Basic Information
VIS ID
TVIS30002865
Fusion event
HIV-CSNK1D 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
q25.3
Reference genome
GRCh37/hg19
Start
80214757/82256881 (Hg38)
End
80214757/82256881 (Hg38)
Orient
+
Location type
Intronic
Target gene
CSNK1D
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-590-3p ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-602 ; hsa-mir-1271-5p ; hsa-mir-1273h-5p ; hsa-mir-183-5p ; hsa-mir-212-5p ; hsa-mir-30b-3p ; hsa-mir-30c-1-3p ; hsa-mir-30c-2-3p ; hsa-mir-3189-3p ; hsa-mir-3622a-3p ; hsa-mir-3622b-3p ; hsa-mir-3689a-3p ; hsa-mir-3689b-3p ; hsa-mir-3689c ; hsa-mir-4268 ; hsa-mir-4448 ; hsa-mir-5192 ; hsa-mir-593-5p ; hsa-mir-6731-5p ; hsa-mir-6765-3p ; hsa-mir-6772-3p ; hsa-mir-6779-5p ; hsa-mir-6780a-5p ; hsa-mir-6788-5p ; hsa-mir-6878-5p ; hsa-mir-8085 ; hsa-mir-887-5p ; hsa-mir-96-5p
Nearest miRNA
hsa-mir-10226/Upstream/20153; hsa-mir-4525/Downstream/411352;
Nearest TSS
ENST00000595228/Upstream/1335; ENST00000566986/Downstream/9919;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/1615, chr17-CpG: 106/Downstream/15902
Upstream sequence
CTCTTCGGTATGTTTTCACAGCACTGGATCCGCAACTATACACATGGCTCTACACACATACGGCTTGTGAACGGCCTGGATAAACCTTTTATGTCCTTCC
Downstream sequence
ATGGCAAGACAGATTTTTAGTTTAGTCTTAAAGCAAGTTTTGGTACCACTAGGGAAATTCAATTCATTTAAAAAAttgtttcattattttattgttttga
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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