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Aliases for SETDB2 Gene

Aliases for SETDB2 Gene

  • SET Domain Bifurcated 2 2 3 4 5
  • Chronic Lymphocytic Leukemia Deletion Region Gene 8 Protein 3 4
  • Lysine N-Methyltransferase 1F 3 4
  • C13orf4 3 4
  • CLLD8 3 4
  • KMT1F 3 4
  • Histone-Lysine N-Methyltransferase SETDB2 3
  • Chromosome 13 Open Reading Frame 4 2
  • SET Domain, Bifurcated 2 2
  • EC 2.1.1.43 4
  • CLLL8 3

External Ids for SETDB2 Gene

Previous HGNC Symbols for SETDB2 Gene

  • C13orf4

Previous GeneCards Identifiers for SETDB2 Gene

  • GC13P048954
  • GC13P047816
  • GC13P048916
  • GC13P050018
  • GC13P030812

Summaries for SETDB2 Gene

Entrez Gene Summary for SETDB2 Gene

  • This gene encodes a member of a family of proteins that contain a methyl-CpG-binding domain (MBD) and a SET domain and function as histone methyltransferases. This protein is recruited to heterochromatin and plays a role in the regulation of chromosome segregation. This region is commonly deleted in chronic lymphocytic leukemia. Naturally-occuring readthrough transcription occurs from this gene to the downstream PHF11 (PHD finger protein 11) gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

GeneCards Summary for SETDB2 Gene

SETDB2 (SET Domain Bifurcated 2) is a Protein Coding gene. Diseases associated with SETDB2 include Chronic Lymphocytic Leukemia. Among its related pathways are Chromatin organization and Lysine degradation. GO annotations related to this gene include histone-lysine N-methyltransferase activity and histone methyltransferase activity (H3-K9 specific). An important paralog of this gene is SETDB1.

UniProtKB/Swiss-Prot for SETDB2 Gene

  • 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.

Additional gene information for SETDB2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETDB2 Gene

Genomics for SETDB2 Gene

Regulatory Elements for SETDB2 Gene

Enhancers for SETDB2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13H050121 2 FANTOM5 Ensembl ENCODE dbSUPER 51.3 +682.7 682701 10.1 PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ZNF766 ZNF143 SETDB2 KCNRG TRIM13 CTAGE10P DLEU1 RNASEH2B-AS1 ENSG00000176882 RNASEH2B EBPL DLEU2
GH13H049494 1.5 Ensembl ENCODE dbSUPER 27.9 +53.6 53638 6.6 HDGF PKNOX1 FOXA2 ARID4B DMAP1 GLI4 ZNF2 YY1 GLIS2 ZNF143 SETDB2 PHF11 TRIM13 KCNRG EBPL ARL11 RCBTB1
GH13H049292 0.9 Ensembl ENCODE 29.1 -151.2 -151189 1 ZSCAN18 NFIA NFIB ZNF195 ZNF16 ZNF662 ZIC2 NFIC LCORL ZNF544 SETDB2 TRIM13 CDADC1 CAB39L GC13P049296 GC13M049248
GH13H050207 1.5 FANTOM5 Ensembl ENCODE 15 +765.0 764965 2.2 PKNOX1 ARNT GLI4 GLIS2 ATF7 SMARCA4 GLIS1 NBN HMBOX1 SP7 SETDB2 RPL34P26 RNASEH2B TRIM13 DLEU7 EBPL GC13P050221 GC13P050185
GH13H049442 1.6 Ensembl ENCODE dbSUPER 12.9 +1.6 1571 5.5 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 PHF11 SETDB2 CAB39L ARL11 EBPL SNRPGP14
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SETDB2 on UCSC Golden Path with GeneCards custom track

Promoters for SETDB2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000062735 344 2801 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766

Genomic Locations for SETDB2 Gene

Genomic Locations for SETDB2 Gene
chr13:49,444,056-49,495,003
(GRCh38/hg38)
Size:
50,948 bases
Orientation:
Plus strand
chr13:50,018,429-50,069,139
(GRCh37/hg19)

Genomic View for SETDB2 Gene

Genes around SETDB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETDB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETDB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETDB2 Gene

Proteins for SETDB2 Gene

  • Protein details for SETDB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96T68-SETB2_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETDB2
    Protein Accession:
    Q96T68
    Secondary Accessions:
    • Q5TC65
    • Q5TC66
    • Q5W0A7
    • Q659A7
    • Q86UD6
    • Q96AI6

    Protein attributes for SETDB2 Gene

    Size:
    719 amino acids
    Molecular mass:
    81894 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAH56265.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=CAI10818.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for SETDB2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETDB2 Gene

Post-translational modifications for SETDB2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SETDB2 Gene

No data available for DME Specific Peptides for SETDB2 Gene

Domains & Families for SETDB2 Gene

Gene Families for SETDB2 Gene

Protein Domains for SETDB2 Gene

Suggested Antigen Peptide Sequences for SETDB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96T68

UniProtKB/Swiss-Prot:

SETB2_HUMAN :
  • In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Domain:
  • In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SETDB2: view

Function for SETDB2 Gene

Molecular function for SETDB2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for SETDB2 Gene

Gene Ontology (GO) - Molecular Function for SETDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SETDB2: view
genes like me logo Genes that share phenotypes with SETDB2: view

Animal Models for SETDB2 Gene

MGI Knock Outs for SETDB2:

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETDB2 Gene

Localization for SETDB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETDB2 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
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 SETDB2 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SETDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 20404330
GO:0005654 nucleoplasm TAS,IDA --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with SETDB2: view

Pathways & Interactions for SETDB2 Gene

genes like me logo Genes that share pathways with SETDB2: view

Pathways by source for SETDB2 Gene

1 BioSystems pathway for SETDB2 Gene
1 KEGG pathway for SETDB2 Gene

Gene Ontology (GO) - Biological Process for SETDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IMP 20404330
GO:0001947 heart looping ISS --
GO:0007049 cell cycle IEA --
GO:0007059 chromosome segregation IMP 20404330
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with SETDB2: view

No data available for SIGNOR curated interactions for SETDB2 Gene

Drugs & Compounds for SETDB2 Gene

(1) Drugs for SETDB2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for SETDB2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
genes like me logo Genes that share compounds with SETDB2: view

Transcripts for SETDB2 Gene

Unigene Clusters for SETDB2 Gene

SET domain, bifurcated 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETDB2 Gene

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: -
SP6:
SP7: - - - -
SP8: - -
SP9:

ExUns: 17a · 17b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SETDB2 Gene

GeneLoc Exon Structure for
SETDB2
ECgene alternative splicing isoforms for
SETDB2

Expression for SETDB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SETDB2 Gene

Protein differential expression in normal tissues from HIPED for SETDB2 Gene

This gene is overexpressed in CD4 Tcells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SETDB2 Gene



Protein tissue co-expression partners for SETDB2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SETDB2 Gene:

SETDB2

SOURCE GeneReport for Unigene cluster for SETDB2 Gene:

Hs.631789

mRNA Expression by UniProt/SwissProt for SETDB2 Gene:

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

Evidence on tissue expression from TISSUES for SETDB2 Gene

  • Intestine(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with SETDB2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETDB2 Gene

Orthologs for SETDB2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETDB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SETDB2 33 34
  • 99.63 (n)
dog
(Canis familiaris)
Mammalia SETDB2 33 34
  • 87.59 (n)
cow
(Bos Taurus)
Mammalia SETDB2 33 34
  • 87.29 (n)
mouse
(Mus musculus)
Mammalia Setdb2 33 16 34
  • 78.95 (n)
oppossum
(Monodelphis domestica)
Mammalia SETDB2 34
  • 54 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETDB2 34
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETDB2 33 34
  • 59.64 (n)
lizard
(Anolis carolinensis)
Reptilia SETDB2 34
  • 43 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia setdb2 33
  • 56.91 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398711 33
zebrafish
(Danio rerio)
Actinopterygii SETDB2 34
  • 29 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Set2 34
  • 4 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea set-11 34
  • 24 (a)
ManyToMany
met-2 34
  • 12 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 34
  • 9 (a)
OneToMany
Species where no ortholog for SETDB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for SETDB2 Gene

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

Paralogs for SETDB2 Gene

Paralogs for SETDB2 Gene

(2) SIMAP similar genes for SETDB2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SETDB2: view

Variants for SETDB2 Gene

Sequence variations from dbSNP and Humsavar for SETDB2 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs1000008576 -- 49,482,315(+) AACAC(C/T)AAGAA intron-variant
rs1000119436 -- 49,454,763(+) GTATC(A/G)TACAC intron-variant
rs1000365556 -- 49,467,766(+) ATCCA(C/T)ATGGG intron-variant
rs1000383891 -- 49,493,224(+) GTTGA(A/G)AAATC intron-variant, utr-variant-3-prime
rs1000418113 -- 49,447,897(+) CAGTT(A/T)GTATA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SETDB2 Gene

Variant ID Type Subtype PubMed ID
nsv561613 CNV loss 21841781
nsv523648 CNV gain 19592680
esv3632048 CNV loss 21293372
esv3404 CNV loss 18987735
esv3374012 CNV insertion 20981092
esv3360364 CNV insertion 20981092
esv2747395 CNV deletion 23290073
esv2747394 CNV deletion 23290073
dgv3139n54 CNV loss 21841781

Variation tolerance for SETDB2 Gene

Residual Variation Intolerance Score: 32.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.70; 46.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SETDB2 Gene

Human Gene Mutation Database (HGMD)
SETDB2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETDB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETDB2 Gene

Disorders for SETDB2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SETDB2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
chronic lymphocytic leukemia
  • b-cell chronic lymphocytic leukemia
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SETDB2

Genetic Association Database (GAD)
SETDB2
Human Genome Epidemiology (HuGE) Navigator
SETDB2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SETDB2
genes like me logo Genes that share disorders with SETDB2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SETDB2 Gene

Publications for SETDB2 Gene

  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. (PMID: 11306461) Mabuchi H … Croce CM (Cancer research 2001) 2 3 4 60
  2. CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation. (PMID: 20404330) Falandry C … Magdinier F (The Journal of biological chemistry 2010) 3 4 60
  3. A multi-centre study of candidate genes for wheeze and allergy: the International Study of Asthma and Allergies in Childhood Phase 2. (PMID: 20085599) Genuneit J … ISAAC Phase 2 Study Group (Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2009) 3 45 60
  4. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 3 4 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for SETDB2 Gene

Sources for SETDB2 Gene

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