Basic Information
VIS ID
TVIS30002226
Fusion event
HIV-SYNE2 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
q23.2
Reference genome
GRCh37/hg19
Start
64329520/63862802 (Hg38)
End
64329520/63862802 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA14B
Target gene
SYNE2
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-193b-3p ; hsa-mir-148b-3p ; hsa-mir-9-5p ; hsa-mir-1-3p ; hsa-mir-34a-5p ; hsa-mir-26b-5p ; hsa-mir-21-5p ; hsa-mir-484 ; hsa-let-7b-5p ; hsa-mir-543 ; hsa-mir-376a-5p ; hsa-mir-485-5p
Nearest miRNA
hsa-mir-208a/Upstream/3214091; hsa-mir-1185-1/Downstream/232222;
Nearest TSS
ENST00000550708/Upstream/9810; ENST00000556725/Downstream/1586;
Nearest CpG islands
None/Target, chr14-CpG: 35/Upstream/8994, chr14-CpG: 45/Downstream/431211
Upstream sequence
AATTTTAATTTGAAAGGCAGGTTTTTAGGAAGGTAGATATTAGGTTTTGGGGCAGTTTTTATTAGAAGGTTTTGGGGCAgttttgttttttttttgtttt
Downstream sequence
gttttgtttttttggagacagagtctcactctgttgccaggctggagtgcagtggcgtgatcttggctcactgcagcctctgcctcctgggttcaagtga
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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