Basic Information
VIS ID
TVIS30002703
Fusion event
HIV-CASC3 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
q21.1
Reference genome
GRCh37/hg19
Start
38305780/40149527 (Hg38)
End
38305780/40149527 (Hg38)
Orient
+
Location type
Intronic
Target gene
CASC3
miRNAs that regulate target gene
hsa-mir-125b-5p ; hsa-mir-128-3p ; hsa-mir-877-5p ; hsa-mir-193b-3p ; hsa-mir-484 ; hsa-mir-378a-3p ; hsa-mir-222-3p ; hsa-mir-182-5p ; hsa-mir-124-3p
Nearest miRNA
hsa-mir-1180/Upstream/123118; hsa-mir-10226/Downstream/12406;
Nearest TSS
ENST00000595228/Upstream/8685; ENST00000474190/Downstream/12270;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/8774, chr17-CpG: 82/Downstream/28079
Upstream sequence
AGAAATTTGACTGAGGGAAGGCTGAAGAGATGGTAGTTGGAGAGGTAGCTTTGAGATCAAGAGGTGATTTGGATGTTTTTTAAAAAGTTAGGAGAGTATC
Downstream sequence
AAATAAGGTCAAAGATTGAAAAAAAGAAAAGAAAGGGGGAAAAAAGAGAGGGAATAGATAATGATATTGAGTACTGGTATTTTTGACTGAGTATATGAGA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate