Basic Information
VIS ID
TVIS30006513
Fusion event
HIV-CCDC88C 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
chr14
Cytoband
q32.11
Reference genome
GRCh37/hg19
Start
91830668/91364324 (Hg38)
End
91830668/91364324 (Hg38)
Orient
+
Location type
Intronic
Target gene
CCDC88C
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-23b-3p ; hsa-mir-1-3p ; hsa-mir-93-5p ; hsa-mir-20a-5p ; hsa-mir-574-5p ; hsa-mir-3659 ; hsa-mir-6818-5p ; hsa-mir-218-5p ; hsa-mir-4658 ; hsa-mir-6790-5p ; hsa-mir-6867-5p ; hsa-mir-636 ; hsa-mir-4720-3p ; hsa-mir-4804-3p ; hsa-mir-191-5p ; hsa-mir-1236-5p ; hsa-mir-4693-3p ; hsa-mir-922 ; hsa-mir-330-3p ; hsa-mir-5586-3p ; hsa-mir-5197-3p ; hsa-mir-424-5p ; hsa-mir-15a-5p ; hsa-mir-195-5p ; hsa-mir-16-5p ; hsa-mir-6838-5p ; hsa-mir-15b-5p ; hsa-mir-497-5p ; hsa-mir-181d-5p ; hsa-mir-181c-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p
Nearest miRNA
hsa-mir-1260a/Upstream/14098034; hsa-mir-1185-1/Downstream/2583902;
Nearest TSS
ENST00000550708/Upstream/25468; ENST00000557524/Downstream/44434;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/60249, chr14-CpG: 16/Downstream/52693
Upstream sequence
CCAAGGGAACCCCCTTCCGCAGAGCACATGGTAGGGGTGTGGCATTGCAATCCAGGGTAGATTGCACTCCTCCCCACTTCTCCTTTAGGTTTGCTTTCGG
Downstream sequence
ATCCTAAAATAAGATTTTGCTTTTCATAAATGACTTGCTTTTCAACTGCATCCTGGAATGACTCCTCGGCCAATTAAATGCTTTAAACAAACCAAAAGAA
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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