Basic Information
VIS ID
TVIS30010816
Fusion event
HIV-SNX4 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
q21.2
Reference genome
GRCh37/hg19
Start
125213981/125495137 (Hg38)
End
125213981/125495137 (Hg38)
Orient
-
Location type
Intronic
Target gene
SNX4
miRNAs that regulate target gene
hsa-mir-125a-5p ; hsa-mir-10a-5p ; hsa-mir-100-5p ; hsa-mir-218-5p ; hsa-mir-4659b-5p ; hsa-mir-4659a-5p ; hsa-mir-3144-3p ; hsa-mir-4732-5p ; hsa-mir-6832-5p ; hsa-mir-548v ; hsa-mir-187-5p ; hsa-mir-203a-3p ; hsa-mir-345-3p ; hsa-mir-511-3p ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-10b-5p ; hsa-mir-504-5p ; hsa-mir-222-3p ; hsa-mir-221-3p ; hsa-mir-3658 ; hsa-mir-580-3p ; hsa-mir-3653-3p ; hsa-mir-6086 ; hsa-mir-377-5p ; hsa-mir-655-5p ; hsa-mir-7162-3p ; hsa-mir-32-3p ; hsa-mir-944 ; hsa-mir-6507-5p ; hsa-mir-513c-3p ; hsa-mir-513a-3p ; hsa-mir-3606-3p
Nearest miRNA
hsa-let-7g/Upstream/343585; hsa-mir-12124/Downstream/295267;
Nearest TSS
ENST00000440867/Upstream/34336; ENST00000610060/Downstream/9607;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/119616, chr3-CpG: 59/Downstream/24515
Upstream sequence
atttgtctgaatacctataataaaattaatgggtctgctacaggaagaccaaagtatagtagtaaagtatagcaggaagccatgttacatccccttgaac
Downstream sequence
atctcagaagtcagttttgcttaagtcccagctttcaactgtgatcagattagctgtaactgccaaacatatgacctccagataagtgaaatgtGATACA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate