Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SETD9 Gene

Aliases for SETD9 Gene

  • SET Domain Containing 9 2 3 5
  • C5orf35 3 4
  • Chromosome 5 Open Reading Frame 35 2
  • SET Domain-Containing Protein 9 3
  • EC 2.1.1.- 4

External Ids for SETD9 Gene

Previous HGNC Symbols for SETD9 Gene

  • C5orf35

Previous GeneCards Identifiers for SETD9 Gene

  • GC05P056206

Summaries for SETD9 Gene

GeneCards Summary for SETD9 Gene

SETD9 (SET Domain Containing 9) is a Protein Coding gene. Among its related pathways are Gene Expression and Regulation of TP53 Activity. Gene Ontology (GO) annotations related to this gene include methyltransferase activity.

Additional gene information for SETD9 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETD9 Gene

Genomics for SETD9 Gene

GeneHancer (GH) Regulatory Elements for SETD9 Gene

Promoters and enhancers for SETD9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I056908 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 620.4 +0.4 399 3.3 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SETD9 LOC105378980 ENSG00000271828 MIER3
GH05I056950 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 74.1 +42.3 42328 2.8 SIN3A FEZF1 YY1 GLIS2 SP5 MXD4 GMEB1 SMARCA4 GLIS1 NR2C1 MIER3 SETD9 LOC105378980 ENSG00000235635
GH05I056814 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 44.3 -92.5 -92500 6.3 HDGF PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 MAP3K1 SETD9 ENSG00000271828 MIER3 C5orf67 GC05P056846 GC05P056845
GH05I056836 Enhancer 1.2 Ensembl ENCODE dbSUPER 43.9 -71.2 -71158 3 MEIS2 CTCF PKNOX1 RAD21 CC2D1A GATA3 ZNF316 ARID2 ZNF143 SMC3 SETD9 MAP3K1 ENSG00000237705 LINC01948 RNU6ATAC2P GC05P056846 GC05P056845
GH05I056848 Enhancer 1 Ensembl ENCODE dbSUPER 52.4 -58.3 -58311 4.3 FOSL1 RXRA BCL6B CEBPA CEBPB CEBPG HNF4A KDM1A ZNF644 SETD9 MAP3K1 LOC105378980 LINC01948 ENSG00000235635 MIER3 C5orf67 GC05P056846 GC05P056845 ENSG00000237705
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SETD9 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SETD9 Gene

Genomic Locations for SETD9 Gene
16,274 bases
Plus strand

Genomic View for SETD9 Gene

Genes around SETD9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD9 Gene

Proteins for SETD9 Gene

  • Protein details for SETD9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    SET domain-containing protein 9
    Protein Accession:
    Secondary Accessions:
    • F5H713

    Protein attributes for SETD9 Gene

    299 amino acids
    Molecular mass:
    34095 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SETD9 Gene


neXtProt entry for SETD9 Gene

Post-translational modifications for SETD9 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SETD9 Gene

Domains & Families for SETD9 Gene

Gene Families for SETD9 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SETD9 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SETD9: view

No data available for Suggested Antigen Peptide Sequences for SETD9 Gene

Function for SETD9 Gene

Enzyme Numbers (IUBMB) for SETD9 Gene

Phenotypes From GWAS Catalog for SETD9 Gene

Gene Ontology (GO) - Molecular Function for SETD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0016278 lysine N-methyltransferase activity TAS --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SETD9: view
genes like me logo Genes that share phenotypes with SETD9: view

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SETD9 Gene

Localization for SETD9 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETD9 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SETD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with SETD9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SETD9 Gene

Pathways & Interactions for SETD9 Gene

genes like me logo Genes that share pathways with SETD9: view

Pathways by source for SETD9 Gene

Interacting Proteins for SETD9 Gene

Gene Ontology (GO) - Biological Process for SETD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032259 methylation IEA --
GO:1901796 regulation of signal transduction by p53 class mediator TAS --
genes like me logo Genes that share ontologies with SETD9: view

No data available for SIGNOR curated interactions for SETD9 Gene

Drugs & Compounds for SETD9 Gene

No Compound Related Data Available

Transcripts for SETD9 Gene

Unigene Clusters for SETD9 Gene

SET domain containing 9:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETD9 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b
SP1: - - - -
SP2: - - - - - -
SP3: - - - - - - -
SP4: - - - - -
SP5: - - - -
SP6: - - -

Relevant External Links for SETD9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SETD9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SETD9 Gene

mRNA differential expression in normal tissues according to GTEx for SETD9 Gene

This gene is overexpressed in Testis (x5.8).

Protein differential expression in normal tissues from HIPED for SETD9 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SETD9 Gene

Protein tissue co-expression partners for SETD9 Gene

NURSA nuclear receptor signaling pathways regulating expression of SETD9 Gene:


SOURCE GeneReport for Unigene cluster for SETD9 Gene:

genes like me logo Genes that share expression patterns with SETD9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD9 Gene

Orthologs for SETD9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SETD9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SETD9 33 34
  • 99.89 (n)
(Canis familiaris)
Mammalia SETD9 33 34
  • 93.31 (n)
(Bos Taurus)
Mammalia SETD9 33 34
  • 92.87 (n)
(Ornithorhynchus anatinus)
Mammalia SETD9 34
  • 72 (a)
(Monodelphis domestica)
Mammalia SETD9 34
  • 67 (a)
(Gallus gallus)
Aves CZH5ORF35 33
  • 67.12 (n)
SETD9 34
  • 66 (a)
(Anolis carolinensis)
Reptilia SETD9 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia setd9 33
  • 65.86 (n)
(Danio rerio)
Actinopterygii SETD9 34
  • 60 (a)
LOC793111 33
  • 59.64 (n)
Dr.16643 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7120 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
Species where no ortholog for SETD9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SETD9 Gene

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

Paralogs for SETD9 Gene

No data available for Paralogs for SETD9 Gene

Variants for SETD9 Gene

Sequence variations from dbSNP and Humsavar for SETD9 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000029254 -- 56,924,297(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000045817 -- 56,907,534(+) T/G upstream_transcript_variant
rs1000505377 -- 56,907,566(+) C/T upstream_transcript_variant
rs1000682167 -- 56,913,405(+) A/G intron_variant
rs1000704966 -- 56,927,202(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SETD9 Gene

Variant ID Type Subtype PubMed ID
nsv598210 CNV loss 21841781

Variation tolerance for SETD9 Gene

Residual Variation Intolerance Score: 35.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.04; 96.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD9 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD9 Gene

Disorders for SETD9 Gene

Additional Disease Information for SETD9

No disorders were found for SETD9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SETD9 Gene

Publications for SETD9 Gene

  1. Uncovering the human methyltransferasome. (PMID: 20930037) Petrossian TC … Clarke SG (Molecular & cellular proteomics : MCP 2011) 2 3 58
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers. (PMID: 28029147) Puzone R … Pfeffer U (European journal of human genetics : EJHG 2017) 3 58
  4. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A … Stelzl U (Molecular systems biology 2015) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for SETD9 Gene

Sources for SETD9 Gene

Loading form....