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VISDB
Viral Integration Site DataBase
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TVIS30006875
Basic Information
VIS ID
TVIS30006875
Fusion event
HIV-NLRC5 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
chr16
Cytoband
q13
Reference genome
GRCh37/hg19
Start
57040873/57006961 (Hg38)
End
57040873/57006961 (Hg38)
Orient
-
Location type
Intronic
Target gene
NLRC5
miRNAs that regulate target gene
hsa-mir-218-5p
;
hsa-mir-216b-5p
;
hsa-mir-6811-5p
;
hsa-mir-6511b-5p
;
hsa-mir-452-3p
;
hsa-mir-6504-5p
;
hsa-mir-4736
;
hsa-mir-3064-5p
;
hsa-mir-664a-5p
;
hsa-mir-4794
;
hsa-mir-17-3p
;
hsa-mir-1205
;
hsa-mir-1184
;
hsa-mir-3158-5p
;
hsa-mir-4692
;
hsa-mir-4514
;
hsa-mir-3126-3p
;
hsa-mir-940
;
hsa-mir-6893-5p
;
hsa-mir-6808-5p
;
hsa-mir-149-5p
;
hsa-mir-34a-5p
Nearest miRNA
hsa-mir-1225/Upstream/102608; hsa-mir-11401/Downstream/765328;
Nearest TSS
ENST00000527434/Upstream/2475;
ENST00000536231/Downstream/10113;
Nearest CpG islands
None/Target,
chr16-CpG: 29/Upstream/17105
,
chr16-CpG: 133/Downstream/85171
Nearby gene
NLRC5
(No orient, 10113)
Upstream sequence
GAGACAGGGTCACAAAACCGTTAACACattattattattattattattattattattTCACATTATTTAGGGAAGTTTCATTTTTTTGTGAGCTATCACT
Downstream sequence
GATAATTTCTTATTTACTCATCATCTTGTATTTCTCTTCCTTGCACATTGGGGAAATGTCTATTCTAGTTTTTAATGTAAATGTTCTTGTGGCTTTTTTA
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
Central Memory CD4+
Sample type
Cell line
Gender
Female
CpG Island Information
×
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