Basic Information
VIS ID
TVIS30002875
Fusion event
HIV-SMCHD1 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
chr18
Cytoband
p11.32
Reference genome
GRCh37/hg19
Start
2658672/2658673 (Hg38)
End
2658672/2658673 (Hg38)
Orient
-
Location type
Intronic
Target gene
SMCHD1
miRNAs that regulate target gene
hsa-mir-210-3p ; hsa-mir-132-3p ; hsa-mir-128-3p ; hsa-mir-181a-5p ; hsa-mir-877-5p ; hsa-mir-421 ; hsa-mir-149-5p ; hsa-mir-221-3p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-100-5p ; hsa-mir-30a-5p ; hsa-mir-18a-5p ; hsa-mir-6768-5p ; hsa-mir-1277-5p ; hsa-mir-4789-5p ; hsa-mir-3941 ; hsa-mir-5011-5p ; hsa-mir-603 ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-1264 ; hsa-mir-3184-3p ; hsa-mir-510-3p ; hsa-mir-203a-3p ; hsa-mir-190a-3p
Nearest miRNA
hsa-mir-8078/Upstream/2546334; hsa-mir-1-2/Downstream/1226680;
Nearest TSS
ENST00000575820/Upstream/2935; ENST00000581226/Downstream/29968;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/1855, chr18-CpG: 150/Downstream/187894
Nearest cancer related gene
SMCHD1(TSG, No orient, 0)
Upstream sequence
TTAGAAATGAGAGGGACCAACTAGTAAGAAAAAAGAAGGCTGAGAAGGCTAACTTTTTTGTTGTTAGACTTCTTTTAAGCATTATTAGATTGTGCCTCGG
Downstream sequence
ATCCCATAACTttgtctccattacgtactcgaagaactgaattaagtcagtgaattaataatctgagattacatggtcaacaagcagtgaaactgggatt
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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