Basic Information
VIS ID
TVIS30002113
Fusion event
HIV-GATC 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
q24.31
Reference genome
GRCh37/hg19
Start
120891736/120453933 (Hg38)
End
120891736/120453933 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA12E ; FRA12C
Target gene
GATC
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-let-7b-5p ; hsa-mir-4279 ; hsa-mir-6778-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-6827-3p ; hsa-mir-340-3p ; hsa-mir-4532 ; hsa-mir-1247-3p ; hsa-mir-4740-3p ; hsa-mir-122-3p
Nearest miRNA
hsa-let-7i/Upstream/298434; hsa-mir-3612/Downstream/269260;
Nearest TSS
ENST00000382841/Upstream/7356; ENST00000549649/Downstream/9463;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/7033, chr12-CpG: 121/Downstream/14942
Upstream sequence
aacaacaacaacaacaacaacaaAAAACCAACCCCAGAAAATGTGTCTATTTTAGGAACAACTCCATCATAACCAATAACTAAATAGAAATGTATGTATG
Downstream sequence
TATGTACATACATACATAAATAGAAAGGTATGTAAAGGGGTGAATTTTGTTTTCCTGGAAATTTCACTTACGCAGGAAACTTAATTATGAAACTTGATTA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate