Basic Information
VIS ID
TVIS30002951
Fusion event
HIV-COL5A3 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
10099944/9989268 (Hg38)
End
10099944/9989268 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA19B
Target gene
COL5A3
miRNAs that regulate target gene
hsa-mir-29b-3p ; hsa-mir-204-5p ; hsa-mir-323a-5p ; hsa-mir-642a-5p ; hsa-mir-6723-5p ; hsa-mir-20b-3p ; hsa-mir-3137 ; hsa-mir-1236-3p ; hsa-mir-877-3p ; hsa-mir-2276-5p ; hsa-mir-6892-3p ; hsa-mir-2114-5p ; hsa-mir-9500
Nearest miRNA
hsa-mir-1227/Upstream/1599888; hsa-let-7e/Downstream/49086;
Nearest TSS
ENST00000633603/Upstream/20381; ENST00000592332/Downstream/6729;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/22500, chr19-CpG: 26/Downstream/20034
Upstream sequence
TGGTGGACCCTGGGAGGAAAATAAGGTCAGTGCCATTCTAGACAGTCCCTTCCACATTCTAAGAGCCCTCATCTCTCTCCTCTGTGGCCCCTGACTGCAG
Downstream sequence
GCCCTGCCTCCCGACCCTCGTCCCCAACCCAGCCTAACCTCCTGGTCACTCACCTGAGCCCCTTTCTCTCCCGTGGGGCCCTCATGTCCTGGGTGACCCT
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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