Basic Information
VIS ID
TVIS30007423
Fusion event
HIV-PRKCSH 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
chr19
Cytoband
p13.2
Reference genome
GRCh37/hg19
Start
11559562/11448747 (Hg38)
End
11559562/11448747 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA19B
Target gene
PRKCSH
miRNAs that regulate target gene
hsa-mir-330-5p ; hsa-mir-454-3p ; hsa-mir-92b-3p ; hsa-mir-324-3p ; hsa-mir-342-3p ; hsa-mir-361-5p
Nearest miRNA
hsa-mir-1181/Upstream/335213; hsa-let-7e/Downstream/46797;
Nearest TSS
ENST00000633603/Upstream/210; ENST00000591510/Downstream/1032;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/13024, chr19-CpG: 20/Downstream/483
Upstream sequence
GGGGCCCCCACTGGCAGGGTGGGAGGCGGGTGGCCCCGGAAGTGGCACCGGCAGTTTCCTGATGGTTGGGGAACCATCTGCGGGTGGGGCCCGAGAGTGC
Downstream sequence
TGCCTTCCATATTGAGGGGGAGCAGAAGCCAGGGGCCAGGTTTAGGGTTGGTCATTGGAGTTGGAGGTACCCTGTGTGTGGGGACTGGAGGAGGCGGTGG
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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