Human Gene KMT5C (ENST00000255613.8) from GENCODE V44
  Description: Homo sapiens lysine methyltransferase 5C (KMT5C), mRNA. (from RefSeq NM_032701)
RefSeq Summary (NM_032701): SUV420H2 and the related enzyme SUV420H1 (MIM 610881) function as histone methyltransferases that specifically trimethylate nucleosomal histone H4 (see MIM 602822) on lysine-20 (K20) (Schotta et al., 2004 [PubMed 15145825]).[supplied by OMIM, Dec 2009].
Gencode Transcript: ENST00000255613.8
Gencode Gene: ENSG00000133247.14
Transcript (Including UTRs)
   Position: hg38 chr19:55,339,876-55,348,121 Size: 8,246 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr19:55,341,937-55,347,449 Size: 5,513 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:55,339,876-55,348,121)mRNA (may differ from genome)Protein (462 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
LynxMalacardsMGIneXtProtOMIMPubMed
ReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SV422_HUMAN
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase SUV420H2; EC=2.1.1.43; AltName: Full=Lysine N-methyltransferase 5C; AltName: Full=Suppressor of variegation 4-20 homolog 2; Short=Su(var)4-20 homolog 2; Short=Suv4-20h2;
FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-20' of histone H4. H4 'Lys-20' trimethylation represents a specific tag for epigenetic transcriptional repression. Mainly functions in pericentric heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin in these regions. SUV420H1 is targeted to histone H3 via its interaction with RB1 family proteins (RB1, RBL1 and RBL2) (By similarity).
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBUNIT: Interacts with HP1 proteins CBX1, CBX3 and CBX5. Interacts with RB1 family proteins RB1, RBL1 and RBL2 (By similarity).
SUBCELLULAR LOCATION: Nucleus. Chromosome (By similarity). Note=Associated with pericentric heterochromatin. CBX1 and CBX5 are required for the localization to pericentric heterochromatin (By similarity).
SIMILARITY: Belongs to the histone-lysine methyltransferase family. Suvar4-20 subfamily.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=AAH05842.1; Type=Erroneous translation; Note=Wrong choice of CDS;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

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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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.51 RPKM in Pituitary
Total median expression: 273.94 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 -99.60225-0.443 Picture PostScript Text
3' UTR -306.60672-0.456 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
IPR025790 - Hist-Lys_N-MTase_Suvar4-20
IPR001214 - SET_dom

Pfam Domains:
PF00856 - SET domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3RQ4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q86Y97
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-  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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0042799 histone methyltransferase activity (H4-K20 specific)

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016571 histone methylation
GO:0032259 methylation
GO:0034773 histone H4-K20 trimethylation

Cellular Component:
GO:0000780 condensed nuclear chromosome, centromeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005720 nuclear heterochromatin
GO:0005721 pericentric heterochromatin


-  Descriptions from all associated GenBank mRNAs
  AK308586 - Homo sapiens cDNA, FLJ98627.
AK304562 - Homo sapiens cDNA FLJ51466 complete cds.
BC044889 - Homo sapiens suppressor of variegation 4-20 homolog 2 (Drosophila), mRNA (cDNA clone MGC:17538 IMAGE:3461265), complete cds.
JD217436 - Sequence 198460 from Patent EP1572962.
JD478222 - Sequence 459246 from Patent EP1572962.
JD406388 - Sequence 387412 from Patent EP1572962.
JD193679 - Sequence 174703 from Patent EP1572962.
JD421339 - Sequence 402363 from Patent EP1572962.
AF289582 - Homo sapiens clone pp7130 unknown mRNA.
BC005842 - Homo sapiens suppressor of variegation 4-20 homolog 2 (Drosophila), mRNA (cDNA clone MGC:2705 IMAGE:2821053), complete cds.
BC019313 - Homo sapiens suppressor of variegation 4-20 homolog 2 (Drosophila), mRNA (cDNA clone MGC:4333 IMAGE:2821053), complete cds.
JD201138 - Sequence 182162 from Patent EP1572962.
JD368799 - Sequence 349823 from Patent EP1572962.
AB590886 - Synthetic construct DNA, clone: pFN21AE1148, Homo sapiens SUV420H2 gene for suppressor of variegation 4-20 homolog 2, without stop codon, in Flexi system.
MP015141 - Sequence 344 from Patent WO2019016252.
JD274243 - Sequence 255267 from Patent EP1572962.
JD453223 - Sequence 434247 from Patent EP1572962.
JD219762 - Sequence 200786 from Patent EP1572962.
JD525754 - Sequence 506778 from Patent EP1572962.
JD419094 - Sequence 400118 from Patent EP1572962.
JD439852 - Sequence 420876 from Patent EP1572962.
JD056047 - Sequence 37071 from Patent EP1572962.
JD123297 - Sequence 104321 from Patent EP1572962.
JD115917 - Sequence 96941 from Patent EP1572962.
JD392743 - Sequence 373767 from Patent EP1572962.
JD373165 - Sequence 354189 from Patent EP1572962.
JD545279 - Sequence 526303 from Patent EP1572962.
JD365660 - Sequence 346684 from Patent EP1572962.
JD548923 - Sequence 529947 from Patent EP1572962.
JD298297 - Sequence 279321 from Patent EP1572962.
JD077617 - Sequence 58641 from Patent EP1572962.
JD486006 - Sequence 467030 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q86Y97 (Reactome details) participates in the following event(s):

R-HSA-5651654 SUV420H1 (KMT5B), SUV420H2 (KMT5C), (possibly SMYD3 (KMT3E)) methylate methyl-lysine-21 of histone H4 (H4K20)
R-HSA-5651657 SUV420H1, SUV420H2, (possibly SMYD3 (KMT3E)) methylate dimethyl-lysine-21 of histone H4 (H4K20)
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: ENST00000255613.1, ENST00000255613.2, ENST00000255613.3, ENST00000255613.4, ENST00000255613.5, ENST00000255613.6, ENST00000255613.7, NM_032701, PP7130, Q86Y97, Q8WZ10, Q9BRZ6, SUV420H2, SV422_HUMAN, uc002qkj.1, uc002qkj.2, uc002qkj.3, uc002qkj.4, uc002qkj.5, uc002qkj.6
UCSC ID: ENST00000255613.8
RefSeq Accession: NM_032701
Protein: Q86Y97 (aka SV422_HUMAN)
CCDS: CCDS12922.1

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