Basic Information
VIS ID
TVIS30005249
Fusion event
HIV-PATJ 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
chr1
Cytoband
p31.3
Reference genome
GRCh37/hg19
Start
62219419/61753747 (Hg38)
End
62219419/61753747 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1L
Target gene
PATJ
miRNAs that regulate target gene
hsa-mir-548b-3p ; hsa-mir-15b-5p ; hsa-mir-155-5p ; hsa-mir-665 ; hsa-mir-6771-5p ; hsa-mir-7160-5p ; hsa-mir-4722-5p ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-1827 ; hsa-mir-4649-3p ; hsa-mir-6746-5p ; hsa-mir-4768-3p ; hsa-mir-5690 ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-578 ; hsa-mir-4639-5p ; hsa-mir-6867-3p ; hsa-mir-211-5p ; hsa-mir-204-5p ; hsa-mir-6845-3p ; hsa-mir-4685-3p ; hsa-mir-7113-3p ; hsa-mir-4287 ; hsa-mir-4469 ; hsa-mir-6832-3p ; hsa-mir-7977 ; hsa-mir-490-3p
Nearest miRNA
hsa-mir-12136/Upstream/2020451; hsa-mir-101-1/Downstream/92328;
Nearest TSS
ENST00000473358/Upstream/11202; ENST00000493967/Downstream/51763;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/10601, chr1-CpG: 33/Downstream/441136
Upstream sequence
tacaggtgtgcatcaccacgtcaagctgatttttgtatttttagtagagatggggtttcaccatattggccaggctggtctcgaactcctgacctcaggt
Downstream sequence
gatccacctgccttggcctcccaaagtgctgagattacaggcatgagccactgtgcccagcctatatattttatttattaagtttttatcttaatcagat
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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