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VISDB
Viral Integration Site DataBase
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TVIS30002223
Basic Information
VIS ID
TVIS30002223
Fusion event
HIV-PRKCH 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
chr14
Cytoband
q23.1
Reference genome
GRCh37/hg19
Start
61855753/61389035 (Hg38)
End
61855753/61389035 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA14B
Target gene
PRKCH
miRNAs that regulate target gene
hsa-mir-376c-3p
;
hsa-mir-432-5p
;
hsa-mir-376a-3p
;
hsa-mir-493-3p
;
hsa-mir-4531
;
hsa-mir-6783-3p
;
hsa-mir-1343-3p
;
hsa-mir-5703
;
hsa-mir-4516
;
hsa-mir-4434
;
hsa-mir-26a-2-3p
;
hsa-mir-26a-1-3p
;
hsa-mir-6731-3p
;
hsa-mir-4254
;
hsa-mir-3690
;
hsa-mir-3938
;
hsa-mir-3675-3p
;
hsa-mir-216b-5p
;
hsa-mir-24-3p
Nearest miRNA
hsa-mir-208a/Upstream/740324; hsa-mir-1185-1/Downstream/2705989;
Nearest TSS
ENST00000550708/Upstream/27961;
ENST00000557473/Downstream/1659;
Nearest CpG islands
None/Target,
chr14-CpG: 35/Upstream/66286
,
chr14-CpG: 112/Downstream/306094
Upstream sequence
GAATCTGAACAAAGCAGGCATCTTTTATTTTGAAAAAGTATATAATCAGGGTGTGGTGGTGACCTAGGGTAAGTCCAGTGCATTTTTGGGGGCTTTGTCA
Downstream sequence
TGGGTAGATACAATAAATTTTAAAAAAGTAAACAGTACTGTTAAGAATCTTTGAGATTggctgggcatggtggctctcgcctgtaatcccagcactctgg
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
Active CD4+
Sample type
Cell line
Gender
Female
CpG Island Information
×
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