Basic Information
VIS ID
TVIS30010549
Fusion event
HIV-ROCK1 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
chr18
Cytoband
q11.1
Reference genome
GRCh37/hg19
Start
18541363/20961402 (Hg38)
End
18541363/20961402 (Hg38)
Orient
-
Location type
Intronic
Target gene
ROCK1
miRNAs that regulate target gene
hsa-mir-146a-5p ; hsa-mir-584-5p ; hsa-mir-124-3p ; hsa-mir-1280 ; hsa-mir-148b-3p ; hsa-mir-335-5p ; hsa-mir-148a-3p ; hsa-mir-135a-5p ; hsa-mir-145-5p ; hsa-mir-340-5p ; hsa-mir-4662a-5p ; hsa-mir-4753-5p ; hsa-mir-6507-5p ; hsa-mir-6768-3p ; hsa-mir-548aw ; hsa-mir-5093 ; hsa-mir-1468-3p ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-3688-3p ; hsa-mir-300 ; hsa-mir-506-3p ; hsa-mir-584-3p ; hsa-mir-126-3p ; hsa-mir-144-5p
Nearest miRNA
hsa-mir-3156-2/Upstream/6131160; hsa-mir-1-2/Downstream/722116;
Nearest TSS
ENST00000575820/Upstream/5935; ENST00000579454/Downstream/7952;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/5630227, chr18-CpG: 113/Downstream/149577
Nearest cancer related gene
ROCK1(OG, No orient, 0)
Upstream sequence
AAAAGCTATAAACTCAGTCTTACAGTAACAGTTAACAATAGGTAACATTTACTGATTTATTTATTCATAAATTTACTATTTGCCACATGCTTTATAATAT
Downstream sequence
CTCATATTTAACCTATGTATAAGTCCATGAATACAGGATATTATATTCCGAGGAATTCGGAAAaggttctactgtcatctttcacttacaaaagaagaga
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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