Human Gene SUV39H2 (uc021png.1)
  Description: Homo sapiens suppressor of variegation 3-9 homolog 2 (Drosophila) (SUV39H2), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr10:14,920,782-14,946,304 Size: 25,523 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr10:14,920,888-14,944,511 Size: 23,624 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:14,920,782-14,946,304)mRNA (may differ from genome)Protein (410 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SUV92_HUMAN
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SUV39H2; EC=2.1.1.43; 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.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SUV39H2
CDC HuGE Published Literature: SUV39H2

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

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

-  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 -45.40106-0.428 Picture PostScript Text
3' UTR -485.861793-0.271 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
PF00856 - SET domain
PF05033 - Pre-SET motif

SCOP Domains:
54160 - Chromo domain-like
82199 - SET domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2R3A - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9H5I1
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 orthologGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
   FlyBase  
   Protein Sequence  
   Alignment  

-  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.
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).
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.
JD037241 - Sequence 18265 from Patent EP1572962.
JD184920 - Sequence 165944 from Patent EP1572962.
JD436635 - Sequence 417659 from Patent EP1572962.
JD355846 - Sequence 336870 from Patent EP1572962.
JD380645 - Sequence 361669 from Patent EP1572962.
JD172352 - Sequence 153376 from Patent EP1572962.
JD490817 - Sequence 471841 from Patent EP1572962.
JD524103 - Sequence 505127 from Patent EP1572962.
JD502548 - Sequence 483572 from Patent EP1572962.
JD082037 - Sequence 63061 from Patent EP1572962.
JD287519 - Sequence 268543 from Patent EP1572962.
JD107353 - Sequence 88377 from Patent EP1572962.
JD533630 - Sequence 514654 from Patent EP1572962.
JD499659 - Sequence 480683 from Patent EP1572962.
JD286713 - Sequence 267737 from Patent EP1572962.
JD511545 - Sequence 492569 from Patent EP1572962.
JD319540 - Sequence 300564 from Patent EP1572962.
JD071050 - Sequence 52074 from Patent EP1572962.
JD159171 - Sequence 140195 from Patent EP1572962.
JD533059 - Sequence 514083 from Patent EP1572962.
JD533058 - Sequence 514082 from Patent EP1572962.
JD430699 - Sequence 411723 from Patent EP1572962.
JD557824 - Sequence 538848 from Patent EP1572962.
JD446995 - Sequence 428019 from Patent EP1572962.
JD177456 - Sequence 158480 from Patent EP1572962.
JD334171 - Sequence 315195 from Patent EP1572962.
JD096358 - Sequence 77382 from Patent EP1572962.
JD308816 - Sequence 289840 from Patent EP1572962.
JD331970 - Sequence 312994 from Patent EP1572962.
JD447603 - Sequence 428627 from Patent EP1572962.
JD084883 - Sequence 65907 from Patent EP1572962.
JD239508 - Sequence 220532 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_001193424, NP_078946, Q5JSS4, Q5JSS5, Q6I9Y3, Q8ND06, Q9H5I1, SUV92_HUMAN
UCSC ID: uc021png.1
RefSeq Accession: NM_001193424
Protein: Q9H5I1 (aka SUV92_HUMAN or SU92_HUMAN)
CCDS: CCDS53494.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001193424.1
exon count: 6CDS single in 3' UTR: no RNA size: 3148
ORF size: 1233CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2658.00frame shift in genome: no % Coverage: 99.49
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.