Basic Information
VIS ID
TVIS30002042
Fusion event
HIV-SPATS2 integration
Validated
No
Detection method
QiaQuick PCR and Sequencing
Data source
download(RID)
Sample type
Cell line
Disease
HIV-infected disease (HID)
Quality evaluation
Normal
Reported year
2013
PubMed ID
23953889
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr12
Cytoband
q13.12
Reference genome
GRCh37/hg19
Start
49813598/49419815 (Hg38)
End
49813598/49419815 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA12A
Target gene
SPATS2
miRNAs that regulate target gene
hsa-mir-590-3p ; hsa-mir-103a-3p ; hsa-mir-296-3p ; hsa-let-7a-5p ; hsa-mir-3154 ; hsa-mir-6873-3p ; hsa-mir-4680-3p ; hsa-mir-5187-3p ; hsa-mir-4427 ; hsa-mir-3921 ; hsa-mir-4653-5p ; hsa-mir-301b-5p ; hsa-mir-301a-5p ; hsa-mir-146a-3p ; hsa-mir-7110-3p ; hsa-mir-6817-3p ; hsa-mir-4639-3p ; hsa-mir-8485 ; hsa-mir-603 ; hsa-mir-1324 ; hsa-mir-4668-5p ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-5695 ; hsa-mir-519d-5p ; hsa-mir-3613-3p ; hsa-mir-3184-3p
Nearest miRNA
hsa-mir-1244-3/Upstream/647778; hsa-let-7i/Downstream/814327;
Nearest TSS
ENST00000382841/Upstream/52268; ENST00000549045/Downstream/41064;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/30405, chr12-CpG: 191/Downstream/118025
Upstream sequence
TGCTTATTCTATCCTTTCATATGACATATACTAGTAGAAGACAGCTATTATTTTGAAAGCAGCATATATATTTAACATTCTTATGATTGTACAGATGTGG
Downstream sequence
ACTGGCATGAGTATTTTGGATCAGAAAAGGCATTTGTCAAATGTAGATTTTTAGTTCATTATGAAAACATACTGTTTTATTGGTGCAATTAACAAAAGTA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
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