Human Gene SETDB2 (ENST00000611815.2_3) from GENCODE V47lift37
  Description: SET domain bifurcated histone lysine methyltransferase 2, transcript variant 10 (from RefSeq NR_172062.1)
Gencode Transcript: ENST00000611815.2_3
Gencode Gene: ENSG00000136169.17_9
Transcript (Including UTRs)
   Position: hg19 chr13:50,018,410-50,069,139 Size: 50,730 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr13:50,026,030-50,065,985 Size: 39,956 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:50,018,410-50,069,139)mRNA (may differ from genome)Protein (707 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedReactomeUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SETB2_HUMAN
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SETDB2; EC=2.1.1.43; AltName: Full=Chronic lymphocytic leukemia deletion region gene 8 protein; AltName: Full=Lysine N-methyltransferase 1F; AltName: Full=SET domain bifurcated 2;
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.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBCELLULAR LOCATION: Nucleus. Chromosome (Probable).
TISSUE SPECIFICITY: Ubiquitous. Highest expression in heart, testis and ovary.
SIMILARITY: Belongs to the histone-lysine methyltransferase family.
SIMILARITY: Contains 1 MBD (methyl-CpG-binding) domain.
SIMILARITY: Contains 1 pre-SET domain.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=CAH56265.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=CAI10818.2; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SETDB2
Diseases sorted by gene-association score: chronic lymphocytic leukemia (9)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -338.50925-0.366 Picture PostScript Text
3' UTR -820.803154-0.260 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016177 - DNA-bd_integrase-typ
IPR001739 - Methyl_CpG_DNA-bd
IPR007728 - Pre-SET_dom
IPR001214 - SET_dom

Pfam Domains:
PF00856 - SET domain
PF01429 - Methyl-CpG binding domain
PF05033 - Pre-SET motif

SCOP Domains:
82199 - SET domain
54171 - DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q96T68
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0046872 metal ion binding
GO:0046974 histone methyltransferase activity (H3-K9 specific)

Biological Process:
GO:0000278 mitotic cell cycle
GO:0001947 heart looping
GO:0006325 chromatin organization
GO:0007049 cell cycle
GO:0007059 chromosome segregation
GO:0007275 multicellular organism development
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051301 cell division
GO:0051567 histone H3-K9 methylation
GO:0070986 left/right axis specification

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  JF729359 - Homo sapiens SETDB2-PHF11 fusion protein variant 1 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729360 - Homo sapiens SETDB2-PHF11 fusion protein variant 2 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729361 - Homo sapiens SETDB2-PHF11 fusion protein variant 3 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729362 - Homo sapiens SETDB2-PHF11 fusion protein variant 4 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729363 - Homo sapiens SETDB2-PHF11 fusion protein variant 5 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729364 - Homo sapiens SETDB2-PHF11 fusion protein variant 6 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729365 - Homo sapiens SETDB2-PHF11 fusion protein variant 7 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729366 - Homo sapiens SETDB2-PHF11 fusion protein variant 8 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729367 - Homo sapiens SETDB2-PHF11 fusion protein variant 9 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729368 - Homo sapiens SETDB2-PHF11 fusion protein variant 10 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729369 - Homo sapiens SETDB2-PHF11 fusion protein variant 11 (SETDB2-PHF11 fusion) mRNA, partial cds.
JF729370 - Homo sapiens SETDB2-PHF11 fusion protein variant 12 (SETDB2-PHF11 fusion) mRNA, partial cds.
AK308220 - Homo sapiens cDNA, FLJ98168.
AF334407 - Homo sapiens CLLL8 protein (CLLD8) mRNA, complete cds.
JD203313 - Sequence 184337 from Patent EP1572962.
AK308354 - Homo sapiens cDNA, FLJ98302.
JD348251 - Sequence 329275 from Patent EP1572962.
JD145875 - Sequence 126899 from Patent EP1572962.
JD336191 - Sequence 317215 from Patent EP1572962.
JD152113 - Sequence 133137 from Patent EP1572962.
JD104819 - Sequence 85843 from Patent EP1572962.
AF277186 - Homo sapiens PNAS-128 mRNA, partial sequence.
JD297363 - Sequence 278387 from Patent EP1572962.
JD120217 - Sequence 101241 from Patent EP1572962.
JD114145 - Sequence 95169 from Patent EP1572962.
JD297087 - Sequence 278111 from Patent EP1572962.
JD465566 - Sequence 446590 from Patent EP1572962.
JD466270 - Sequence 447294 from Patent EP1572962.
BC028202 - Homo sapiens cDNA clone IMAGE:5202379.
JD102634 - Sequence 83658 from Patent EP1572962.
JD435784 - Sequence 416808 from Patent EP1572962.
BC047434 - Homo sapiens SET domain, bifurcated 2, mRNA (cDNA clone MGC:48295 IMAGE:5266911), complete cds.
JD251807 - Sequence 232831 from Patent EP1572962.
AK307593 - Homo sapiens cDNA, FLJ97541.
JD546619 - Sequence 527643 from Patent EP1572962.
JD554273 - Sequence 535297 from Patent EP1572962.
CU690416 - Synthetic construct Homo sapiens gateway clone IMAGE:100020961 5' read SETDB2 mRNA.
KJ899724 - Synthetic construct Homo sapiens clone ccsbBroadEn_09118 SETDB2 gene, encodes complete protein.
AB209349 - Homo sapiens mRNA for CLLL8 protein variant protein.
AL831937 - Homo sapiens mRNA; cDNA DKFZp761J1217 (from clone DKFZp761J1217).
BC017078 - Homo sapiens SET domain, bifurcated 2, mRNA (cDNA clone IMAGE:3847827), partial cds.
AK311602 - Homo sapiens cDNA, FLJ18644.
AF086317 - Homo sapiens full length insert cDNA clone ZD53A03.
AL833957 - Homo sapiens mRNA; cDNA DKFZp586I0123 (from clone DKFZp586I0123).
JD091161 - Sequence 72185 from Patent EP1572962.
JD061524 - Sequence 42548 from Patent EP1572962.
JD429356 - Sequence 410380 from Patent EP1572962.
JD552093 - Sequence 533117 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96T68 (Reactome details) participates in the following event(s):

R-HSA-4827382 SUV39H1 (KMT1A), SUV39H2 (KTM1B), SETDB1 (KMT1E), SETDB2 (KMT1F) methylate dimethyl-lysine-10 of histone H3 (H3K9)
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: C13orf4, CLLD8, ENST00000611815.1, KMT1F, NR_172062, Q5TC65, Q5TC66, Q5W0A7, Q659A7, Q86UD6, Q96AI6, Q96T68, SETB2_HUMAN, uc327nos.1, uc327nos.2
UCSC ID: ENST00000611815.2_3
RefSeq Accession: NM_001160308.3
Protein: Q96T68 (aka SETB2_HUMAN or SEB2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.