Basic Information
VIS ID
TVIS30007667
Fusion event
HIV-RTN4 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
p16.1
Reference genome
GRCh37/hg19
Start
55264314/55037178 (Hg38)
End
55264314/55037178 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA2S
Target gene
RTN4
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-16-5p ; hsa-mir-148b-3p ; hsa-mir-132-3p ; hsa-mir-183-5p ; hsa-mir-34a-5p ; hsa-mir-101-3p ; hsa-mir-33a-5p ; hsa-mir-320a ; hsa-mir-30c-5p ; hsa-mir-3148 ; hsa-mir-4330 ; hsa-mir-4496 ; hsa-mir-605-5p ; hsa-mir-4524b-5p ; hsa-mir-4524a-5p ; hsa-mir-1272 ; hsa-mir-646 ; hsa-mir-376c-3p ; hsa-mir-4643 ; hsa-mir-338-5p ; hsa-mir-4662b ; hsa-mir-4647 ; hsa-mir-4426 ; hsa-mir-497-5p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-6838-5p ; hsa-mir-424-5p ; hsa-mir-15a-5p ; hsa-mir-503-5p
Nearest miRNA
hsa-mir-1301/Upstream/1187973; hsa-mir-10b/Downstream/945789;
Nearest TSS
ENST00000437798/Upstream/26729; ENST00000463185/Downstream/9708;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/311827, chr2-CpG: 129/Downstream/12241
Nearest cancer related gene
RTN4(TSG, No orient, 0)
Upstream sequence
tatttccatacagtagcaacaaagagaaaatgaaaatattttctaaatatcactcactgtaacaaaaaaacataaaatatttaggcataaatttgacaag
Downstream sequence
agatgcacaaaactgctatactgaaacacactgctgagagaaattacagatgatctaaacaacagagatatcacattcatgggttgaaagatataatatt
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate