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Aliases for SETDB2 Gene

Aliases for SETDB2 Gene

  • SET Domain, Bifurcated 2 2 3
  • CLLD8 3 4 6
  • Chronic Lymphocytic Leukemia Deletion Region Gene 8 Protein 3 4
  • Lysine N-Methyltransferase 1F 3 4
  • C13orf4 3 4
  • KMT1F 3 4
  • Chronic Lymphocytic Leukemia Deletion Region 8 3
  • Histone-Lysine N-Methyltransferase SETDB2 3
  • Chromosome 13 Open Reading Frame 4 2
  • SET Domain Bifurcated 2 4
  • EC 2.1.1.43 4
  • CLLL8 3

External Ids for SETDB2 Gene

Previous Symbols for SETDB2 Gene

  • C13orf4

Summaries for SETDB2 Gene

Entrez Gene Summary for SETDB2 Gene

  • Proteins that contain a SET domain, such as SETDB2, modulate gene expression epigenetically through histone H3 (see MIM 601128) methylation. SETDB2 is likely a histone H3 methyltransferase, as it contains both the active site and flanking cysteine residues required for catalytic activity (Zhang et al., 2003 [PubMed 12754510]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SETDB2 Gene

SETDB2 (SET Domain, Bifurcated 2) is a Protein Coding gene. Diseases associated with SETDB2 include chronic lymphocytic leukemia and leukemia. Among its related pathways are Lysine degradation. GO annotations related to this gene include 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

Genomic Location for SETDB2 Gene

Start:
49,444,166 bp from pter
End:
49,495,003 bp from pter
Size:
50,838 bases
Orientation:
Plus strand

Genomic View for SETDB2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SETDB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETDB2 Gene

Regulatory Elements 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 for SETDB2 Gene

Gene Families for SETDB2 Gene

HGNC:
  • KMT :Chromatin-modifying enzymes / K-methyltransferases

Protein Domains for SETDB2 Gene

UniProtKB/Swiss-Prot:

SETB2_HUMAN
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.:
    • Q96T68
  • Contains 1 MBD (methyl-CpG-binding) domain.:
    • Q96T68
  • Contains 1 pre-SET domain.:
    • Q96T68
  • Contains 1 SET domain.:
    • Q96T68
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.:
    • Q96T68
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:0008270 zinc ion binding IEA --
GO:0018024 histone-lysine N-methyltransferase activity --
GO:0046974 histone methyltransferase activity (H3-K9 specific) IDA 20404330
genes like me logo Genes that share ontologies with SETDB2: view

No data available for Phenotypes , Animal Models , miRNA , Transcription Factor Targeting 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
plasma membrane 3
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SETDB2 Gene

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

Pathways for SETDB2 Gene

SuperPathways for SETDB2 Gene

Superpath Contained pathways
1 Lysine degradation
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:0001947 heart looping ISS --
GO:0006325 chromatin organization TAS --
GO:0007059 chromosome segregation IMP 20404330
GO:0007067 mitotic nuclear division IMP 20404330
GO:0034968 histone lysine methylation --
genes like me logo Genes that share ontologies with SETDB2: view

Compounds for SETDB2 Gene

(2) HMDB Compounds for SETDB2 Gene

Compound Synonyms Cas Number PubMed IDs
S-Adenosylhomocysteine
  • (S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine
979-92-0
S-Adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
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:

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with SETDB2: view

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 36
  • 99.63 (n)
  • 99.58 (a)
SETDB2 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SETDB2 36
  • 87.29 (n)
  • 79.43 (a)
SETDB2 37
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETDB2 36
  • 87.59 (n)
  • 81.39 (a)
SETDB2 37
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setdb2 36
  • 78.95 (n)
  • 68.22 (a)
Setdb2 16
Setdb2 37
  • 67 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SETDB2 37
  • 54 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETDB2 37
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETDB2 36
  • 59.64 (n)
  • 50 (a)
SETDB2 37
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETDB2 37
  • 43 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC398711 36
tropical clawed frog
(Silurana tropicalis)
Amphibia setdb2 36
  • 56.91 (n)
  • 46.79 (a)
zebrafish
(Danio rerio)
Actinopterygii SETDB2 37
  • 29 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Set2 37
  • 4 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea met-2 37
  • 12 (a)
ManyToMany
set-11 37
  • 24 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 37
  • 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

Selected 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 MAF
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
rs728445 -- 49,480,790(+) TACAG(C/T)TAGTA intron-variant
rs959421 -- 49,488,191(-) TTATC(A/G)ATCCT 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

Relevant External Links for SETDB2 Gene

HapMap Linkage Disequilibrium report
SETDB2
Human Gene Mutation Database (HGMD)
SETDB2

Disorders for SETDB2 Gene

Relevant External Links for SETDB2

Genetic Association Database (GAD)
SETDB2
Human Genome Epidemiology (HuGE) Navigator
SETDB2
genes like me logo Genes that share disorders with SETDB2: view

No data available for UniProtKB/Swiss-Prot 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
  2. 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. … Moffatt M.F. (Clin. Exp. Allergy 2009) 3 49
  3. CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation. (PMID: 20404330) Falandry C. … Magdinier F. (J. Biol. Chem. 2010) 3 4
  4. Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. (PMID: 12754510) Zhang Y. … Cookson W.O.C.M. (Nat. Genet. 2003) 3 4
  5. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A. … Ross M.T. (Nature 2004) 3 4

Products for SETDB2 Gene

Sources for SETDB2 Gene

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