Basic Information
VIS ID
TVIS30004862
Fusion event
HIV-SMARCC1 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
chr3
Cytoband
p21.31
Reference genome
GRCh37/hg19
Start
47653807/47612317 (Hg38)
End
47653807/47612317 (Hg38)
Orient
+
Location type
Intronic
Target gene
SMARCC1
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-34a-5p ; hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-mir-29b-3p ; hsa-let-7f-5p ; hsa-let-7c-5p ; hsa-mir-320c ; hsa-mir-544a ; hsa-mir-6738-3p ; hsa-mir-570-3p ; hsa-mir-4793-3p ; hsa-mir-3130-3p ; hsa-mir-3140-5p ; hsa-mir-4705 ; hsa-mir-34b-3p
Nearest miRNA
hsa-mir-12127/Upstream/2750336; hsa-let-7g/Downstream/237238;
Nearest TSS
ENST00000440867/Upstream/1519; ENST00000472718/Downstream/66048;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/32676, chr3-CpG: 109/Downstream/169114
Nearest cancer related gene
SMARCC1(TSG, No orient, 0)
Upstream sequence
AAGGTGGGGTGGGAAATCTAAATATTCTGGCTACAGATCCTTGGTTTTGCTTTCTTCTAATCATTCTTTCTAGGAATTTAGGACTCTGAATTTGCTTAAG
Downstream sequence
AGGTGGCCAGAAAACATCCTCTTATCTGTTTTTGTTGAGTGACTACTGGTCTGAACAGCTTGGCTGTAGTCCTACTGTTATGTAAGAACTATGGAATTTA
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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