Basic Information
VIS ID
TVIS30003248
Fusion event
HIV-RBCK1 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
chr20
Cytoband
p13
Reference genome
GRCh37/hg19
Start
402546/421902 (Hg38)
End
402546/421902 (Hg38)
Orient
+
Location type
Intronic
Target gene
RBCK1
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-124-3p ; hsa-mir-34a-5p ; hsa-mir-1245b-3p ; hsa-mir-3659 ; hsa-mir-4658 ; hsa-mir-514a-3p ; hsa-mir-514b-3p ; hsa-mir-541-3p ; hsa-mir-5683 ; hsa-mir-574-5p ; hsa-mir-654-5p ; hsa-mir-6769a-5p ; hsa-mir-6769b-5p ; hsa-mir-6790-5p ; hsa-mir-92a-2-5p
Nearest miRNA
hsa-mir-1-1/Downstream/970998;
Nearest TSS
ENST00000382410/Upstream/12018; ENST00000621487/Downstream/40;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/2077, chr20-CpG: 97/Downstream/39984
Upstream sequence
gagtcactggggagacatggctgctgttctgagatagactctaggggccagatggatgcagggagcccagcgaggaggctcctggagtcacccaggtggg
Downstream sequence
ggatgtggggcctggaccagagAATCAGAGCGGCAGTATGGAGGCAGGGTGGAGGCCTTGGTGATGGGTTGGTGAGAGGGATGGGAAGGAAGGAGATATT
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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