Basic Information
VIS ID
TVIS30003507
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
47740568/47699078 (Hg38)
End
47740568/47699078 (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/2837097; hsa-let-7g/Downstream/150477;
Nearest TSS
ENST00000440867/Upstream/20713; ENST00000472718/Downstream/2324;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/119437, chr3-CpG: 109/Downstream/82353
Nearest cancer related gene
SMARCC1(TSG, No orient, 0)
Upstream sequence
atgtggggaataaaattaacttcaacccttaattcataacatcctcaaaaacaactttaaattgggtcacagacctaactataaaagcagaaggcataag
Downstream sequence
ctttctacaagaaaacacagaaaaacacatttgcaacactaatataggcaaaaaatttcttaggacacaagaaAAGTTAAGAGCACCTGTCCTCCAAAAA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate