Basic Information
VIS ID
TVIS30002342
Fusion event
HIV-SMAD3 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
chr15
Cytoband
q22.33
Reference genome
GRCh37/hg19
Start
67388647/67096309 (Hg38)
End
67388647/67096309 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA15A
Target gene
SMAD3
miRNAs that regulate target gene
hsa-mir-200a-3p ; hsa-mir-18a-5p ; hsa-mir-335-5p ; hsa-mir-155-5p ; hsa-mir-193b-3p ; hsa-mir-17-5p ; hsa-mir-143-3p ; hsa-mir-145-5p ; hsa-mir-3529-3p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-497-5p ; hsa-mir-142-5p ; hsa-mir-491-5p ; hsa-mir-92b-3p ; hsa-mir-4290 ; hsa-mir-18a-3p ; hsa-mir-323a-3p ; hsa-mir-708-5p ; hsa-mir-199a-5p ; hsa-mir-145-3p ; hsa-mir-590-5p ; hsa-mir-23a-3p ; hsa-mir-23b-5p ; hsa-mir-424-5p ; hsa-mir-29b-1-5p
Nearest miRNA
hsa-mir-10393/Upstream/599275; hsa-mir-11181/Downstream/1705541;
Nearest TSS
ENST00000557528/Upstream/18323; ENST00000559092/Downstream/2273;
Nearest CpG islands
None/Target, chr15-CpG: 55/Upstream/29885, chr15-CpG: 62/Downstream/158142
Upstream sequence
gaagggaaaggaaagatagggcacccatattgccttttcctttcagatcttccttactcctcaggcagcataaagagtgaggtagaatggacacatagcg
Downstream sequence
agaagtgaagtaaaaacgattgagttagctttatggatgtttctctggttctggtacatcacaaaatgcacatccaagtcctaaaatacaattcatgtaa
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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