Basic Information
VIS ID
TVIS30003750
Fusion event
HIV-CDC42SE2 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
chr5
Cytoband
q31.1
Reference genome
GRCh37/hg19
Start
130676796/131341103 (Hg38)
End
130676796/131341103 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA5C
Target gene
CDC42SE2
miRNAs that regulate target gene
hsa-mir-421 ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-103a-3p ; hsa-mir-107 ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-545-3p ; hsa-mir-4524a-5p ; hsa-mir-4641 ; hsa-mir-4690-3p ; hsa-mir-4524b-5p ; hsa-mir-5685 ; hsa-mir-6838-5p ; hsa-mir-5680 ; hsa-mir-885-3p ; hsa-mir-203a-3p ; hsa-mir-646 ; hsa-mir-503-5p
Nearest miRNA
hsa-mir-10397/Upstream/1943956; hsa-mir-103a-1/Downstream/876746;
Nearest TSS
ENST00000502646/Upstream/77003; ENST00000506929/Downstream/44503;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/76390, chr5-CpG: 85/Downstream/293619
Upstream sequence
TTGAACTTCAAAGGAAGGATTGAGAGGCAAGAAGCAATAATCAAATCAATTGGCAAATTTGGAAAAATATTAATCATCAGCATCATTGTGTACTTACTGT
Downstream sequence
ATACTAAGTGTTTTGtttaattttcacaatagtcccatggtataggtactattattttccTggacaacattttccagtttgaaagaggtcattcagaccc
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate