Basic Information
VIS ID
TVIS30004630
Fusion event
HIV-RAD51L3-RFFL 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
chr17
Cytoband
q12
Reference genome
GRCh37/hg19
Start
33392366/35065347 (Hg38)
End
33392366/35065347 (Hg38)
Orient
-
Location type
ncRNA_intronic
Target gene
RAD51L3-RFFL
miRNAs that regulate target gene
hsa-mir-216a-5p ; hsa-mir-6867-3p ; hsa-mir-3160-5p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-7113-3p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-3613-3p ; hsa-mir-888-5p ; hsa-mir-7162-5p ; hsa-mir-516b-3p ; hsa-mir-516a-3p ; hsa-mir-4772-3p ; hsa-mir-6787-3p ; hsa-mir-1304-3p ; hsa-mir-4532 ; hsa-mir-1247-3p ; hsa-mir-6736-3p ; hsa-mir-6890-3p ; hsa-mir-2115-5p ; hsa-mir-6728-3p ; hsa-mir-1255b-2-3p ; hsa-mir-1273g-3p ; hsa-mir-455-3p ; hsa-mir-6516-5p
Nearest miRNA
hsa-mir-1180/Upstream/2715145; hsa-mir-10226/Downstream/1968398;
Nearest TSS
ENST00000595228/Upstream/1495; ENST00000158009/Downstream/9027;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/84120, chr17-CpG: 43/Downstream/23775
Upstream sequence
CTGTATTTGCGAACTTTAAATAAGAGggccgggcacagcggttcacgcctataattgcagcactttggaaggccgaggtgggcggatcacctgaggtcgg
Downstream sequence
gagttcaagactagcctaaccaacatggagaaacccccatctctactaaaaatacaaaattagccaggtgtggtggcacatgcctgtaatcccagctact
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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