Basic Information
VIS ID
TVIS30003462
Fusion event
HIV-RAF1 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
chr3
Cytoband
p25.2
Reference genome
GRCh37/hg19
Start
12648730/12607231 (Hg38)
End
12648730/12607231 (Hg38)
Orient
-
Location type
Intronic
Target gene
RAF1
miRNAs that regulate target gene
hsa-mir-7-5p ; hsa-mir-125b-5p ; hsa-mir-195-5p ; hsa-mir-497-5p ; hsa-mir-186-5p ; hsa-mir-23b-3p ; hsa-mir-16-5p ; hsa-mir-4799-5p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-6516-3p ; hsa-mir-7111-3p ; hsa-mir-3682-5p ; hsa-mir-520f-5p ; hsa-mir-4291 ; hsa-mir-6789-5p ; hsa-mir-6077 ; hsa-mir-486-3p ; hsa-mir-4254 ; hsa-mir-4660 ; hsa-mir-3690 ; hsa-mir-6736-3p ; hsa-mir-7157-5p ; hsa-mir-4310 ; hsa-mir-6813-5p ; hsa-mir-6085 ; hsa-mir-6743-5p ; hsa-mir-4688 ; hsa-mir-3134 ; hsa-mir-8082 ; hsa-mir-4534 ; hsa-mir-19b-3p ; hsa-mir-19a-3p ; hsa-mir-132-3p ; hsa-mir-7-1-3p ; hsa-mir-125a-5p
Nearest miRNA
hsa-mir-12127/Upstream/2212669; hsa-let-7g/Downstream/2889008;
Nearest TSS
ENST00000440867/Upstream/3018; ENST00000626378/Downstream/1636;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/49679, chr3-CpG: 89/Downstream/56329
Nearest cancer related gene
RAF1(OG, No orient, 0)
Upstream sequence
GACTAAAATAGAAGGAATAAATCACAGAAAAGTGAGTAATTAGGCACCTTTTTTCCATGAGGTGggcacttgtgcttagtaatttcacaggttatgtcag
Downstream sequence
caagcctcataagaacaatgcaaggaaggtaatatcccctttattcagatgcatgaacgaaaactcagatgtggttatggttaatgacaacactgagatt
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate