Basic Information
VIS ID
TVIS30007744
Fusion event
HIV-NCK2 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
q12.2
Reference genome
GRCh37/hg19
Start
106435600/105819143 (Hg38)
End
106435600/105819143 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA2S
Target gene
NCK2
miRNAs that regulate target gene
hsa-mir-128-3p ; hsa-mir-877-3p ; hsa-mir-337-5p ; hsa-mir-495-3p ; hsa-mir-505-3p ; hsa-mir-3065-5p ; hsa-mir-4742-3p ; hsa-mir-3591-5p ; hsa-mir-5688 ; hsa-mir-7159-5p ; hsa-mir-190a-3p ; hsa-mir-1277-5p ; hsa-mir-5011-5p ; hsa-mir-5692c ; hsa-mir-5692b ; hsa-mir-548v ; hsa-mir-452-3p ; hsa-mir-496 ; hsa-mir-5683 ; hsa-mir-142-3p ; hsa-mir-574-5p ; hsa-mir-6867-5p ; hsa-mir-648 ; hsa-mir-4436a ; hsa-mir-4700-3p ; hsa-mir-5000-3p ; hsa-mir-505-5p ; hsa-mir-6827-5p
Nearest miRNA
hsa-mir-1285-2/Upstream/3386777; hsa-mir-10b/Downstream/3322347;
Nearest TSS
ENST00000437798/Upstream/2585; ENST00000425756/Downstream/32605;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/73382, chr2-CpG: 78/Downstream/62188
Upstream sequence
ATGCCATATTGTCCCGTTGATTTAGGGTGTTGTGTGTTGTGATTTCCAGAGCTAGCTCCTGGTCGGCAGTCGGGGGTTGGCACTCACACTGCATACCTGA
Downstream sequence
CTTCACCCCAGCCATTGTTGGCTCTTCTAGCTTTGGGTCCCCTCATGCATTCATAGGGCATTCCCAGGTCTCTCTTCCAGACCTTGTGCAAGACAGACAC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate