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Aliases for SETDB2 Gene

Aliases for SETDB2 Gene

  • SET Domain Bifurcated 2 2 3 4
  • Chronic Lymphocytic Leukemia Deletion Region Gene 8 Protein 3 4
  • Lysine N-Methyltransferase 1F 3 4
  • SET Domain, Bifurcated 2 2 5
  • C13orf4 3 4
  • CLLD8 3 4
  • KMT1F 3 4
  • Chromosome 13 Open Reading Frame 4 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 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. 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 EHMT1.

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.

No data available for 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around SETDB2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SETDB2 Gene

Chromosome:
13
Start:
49,444,056 bp from pter
End:
49,495,003 bp from pter
Size:
50,948 bases
Orientation:
Plus strand

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

Proteomics data for SETDB2 Gene at MOPED

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

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.
  • Contains 1 MBD (methyl-CpG-binding) domain.
  • Contains 1 pre-SET domain.
  • Contains 1 SET domain.
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

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

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , 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
Jensen Localization Image for SETDB2 Gene COMPARTMENTS Subcellular localization image for SETDB2 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 2
mitochondrion 1

No data available for Gene Ontology (GO) - Cellular Components for SETDB2 Gene

Pathways & Interactions for SETDB2 Gene

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

Pathways by source 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:0007059 chromosome segregation IMP 20404330
GO:0045892 negative regulation of transcription, DNA-templated ISS --
GO:0051301 cell division IEA --
GO:0051567 histone H3-K9 methylation IDA 20404330
GO:0070986 left/right axis specification ISS --
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

(2) Drugs for SETDB2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 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:

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 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



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.
genes like me logo Genes that share expression patterns with SETDB2: view

Protein tissue co-expression partners for SETDB2 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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
cow
(Bos Taurus)
Mammalia SETDB2 35
  • 87.29 (n)
  • 79.43 (a)
SETDB2 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETDB2 35
  • 87.59 (n)
  • 81.39 (a)
SETDB2 36
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setdb2 35
  • 78.95 (n)
  • 68.22 (a)
Setdb2 16
Setdb2 36
  • 67 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SETDB2 35
  • 99.63 (n)
  • 99.58 (a)
SETDB2 36
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SETDB2 36
  • 54 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETDB2 36
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETDB2 35
  • 59.64 (n)
  • 50 (a)
SETDB2 36
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETDB2 36
  • 43 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia setdb2 35
  • 56.91 (n)
  • 46.79 (a)
African clawed frog
(Xenopus laevis)
Amphibia LOC398711 35
zebrafish
(Danio rerio)
Actinopterygii SETDB2 36
  • 29 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Set2 36
  • 4 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea met-2 36
  • 12 (a)
ManyToMany
set-11 36
  • 24 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 36
  • 9 (a)
OneToMany
Species with no ortholog for SETDB2:
  • 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

(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
rs2057413 - 49,482,961(+) TTACT(A/G)TGTAA nc-transcript-variant, reference, missense
rs7998427 - 49,476,484(+) AACAG(A/G)AAATA nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs1812 -- 49,489,375(-) GATAG(C/T)CATTA intron-variant
rs721457 -- 49,461,015(+) AATGA(C/G)ATAAA intron-variant
rs721458 -- 49,460,912(+) TAGCT(A/G)AATGT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv523648 CNV Gain 19592680
nsv900070 CNV Loss 21882294
esv2747394 CNV Deletion 23290073
esv3404 CNV Deletion 18987735
esv2747395 CNV Deletion 23290073
esv272759 CNV Insertion 20981092
esv267803 CNV Insertion 20981092

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

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: DISEASES and GeneCards

Disorder Aliases PubMed IDs
chronic lymphocytic leukemia
  • cll
- 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 C.M. (Cancer Res. 2001) 2 3 4 67
  2. A functional AT/G polymorphism in the 5'-untranslated region of SETDB2 in the IgE locus on human chromosome 13q14. (PMID: 26378653) Holt R.J. … Zhang Y. (Genes Immun. 2015) 3
  3. Left-Right Axis Differentiation and Functional Lateralization: a Haplotype in the Methyltransferase Encoding Gene SETDB2 Might Mediate Handedness in Healthy Adults. (PMID: 26572639) Ocklenburg S. … Akkad D.A. (Mol. Neurobiol. 2015) 3
  4. Type I Interferon Induced Epigenetic Regulation of Macrophages Suppresses Innate and Adaptive Immunity in Acute Respiratory Viral Infection. (PMID: 26709698) Kroetz D.N. … Kunkel S.L. (PLoS Pathog. 2015) 3
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3

Products for SETDB2 Gene

Sources for SETDB2 Gene

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