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Viral Integration Site DataBase
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TVIS30011178
Basic Information
VIS ID
TVIS30011178
Fusion event
HIV-USP48 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
p36.12
Reference genome
GRCh37/hg19
Start
22098054/21771561 (Hg38)
End
22098054/21771561 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
USP48
miRNAs that regulate target gene
hsa-mir-124-3p
;
hsa-mir-148b-3p
;
hsa-mir-580-3p
;
hsa-mir-7153-5p
;
hsa-mir-146b-5p
;
hsa-mir-146a-5p
;
hsa-mir-589-5p
;
hsa-mir-4539
;
hsa-mir-545-5p
;
hsa-mir-8063
;
hsa-mir-374b-3p
;
hsa-let-7i-3p
;
hsa-mir-4524b-5p
;
hsa-mir-4524a-5p
;
hsa-mir-1468-3p
;
hsa-mir-5590-3p
;
hsa-mir-545-3p
;
hsa-mir-142-5p
;
hsa-mir-646
;
hsa-mir-548p
;
hsa-mir-561-3p
;
hsa-mir-548at-5p
;
hsa-mir-503-5p
;
hsa-mir-6838-5p
;
hsa-mir-497-5p
;
hsa-mir-424-5p
;
hsa-mir-195-5p
;
hsa-mir-16-5p
;
hsa-mir-15b-5p
;
hsa-mir-15a-5p
;
hsa-mir-1305
;
hsa-mir-943
;
hsa-mir-3118
;
hsa-mir-134-5p
;
hsa-mir-1290
;
hsa-mir-876-5p
;
hsa-mir-3167
;
hsa-mir-1246
;
hsa-mir-892a
;
hsa-mir-4796-3p
;
hsa-mir-3609
;
hsa-mir-548ah-5p
;
hsa-mir-20a-5p
;
hsa-mir-20b-5p
;
hsa-mir-519d-3p
;
hsa-mir-17-5p
;
hsa-mir-93-5p
;
hsa-mir-526b-3p
;
hsa-mir-106a-5p
;
hsa-mir-106b-5p
Nearest miRNA
hsa-mir-12136/Upstream/783129; hsa-mir-101-1/Downstream/494678;
Nearest TSS
ENST00000473358/Upstream/23370;
ENST00000484271/Downstream/10459;
Nearest CpG islands
None/Target,
chr1-CpG: 111/Upstream/101645
,
chr1-CpG: 111/Downstream/11075
Upstream sequence
taattataaattatttatttatttatttttCATGAGAACCATGAGAAAAATTCTAAAAGGAATTAaggtcttgccttatcagatatttttcaaatactat
Downstream sequence
aaaataattagaattgtggtatcactacagagttattcaacgaaattaatcaatggcaaaaaaaacagggttgagaggctgggtgcagtggcttacacct
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Sample Information
×
Sample name
Resting CD4+
Sample type
Cell line
Gender
Female
CpG Island Information
×
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