Basic Information
VIS ID
TVIS30009093
Fusion event
HIV-COL12A1 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
q13
Reference genome
GRCh37/hg19
Start
75898559/75188843 (Hg38)
End
75898559/75188843 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA6D
Target gene
COL12A1
miRNAs that regulate target gene
hsa-mir-375 ; hsa-mir-9-5p ; hsa-mir-124-3p ; hsa-mir-1-3p ; hsa-mir-26b-5p ; hsa-mir-6516-5p ; hsa-mir-455-3p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-5004-5p ; hsa-mir-935 ; hsa-mir-4712-3p ; hsa-mir-1252-3p ; hsa-mir-548as-3p ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-605-3p ; hsa-mir-545-3p ; hsa-mir-5582-5p ; hsa-mir-548p ; hsa-mir-3120-3p ; hsa-mir-8485 ; hsa-mir-3202 ; hsa-mir-4533 ; hsa-mir-6079 ; hsa-mir-551b-5p
Nearest miRNA
hsa-mir-10398/Upstream/2221090; hsa-mir-10524/Downstream/239564;
Nearest TSS
ENST00000381078/Upstream/379; ENST00000607221/Downstream/13949;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/103471, chr6-CpG: 43/Downstream/13020
Upstream sequence
AAAGAGGAAAAAAGTGGTTGGTTAAACAGAGTGGGCTTTCATCCCAACCATACCATCGTATGTCTTTGCCATCTGTAAAGATAATACTTTTTTCTTCCAG
Downstream sequence
AGTCCTCAATAAGCTGGAGCCCTCTGAATTCTTCAAGTATTACATAATATAGGAAACACATAAAAAACACTTAATGATAATACAAGGAGGATCTTTATTA
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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