Basic Information
VIS ID
TVIS30012728
Fusion event
HIV-AFF3 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
chr2
Cytoband
q11.2
Reference genome
GRCh37/hg19
Start
100595538/99979076 (Hg38)
End
100595538/99979076 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA2S ; FRA2A
Target gene
AFF3
miRNAs that regulate target gene
hsa-mir-574-5p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-6867-5p ; hsa-mir-3177-5p ; hsa-mir-7703 ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-1227-3p ; hsa-mir-4252 ; hsa-mir-4793-3p ; hsa-mir-766-3p ; hsa-mir-1273g-3p ; hsa-mir-508-5p ; hsa-mir-6849-3p
Nearest miRNA
hsa-mir-1285-2/Upstream/3180723; hsa-mir-10b/Downstream/1330374;
Nearest TSS
ENST00000437798/Upstream/400706; ENST00000434301/Downstream/27769;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/385047, chr2-CpG: 138/Downstream/124847
Nearest cancer related gene
AFF3(OG, No orient, 0)
Upstream sequence
GGATCAAAGGCAGGTGGTGGAAGGACTGACTACATGGGCTCTTCAACTGAAGAGATCAACGCAATGATCTCTTCAATAGAATAGTCTGTTGAAGATCTGG
Downstream sequence
AAGTATATAAATAGGGCATATTGTATTAATAGATATATTTGCTTGCCTCCCTAGTATCCTCAAAAGATGAGGACCGGGACTAAGTTGTTCTTGTATCGTG
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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