Basic Information
VIS ID
TVIS30008600
Fusion event
HIV-LINC01088 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
chr4
Cytoband
q21.21
Reference genome
GRCh37/hg19
Start
79916111/78994957 (Hg38)
End
79916111/78994957 (Hg38)
Orient
+
Location type
ncRNA_intronic
Target gene
LINC01088
Nearest miRNA
hsa-mir-12113/Upstream/2419331; hsa-mir-1243/Downstream/3758380;
Nearest TSS
ENST00000502981/Upstream/23209; ENST00000511895/Downstream/90282;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/55366, chr4-CpG: 39/Downstream/969733
Upstream sequence
atctgttcgtgtcaatccttgcacaataccatactttcatagttattttagctttataaaaggtattgatatcttatagagcaggccctcTGTATAGGTG
Downstream sequence
TGTTGCCTTTCTTTCtttttttttttttaaaaaaaacaaaaaaaCAAAAACATGTttcctagatgtttgataatgctaatgctatcgtaaatgggatttt
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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