Basic Information
VIS ID
TVIS30012355
Fusion event
HIV-RNFT1 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
chr17
Cytoband
q23.1
Reference genome
GRCh37/hg19
Start
58029782/59952421 (Hg38)
End
58029782/59952421 (Hg38)
Orient
-
Location type
UTR3
Target gene
RNFT1
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-889-3p ; hsa-mir-4451 ; hsa-mir-202-3p ; hsa-mir-6831-5p ; hsa-mir-3927-3p ; hsa-mir-6858-3p ; hsa-mir-4517 ; hsa-mir-5583-3p ; hsa-mir-561-3p ; hsa-mir-98-5p ; hsa-let-7a-5p ; hsa-let-7c-5p ; hsa-let-7d-5p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-let-7g-5p ; hsa-let-7i-5p ; hsa-let-7b-5p ; hsa-mir-4458 ; hsa-mir-4500
Nearest miRNA
hsa-mir-10226/Upstream/111084; hsa-mir-1250/Downstream/90604;
Nearest TSS
ENST00000595228/Upstream/4843; ENST00000593015/Downstream/6216;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/58761, chr17-CpG: 23/Downstream/12064
Upstream sequence
AGCTGATGGCAGGAAGAATTTATGACGTCCAGAGACAAAATGAATTTAAATCATTTATTTTCACTTATTACTAATCTTACTACAGAGAATAATACAATAC
Downstream sequence
TATAATGTATCATCCTCAGTAAATTAATCTTCACTTAGAAAATGTTACTGATAAAATACAACATTTAGAATTTTCATTTAAAAATACAAATTTTATGAAA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate