Basic Information
VIS ID
TVIS30009584
Fusion event
HIV-SDC2 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
chr8
Cytoband
q22.1
Reference genome
GRCh37/hg19
Start
97510804/96498576 (Hg38)
End
97510804/96498576 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA8B
Target gene
SDC2
miRNAs that regulate target gene
hsa-mir-3202 ; hsa-mir-2467-3p ; hsa-mir-3616-3p ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-3179 ; hsa-mir-6847-5p ; hsa-mir-7843-5p ; hsa-mir-6879-5p ; hsa-mir-6735-5p ; hsa-mir-4632-5p ; hsa-mir-4436b-3p ; hsa-mir-6876-5p ; hsa-mir-4476 ; hsa-mir-577 ; hsa-mir-6859-5p ; hsa-mir-3916 ; hsa-mir-3125 ; hsa-mir-7-2-3p ; hsa-mir-7-1-3p ; hsa-mir-5688 ; hsa-mir-495-3p
Nearest miRNA
hsa-mir-12123/Upstream/1425580; hsa-mir-10400/Downstream/1895069;
Nearest TSS
ENST00000518652/Upstream/4568; ENST00000521590/Downstream/81773;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/3197, chr8-CpG: 67/Downstream/146370
Upstream sequence
ttttttcctcttgagatggagtctcactctgtcacccaggctggagtacaatggcactctgcaaccaccacctcactgcagccacctcactgcaaccacc
Downstream sequence
acctcccaggttcaagcgattctcctgcctcagcctcccgagtagctgggactacaggcacatgccactgcacctggctaaattttgtatttttagtagg
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate