Basic Information
VIS ID
TVIS30002785
Fusion event
HIV-CCDC47 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
q23.3
Reference genome
GRCh37/hg19
Start
61831201/63753841 (Hg38)
End
61831201/63753841 (Hg38)
Orient
-
Location type
Intronic
Target gene
CCDC47
miRNAs that regulate target gene
hsa-mir-215-5p ; hsa-mir-196a-5p ; hsa-mir-192-5p ; hsa-mir-1226-3p ; hsa-mir-500a-3p ; hsa-mir-484 ; hsa-mir-106b-5p ; hsa-mir-222-3p ; hsa-mir-106a-5p ; hsa-mir-93-5p ; hsa-mir-20a-5p ; hsa-mir-17-5p ; hsa-mir-1255b-2-3p ; hsa-mir-6763-3p ; hsa-mir-5591-3p ; hsa-mir-5587-3p ; hsa-mir-4707-5p ; hsa-mir-6729-3p ; hsa-mir-7851-3p ; hsa-mir-619-3p ; hsa-mir-660-5p
Nearest miRNA
hsa-mir-10226/Upstream/809529; hsa-mir-1250/Downstream/746933;
Nearest TSS
ENST00000595228/Upstream/1744; ENST00000581135/Downstream/7696;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/11804, chr17-CpG: 118/Downstream/19483
Upstream sequence
AAATTACAAAACACACAGATTTGTAATCAGACATAAGTCAAACATCACACACAAATTATTATCATAAAAAAAAAGAACCTATGGACTGgggcatggtggc
Downstream sequence
tcacgcttataattccagcactttgggaggccaaggcaggtggatcacgaggtcaggagttcgagaccagcctgaccaacatggtgaaaccccatctcta
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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