Basic Information
VIS ID
TVIS30010183
Fusion event
HIV-RTN3 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
chr11
Cytoband
q13.1
Reference genome
GRCh37/hg19
Start
63490278/63722806 (Hg38)
End
63490278/63722806 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA11H
Target gene
RTN3
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-760 ; hsa-mir-484 ; hsa-mir-378a-3p ; hsa-mir-106a-5p ; hsa-mir-17-5p ; hsa-mir-205-5p ; hsa-mir-6515-5p ; hsa-mir-4443 ; hsa-mir-4725-3p ; hsa-mir-6780b-5p ; hsa-mir-4271 ; hsa-mir-6797-5p ; hsa-mir-1249-5p ; hsa-mir-6783-5p ; hsa-mir-671-5p ; hsa-mir-4511 ; hsa-mir-33b-5p ; hsa-mir-33a-5p ; hsa-mir-4684-3p ; hsa-mir-4694-5p ; hsa-mir-367-5p ; hsa-mir-802 ; hsa-mir-522-3p ; hsa-mir-224-3p ; hsa-mir-4694-3p ; hsa-mir-335-3p ; hsa-mir-4775 ; hsa-mir-5692a ; hsa-mir-590-3p ; hsa-mir-6793-3p
Nearest miRNA
hsa-mir-129-2/Upstream/930035; hsa-let-7a-2/Downstream/619043;
Nearest TSS
ENST00000527297/Upstream/41233; ENST00000535820/Downstream/43146;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/40892, chr11-CpG: 188/Downstream/39610
Upstream sequence
tctaattcttgctgtgctgtgtctagaagtatgactttgaacaagtaacttacataacctttcgggggcctcagttttaatatctgtaaagtgaggatgt
Downstream sequence
aaagtgaagtagatggtcttcaaTTATCATTTAAATAATATGATTCTCTGGCTCTGGTACATTCTAGATTTCTTCCTCAGTTGTCATAATTCTTACAGGT
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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