Basic Information
VIS ID
TVIS30001939
Fusion event
HIV-PICALM 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
chr11
Cytoband
q14.2
Reference genome
GRCh37/hg19
Start
85703882/85992839 (Hg38)
End
85703882/85992839 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA11F
Target gene
PICALM
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-155-5p ; hsa-mir-124-3p ; hsa-mir-98-5p ; hsa-mir-30a-5p ; hsa-mir-889-3p ; hsa-mir-3158-5p ; hsa-mir-205-5p ; hsa-mir-17-3p ; hsa-mir-1205 ; hsa-mir-1184 ; hsa-mir-3121-3p ; hsa-mir-30d-5p ; hsa-mir-30e-5p ; hsa-mir-30c-5p ; hsa-mir-30b-5p ; hsa-mir-510-3p ; hsa-mir-5007-3p ; hsa-mir-3163 ; hsa-mir-4760-3p
Nearest miRNA
hsa-mir-10392/Upstream/4102003; hsa-let-7a-2/Downstream/285494;
Nearest TSS
ENST00000527297/Upstream/2581; ENST00000533228/Downstream/4090;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/57691, chr11-CpG: 56/Downstream/75844
Upstream sequence
CATTGGTTTATGAGAAAACACATGTTCAGGAAAGGTTACCAGTCATCCGCTGTTCTACTGACAGATAGGTTTTATCTAGCACCTAATTTCAATCACTTCC
Downstream sequence
TATTACGTGAAACACCTTAGAGAAGAATATTCAGAAATATTTGCAAATGCATTCATAATTAGATCAATCAGATAAGGAAAACCAGTTCCTAATCTACTTG
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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