Basic Information
VIS ID
TVIS30010889
Fusion event
HIV-LYSMD3 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
chr5
Cytoband
q14.3
Reference genome
GRCh37/hg19
Start
89814936/90519119 (Hg38)
End
89814936/90519119 (Hg38)
Orient
+
Location type
Exonic
Target gene
LYSMD3
miRNAs that regulate target gene
hsa-mir-340-5p ; hsa-mir-128-3p ; hsa-mir-124-3p ; hsa-mir-181a-5p ; hsa-mir-192-5p ; hsa-mir-101-3p ; hsa-mir-27a-3p ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-93-5p ; hsa-mir-106b-5p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-410-3p ; hsa-mir-205-5p ; hsa-mir-384 ; hsa-mir-3685 ; hsa-mir-374a-3p ; hsa-mir-5009-3p ; hsa-mir-3908 ; hsa-mir-3120-3p ; hsa-mir-944 ; hsa-mir-580-5p ; hsa-mir-651-3p ; hsa-mir-27b-3p ; hsa-mir-216a-3p ; hsa-mir-3681-3p ; hsa-mir-144-3p ; hsa-mir-502-3p ; hsa-mir-501-3p ; hsa-mir-5583-3p ; hsa-mir-4517 ; hsa-mir-380-3p ; hsa-mir-3910 ; hsa-mir-3714 ; hsa-mir-4422 ; hsa-mir-6835-3p ; hsa-mir-506-3p
Nearest miRNA
hsa-mir-10397/Upstream/502399; hsa-mir-103a-1/Downstream/3101577;
Nearest TSS
ENST00000502646/Upstream/44224; ENST00000508842/Downstream/10225;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/44080, chr5-CpG: 50/Downstream/10180
Upstream sequence
ATAATACAACAAATAAAACACTGGTGTTATTATACCTACTATCAACATTATCACTACAGCTGTCCACCACCCTATTCCCCAGTCTGCTCCATAATAGGGG
Downstream sequence
TCTTTACGTTGAGTGTTTTTGTTATCAGGTTCAAAACGCATTTGTTGTGCTGTTAAGGCCGATACTACCTCATTGAGGTTCTCTCTCTTATTGTCTGTAC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate