Homo sapiens gene SUV39H2, encoding suppressor of variegation 3-9 homolog 2 (Drosophila).
SUMMARY back to top
RefSeq annotates 6 representative transcripts (NM included in AceView variants .a, .b, .c, .d, .f and .h), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 10 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.4 times the average gene in this release. The sequence of this gene is defined by 180 GenBank accessions from 158 cDNA clones, some from testis (seen 19 times), brain (12), colon (5), coronary artery (4), liver (4), muscle (4), prostate (4) and 69 other tissues. We annotate structural defects or features in 10 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 13 distinct introns (11 gt-ag, 2 gc-ag). Transcription produces 11 different mRNAs, 10 alternatively spliced variants and 1 unspliced form. There are 3 probable alternative promotors and 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of 6 cassette exons, overlapping exons with different boundaries. 1909 bp of this gene are antisense to spliced gene DCLRE1C, raising the possibility of regulated alternate expression.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant aAug10, bAug10, dAug10, fAug10).
Function: There are 9 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in pathway (Lysine degradation) and processes (chromatin assembly or disassembly, chromatin remodeling, cell cycle, cell differentiation, male meiosis, regulation of transcription). Proteins are expected to have molecular functions (histone methyltransferase activity (H3-K9 specific), protein binding, chromatin binding, protein methyltransferase activity, zinc ion binding) and to localize in various compartments (chromatin, cytoplasm, chromosome, chromosome, centromeric region, nuclear heterochromatin, nucleus). Putative protein interactors have been described (CGGBP1, EWSR1, SASH1, SMAD5, UBE2V2).
Protein coding potential: 8 spliced and the unspliced mRNAs putatively encode good proteins, altogether 7 different isoforms (5 complete, 2 partial), some containing domains 'chromo' (CHRromatin Organisation MOdifier) domain, Pre-SET motif [Pfam]. The remaining 2 mRNA variants (2 spliced; 1 partial) appear not to encode good proteins.
Isoform SUV39H2.iAug10 is annotated using as Met a Kozak-compatible a..AGG. start, thereby gaining 62 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 10, links to other databases and other names
Map: This gene SUV39H2 maps on chromosome 10, at 10p13 according to Entrez Gene. In AceView, it covers 25.55 kb, from 14920765 to 14946311 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from KEGG_00310, PhosphoSite, the SNP view, gene overviews from Entrez Gene 79723, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as SUV39H2, RP11-2K17.2, KMT1B or FLJ23414, LOC79723. It has been described as histone-lysine N-methyltransferase SUV39H2, H3-K9-HMTase 2, OTTHUMP00000019182, su(var)3-9 homolog 2, lysine N-methyltransferase 1B, histone H3-K9 methyltransferase 2.
EC number: This gene encodes protein number:
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Suv39h2 (e=3 10-63).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes hpl-1 (e=10-06), hpl-2 (e=3 10-05), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene TFL2 (e=10-07), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
Downstream sequence
aAug10 3147 bp 410 aa 123 bp 1791 bp 75 bp 2kb including Promoter 25538 bp 1kb
bAug10 3087 bp 350 aa 243 bp 1791 bp 48 bp 2kb including Promoter 25437 bp 1kb
cAug10 3076 bp 350 aa 232 bp 1791 bp 2kb probably including promoter 25405 bp 1kb
dAug10 2994 bp 350 aa 148 bp 1793 bp 66 bp 2kb including Promoter 25531 bp 1kb
eAug10-unspliced 1279 bp 263 aa 399 bp 88 bp 51 bp 2kb possibly including promoter 1279 bp 1kb
fAug10 2590 bp 230 aa 106 bp 1791 bp 75 bp 2kb possibly including promoter 25521 bp 1kb
gAug10 631 bp 209 aa 2kb 18516 bp 1kb
hAug10 2569 bp 170 aa 265 bp 1791 bp 48 bp 2kb possibly including promoter 25459 bp 1kb
iAug10 782 bp 151 aa 329 bp 2kb possibly including promoter 17981 bp 1kb
jAug10 737 bp 87 aa 475 bp 2kb 17369 bp 1kb
kAug10 330 bp 16 aa 6 bp 273 bp 2kb including Promoter 22396 bp 1kb

Gene neighbors and Navigator on chromosome 10p13 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               9 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e-u, .f, .g, .h, .i, .j, .k Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !