Basic Information
VIS ID
TVIS30006128
Fusion event
HIV-SCAF11 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
chr12
Cytoband
q12
Reference genome
GRCh37/hg19
Start
46362211/45968428 (Hg38)
End
46362211/45968428 (Hg38)
Orient
-
Location type
Intronic
Target gene
SCAF11
miRNAs that regulate target gene
hsa-mir-29c-3p ; hsa-mir-124-3p ; hsa-mir-1-3p ; hsa-mir-21-5p ; hsa-mir-92b-3p ; hsa-mir-32-5p ; hsa-mir-92a-3p
Nearest miRNA
hsa-mir-1244-3/Upstream/3644569; hsa-let-7i/Downstream/1219384;
Nearest TSS
ENST00000382841/Upstream/19898; ENST00000550319/Downstream/22137;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/237756, chr12-CpG: 115/Downstream/21350
Upstream sequence
AATATCTTTTTAGTCTGTGACCCCTAATATAATGATCTAACATACTTCTATCGTCCAGTTGCTCTTTTCCATTTCATAACATATTGTTTCTGCTAGATAC
Downstream sequence
TGAAAGTGATACTCCAAATATGTTCATATAATAATTGGGGAAGAATGGTCTAAGTTTTAAATTTTATTTATCATATAAGAAGGTATTAAAGCTTGGaatt
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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