Basic Information
VIS ID
TVIS30004857
Fusion event
HIV-PDCD6IP 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
chr3
Cytoband
p22.3
Reference genome
GRCh37/hg19
Start
33889855/33848363 (Hg38)
End
33889855/33848363 (Hg38)
Orient
+
Location type
Intronic
Target gene
PDCD6IP
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-15a-5p ; hsa-mir-760 ; hsa-mir-23b-3p ; hsa-mir-92a-3p ; hsa-mir-23a-3p
Nearest miRNA
hsa-mir-12127/Upstream/1341974; hsa-let-7g/Downstream/1896113;
Nearest TSS
ENST00000440867/Upstream/4272; ENST00000495235/Downstream/4245;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/49184, chr3-CpG: 86/Downstream/1790654
Upstream sequence
tctaggttacctttagtgtagggTAAATGTATCAAGTTTCTGCGTTCGTTGCTGTAGACATAGTTGCTTATTTGCCTTTTCTGAAAATAAAATGACAAGG
Downstream sequence
TTATAAAAGTAAAATAGAAGATTTTGTTGAGGGCAtttctttctttcttttttttttttgagacggagtcttgctctgtcacccaggctggagagcagtg
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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