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 SETD9 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 SETD9 gene:
    Search GeneIP for patents involving SETD9

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
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