Basic Information
VIS ID
TVIS30003275
Fusion event
HIV-PHF20 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
chr20
Cytoband
q11.23
Reference genome
GRCh37/hg19
Start
34470331/35882409 (Hg38)
End
34470331/35882409 (Hg38)
Orient
-
Location type
Intronic
Target gene
PHF20
miRNAs that regulate target gene
hsa-mir-197-3p ; hsa-mir-21-5p ; hsa-mir-1303 ; hsa-mir-5096 ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-6802-3p ; hsa-mir-411-5p ; hsa-mir-6832-5p ; hsa-mir-193b-5p ; hsa-mir-3620-3p ; hsa-mir-6865-3p ; hsa-mir-483-5p ; hsa-mir-10b-5p ; hsa-mir-10a-5p
Nearest miRNA
hsa-mir-103a-2/Upstream/428312; hsa-mir-1-1/Downstream/2634154;
Nearest TSS
ENST00000382410/Upstream/12879; ENST00000420233/Downstream/34771;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/110081, chr20-CpG: 146/Downstream/71271
Upstream sequence
CTCCTACCTCTGGGCCTTGTTCAAGCACACTTTTATTGAGTACTTTTTATCCCCAGCCAGAGCAAGTAGATCCATTGGGAACATATCAGTAATGTGATGG
Downstream sequence
GTAATATTTATTTATGTATTCATTCAtttatttgtttgagaagggttttgctctgtcatccaggctggagtgtaatggcatgatcatagctcactgcagc
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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