Human Gene SUV39H2 (ENST00000378325.7) Description and Page Index
  Description: Homo sapiens suppressor of variegation 3-9 homolog 2 (SUV39H2), transcript variant 4, mRNA. (from RefSeq NM_001193426)
Gencode Transcript: ENST00000378325.7
Gencode Gene: ENSG00000152455.16
Transcript (Including UTRs)
   Position: hg38 chr10:14,878,863-14,903,085 Size: 24,223 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr10:14,878,889-14,902,512 Size: 23,624 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:14,878,863-14,903,085)mRNA (may differ from genome)Protein (230 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SUV39H2; EC=; AltName: Full=Histone H3-K9 methyltransferase 2; Short=H3-K9-HMTase 2; AltName: Full=Lysine N-methyltransferase 1B; AltName: Full=Suppressor of variegation 3-9 homolog 2; Short=Su(var)3-9 homolog 2;
FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3 using monomethylated H3 'Lys- 9' as substrate. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. H3 'Lys-9' trimethylation is also required to direct DNA methylation at pericentric repeats. SUV39H1 is targeted to histone H3 via its interaction with RB1 and is involved in many processes, such as cell cycle regulation, transcriptional repression and regulation of telomere length. May participate in regulation of higher-order chromatin organization during spermatogenesis.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBUNIT: Interacts with SMAD5.
INTERACTION: P16333:NCK1; NbExp=2; IntAct=EBI-723127, EBI-389883;
SUBCELLULAR LOCATION: Nucleus (By similarity). Chromosome, centromere (By similarity). Note=Associates with centromeric constitutive heterochromatin (By similarity).
DOMAIN: Although the SET domain contains the active site of enzymatic activity, both pre-SET and post-SET domains are required for methyltransferase activity. The SET domain also participates to stable binding to heterochromatin (By similarity).
SIMILARITY: Belongs to the histone-lysine methyltransferase family. Suvar3-9 subfamily.
SIMILARITY: Contains 1 chromo domain.
SIMILARITY: Contains 1 post-SET domain.
SIMILARITY: Contains 1 pre-SET domain.
SIMILARITY: Contains 1 SET domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.64 RPKM in Testis
Total median expression: 74.66 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  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 -2.3026-0.088 Picture PostScript Text
3' UTR -118.80573-0.207 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
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS
IPR011381 - Histone_H3-K9_MeTrfase
IPR003616 - Post-SET_dom
IPR007728 - Pre-SET_dom
IPR001214 - SET_dom

Pfam Domains:
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF05033 - Pre-SET motif
PF00856 - SET domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9H5I1
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific 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)
GO:1904047 S-adenosyl-L-methionine binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006333 chromatin assembly or disassembly
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007049 cell cycle
GO:0030154 cell differentiation
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0036123 histone H3-K9 dimethylation
GO:0036124 histone H3-K9 trimethylation
GO:0042754 negative regulation of circadian rhythm
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048511 rhythmic process
GO:0071456 cellular response to hypoxia

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome

-  Descriptions from all associated GenBank mRNAs
  BC029360 - Homo sapiens suppressor of variegation 3-9 homolog 2 (Drosophila), mRNA (cDNA clone MGC:32534 IMAGE:4079431), complete cds.
AK222565 - Homo sapiens mRNA, Histone-lysine N-methyltransferase, H3 lysine-9 specific 2 variant, clone: CAE05215.
AK225369 - Homo sapiens mRNA for Histone-lysine N-methyltransferase, H3 lysine-9 specific 2 variant, clone: HEP20704.
AK027067 - Homo sapiens cDNA: FLJ23414 fis, clone HEP20704.
CU688630 - Synthetic construct Homo sapiens gateway clone IMAGE:100022165 5' read SUV39H2 mRNA.
KJ894721 - Synthetic construct Homo sapiens clone ccsbBroadEn_04115 SUV39H2 gene, encodes complete protein.
BC007754 - Homo sapiens suppressor of variegation 3-9 homolog 2 (Drosophila), mRNA (cDNA clone MGC:13305 IMAGE:4109807), complete cds.
JD127973 - Sequence 108997 from Patent EP1572962.
DQ572247 - Homo sapiens piRNA piR-40359, complete sequence.
CU675795 - Synthetic construct Homo sapiens gateway clone IMAGE:100019054 5' read SUV39H2 mRNA.
CR457372 - Homo sapiens full open reading frame cDNA clone RZPDo834C0214D for gene SUV39H2, suppressor of variegation 3-9 homolog 2 (Drosophila); complete cds, incl. stopcodon.
AB528357 - Synthetic construct DNA, clone: pF1KE1041, Homo sapiens SUV39H2 gene for suppressor of variegation 3-9 homolog 2, without stop codon, in Flexi system.
DQ896015 - Synthetic construct Homo sapiens clone IMAGE:100010475; FLH189506.01L; RZPDo839F1264D suppressor of variegation 3-9 homolog 2 (Drosophila) (SUV39H2) gene, encodes complete protein.
EU176399 - Synthetic construct Homo sapiens clone IMAGE:100006484; FLH189513.01X; RZPDo839D03252D suppressor of variegation 3-9 homolog 2 (Drosophila) (SUV39H2) gene, encodes complete protein.
KJ894720 - Synthetic construct Homo sapiens clone ccsbBroadEn_04114 SUV39H2 gene, encodes complete protein.
AL834488 - Homo sapiens mRNA; cDNA DKFZp434E1831 (from clone DKFZp434E1831).
JD037241 - Sequence 18265 from Patent EP1572962.
JD184920 - Sequence 165944 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00310 - Lysine degradation

Reactome (by CSHL, EBI, and GO)

Protein Q9H5I1 (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: D3DRT4, KMT1B, NM_001193426, Q5JSS4, Q5JSS5, Q6I9Y3, Q8ND06, Q9H5I1, SUV92_HUMAN, uc001ing.1, uc001ing.2, uc001ing.3, uc001ing.4
UCSC ID: uc001ing.4
RefSeq Accession: NM_001193426
Protein: Q9H5I1 (aka SUV92_HUMAN or SU92_HUMAN)
CCDS: CCDS53493.1

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