Basic Information
VIS ID
TVIS30006340
Fusion event
HIV-GTF2F2 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
chr13
Cytoband
q14.13
Reference genome
GRCh37/hg19
Start
45780314/45206179 (Hg38)
End
45780314/45206179 (Hg38)
Orient
-
Location type
Intronic
Target gene
GTF2F2
miRNAs that regulate target gene
hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-500a-5p ; hsa-mir-548as-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-548ac
Nearest miRNA
hsa-mir-2276/Upstream/1009979; hsa-mir-1267/Downstream/4790236;
Nearest TSS
ENST00000623511/Upstream/11462; ENST00000494087/Downstream/176;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/85348, chr13-CpG: 37/Downstream/105440
Upstream sequence
aCGGCTTTTAAAATATTTTCTTCCTGCCATATTTTGGTATAAGGTAGTCATGCTTCTCATCATTGCTTTTTCTGCATCTTCTTGAGATTTGTTGCATATG
Downstream sequence
TTGCATTAAGGGACCCTGGATACATTGATTATATACGGTGTGCTTGTAATTAGTTCGTACAGAGTCTCCTAGATTTTGGAGACATCCAAAGATCACTAAA
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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