Basic Information
VIS ID
TVIS30009646
Fusion event
HIV-PTK2 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
chr8
Cytoband
q24.3
Reference genome
GRCh37/hg19
Start
141731242/140721143 (Hg38)
End
141731242/140721143 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA8D
Target gene
PTK2
miRNAs that regulate target gene
hsa-mir-193a-3p ; hsa-mir-138-5p ; hsa-mir-7-5p ; hsa-mir-21-5p ; hsa-let-7e-5p ; hsa-let-7c-5p ; hsa-mir-543 ; hsa-mir-379-5p ; hsa-mir-135a-5p
Nearest miRNA
hsa-mir-1204/Upstream/5916198; hsa-mir-10400/Downstream/11421;
Nearest TSS
ENST00000518652/Upstream/2409; ENST00000522882/Downstream/645;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/84728, chr8-CpG: 176/Downstream/279198
Upstream sequence
accatgcctggccTCCTACCTTTCTTTCTTTAtttttttttttttaaaagagatggaatggtactaagttgctcaggctggtcctgaactcctgcgttcc
Downstream sequence
agAGTAACTGGGACTACAGGCTTACACCATATGCCTGTGCAAGTATTTCAAATGAGTTAATATCCAAGTAGAGCTTGAGATACAAAGGAGCAACCATGTC
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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