Basic Information
VIS ID
TVIS30005118
Fusion event
HIV-RCAN3 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
chr1
Cytoband
p36.11
Reference genome
GRCh37/hg19
Start
24844135/24517645 (Hg38)
End
24844135/24517645 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
RCAN3
miRNAs that regulate target gene
hsa-mir-6855-5p ; hsa-mir-3170 ; hsa-mir-6742-5p ; hsa-mir-193b-5p ; hsa-mir-564 ; hsa-mir-6838-5p ; hsa-mir-6767-3p ; hsa-mir-497-5p ; hsa-mir-424-5p ; hsa-mir-195-5p ; hsa-mir-16-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p ; hsa-mir-451b ; hsa-mir-6507-5p ; hsa-mir-5583-3p ; hsa-mir-548e-5p ; hsa-mir-183-5p ; hsa-mir-4762-3p ; hsa-mir-5006-5p ; hsa-mir-3192-3p ; hsa-mir-6749-3p ; hsa-mir-1260b ; hsa-mir-1260a ; hsa-mir-4755-3p ; hsa-mir-4502 ; hsa-mir-532-3p ; hsa-mir-1224-3p ; hsa-mir-532-5p ; hsa-mir-186-5p
Nearest miRNA
hsa-mir-12136/Upstream/588498; hsa-mir-101-1/Downstream/401700;
Nearest TSS
ENST00000473358/Upstream/3272; ENST00000482807/Downstream/15469;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/14257, chr1-CpG: 19/Downstream/17567
Upstream sequence
TGGAAATCATCCCAGCAGAAATTCTAATAACAGCAGTTCAGCGGACTTCCTAGTAAATTGTATTTAATACCCTTAACAGTAATATCTGAAATGACAAAAT
Downstream sequence
ATAAAATGTTTATATTATGGTTATCTATAGATCATCAGTTGGATATAAAATATGGACAGAATCAAggccagatatgatggctcatgcttgtaatcccagc
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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