Basic Information
VIS ID
TVIS30013395
Fusion event
HIV-MDC1 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
chr6
Cytoband
p21.33
Reference genome
GRCh37/hg19
Start
30676062/30708285 (Hg38)
End
30676062/30708285 (Hg38)
Orient
+
Location type
Exonic
Fragile sites / regions
FRA6H
Target gene
MDC1
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-215-5p ; hsa-mir-877-3p ; hsa-mir-615-3p ; hsa-mir-18a-3p ; hsa-mir-505-3p ; hsa-mir-324-5p ; hsa-mir-361-5p ; hsa-mir-18a-5p ; hsa-mir-17-3p ; hsa-mir-335-3p ; hsa-mir-4474-3p ; hsa-mir-664b-3p ; hsa-mir-579-3p ; hsa-mir-5696 ; hsa-mir-6815-3p ; hsa-mir-2115-5p ; hsa-mir-627-3p ; hsa-mir-4729 ; hsa-mir-6866-3p ; hsa-mir-188-5p ; hsa-mir-605-5p ; hsa-mir-1253 ; hsa-mir-185-5p ; hsa-mir-3180-5p ; hsa-mir-33a-3p ; hsa-mir-411-5p ; hsa-mir-4306 ; hsa-mir-4307 ; hsa-mir-4644 ; hsa-mir-4768-3p ; hsa-mir-516a-3p ; hsa-mir-516b-3p ; hsa-mir-520a-5p ; hsa-mir-525-5p ; hsa-mir-665 ; hsa-mir-7162-5p
Nearest miRNA
hsa-mir-3143/Upstream/123868; hsa-mir-10398/Downstream/182598;
Nearest TSS
ENST00000381078/Upstream/600; ENST00000327892/Downstream/3629;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/17037, chr6-CpG: 52/Downstream/8774
Nearest cancer related gene
MDC1(TSG, No orient, 0)
Upstream sequence
TCTGTGTGAACTGGGCTCTCTGGATGTTGGTCTCCTGGTATTGCCCTAGGTGGAGACAGGCAAGGTCCATAGGCCTCAAGGTGCGTGTCAAAAGGCTGGG
Downstream sequence
TCTCAGAGTCCTCAGACTCTCTCAGACAGAATGGCTGTGTAGCCAGGACCTCCCATGGTTCATCTAGGGTACCTGgaaggggaggaaggaagagagagag
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate