Basic Information
VIS ID
TVIS30010967
Fusion event
HIV-PTPRK 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
chr6
Cytoband
q22.33
Reference genome
GRCh37/hg19
Start
128306029/127984884 (Hg38)
End
128306029/127984884 (Hg38)
Orient
+
Location type
Intronic
Target gene
PTPRK
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-mir-133b ; hsa-mir-9-5p ; hsa-mir-935 ; hsa-mir-877-3p ; hsa-mir-615-3p ; hsa-mir-423-3p ; hsa-mir-149-5p ; hsa-mir-218-5p ; hsa-mir-1283 ; hsa-mir-7849-3p ; hsa-mir-548c-3p
Nearest miRNA
hsa-mir-10398/Upstream/1500171; hsa-mir-1202/Downstream/3807288;
Nearest TSS
ENST00000381078/Upstream/66253; ENST00000417390/Downstream/23193;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/468323, chr6-CpG: 173/Downstream/534129
Nearest cancer related gene
PTPRK(TSG, No orient, 0)
Upstream sequence
TCCCAGAGTTGGAGACAGGAATGTAATTTAAGAGTACATCAGATTTCATGAGGAGGATTGAAAGGAAGTTTTTTTTGTTTTCAGGGTACATAGTATCTGA
Downstream sequence
TCCTATGGGACGTTTTACCTTTACTTCATTCTCTGCTTTTTTTCCCCTCTTTTATACATGGTTATTTAAATCCTGAATAGGTTGGATTTTCAGAAAGCAA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate