Basic Information
VIS ID
TVIS30012861
Fusion event
HIV-SAMHD1 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
chr20
Cytoband
q11.23
Reference genome
GRCh37/hg19
Start
35564272/36935869 (Hg38)
End
35564272/36935869 (Hg38)
Orient
-
Location type
Intronic
Target gene
SAMHD1
miRNAs that regulate target gene
hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-30a-5p ; hsa-mir-642a-5p ; hsa-mir-6868-3p ; hsa-mir-3667-3p ; hsa-mir-6734-3p ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6873-3p ; hsa-mir-627-3p ; hsa-mir-3124-3p ; hsa-mir-130b-5p ; hsa-mir-6817-3p ; hsa-mir-7110-3p ; hsa-mir-181a-5p ; hsa-mir-155-5p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4279 ; hsa-mir-4722-3p ; hsa-mir-4740-3p ; hsa-mir-498 ; hsa-mir-6727-3p ; hsa-mir-6747-3p ; hsa-mir-6778-3p
Nearest miRNA
hsa-mir-103a-2/Upstream/1481772; hsa-mir-1-1/Downstream/1580694;
Nearest TSS
ENST00000382410/Upstream/666; ENST00000598590/Downstream/10911;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/71467, chr20-CpG: 90/Downstream/15065
Upstream sequence
tatgttggccaggctggccgcgaactcctgacctcaagtgatccgcccacctcggcctcccaaagtgttgggattacaggcgtgagccaccgtgcccggc
Downstream sequence
cTAAATTTTTTTTTTTCTAAATGTATCTATACAGCACTCATCATTAAAACAGAAAAGAAAGAAGGGAGGCAGGGAAAGAAAGAAAGATGGAAATTCCTCT
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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