Basic Information
VIS ID
TVIS30002224
Fusion event
HIV-PRKCH 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
q23.1
Reference genome
GRCh37/hg19
Start
61908641/61441923 (Hg38)
End
61908641/61441923 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA14B
Target gene
PRKCH
miRNAs that regulate target gene
hsa-mir-376c-3p ; hsa-mir-432-5p ; hsa-mir-376a-3p ; hsa-mir-493-3p ; hsa-mir-4531 ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-5703 ; hsa-mir-4516 ; hsa-mir-4434 ; hsa-mir-26a-2-3p ; hsa-mir-26a-1-3p ; hsa-mir-6731-3p ; hsa-mir-4254 ; hsa-mir-3690 ; hsa-mir-3938 ; hsa-mir-3675-3p ; hsa-mir-216b-5p ; hsa-mir-24-3p
Nearest miRNA
hsa-mir-208a/Upstream/793212; hsa-mir-1185-1/Downstream/2653101;
Nearest TSS
ENST00000550708/Upstream/51229; ENST00000557473/Downstream/635;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/119174, chr14-CpG: 112/Downstream/253206
Upstream sequence
AAtttttttaagagatggggcctcagtatattgtccaggtggtcttgaactcctggactcaagcagtcctcctgcctcagcctcccaaagtgttggtatt
Downstream sequence
acagacatgagctactgtacccggccAAGTTTTATTATCCTTATCTTATCCTAGGAGTATAATATTTTTCTGTGTTTTCTTATTGTTCTATAATTTCCTT
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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