Basic Information
VIS ID
TVIS30010112
Fusion event
HIV-CDC42BPA 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
chr1
Cytoband
q42.13
Reference genome
GRCh37/hg19
Start
227256544/227068843 (Hg38)
End
227256544/227068843 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1H
Target gene
CDC42BPA
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-98-5p ; hsa-let-7c-5p ; hsa-mir-485-5p ; hsa-mir-218-5p ; hsa-mir-4753-3p ; hsa-mir-6868-3p ; hsa-mir-1468-3p ; hsa-mir-3124-3p ; hsa-mir-130b-5p ; hsa-mir-8063 ; hsa-mir-6856-5p ; hsa-mir-6758-5p ; hsa-mir-216b-5p ; hsa-mir-4311
Nearest miRNA
hsa-mir-101-1/Upstream/1146701; hsa-mir-1182/Downstream/872747;
Nearest TSS
ENST00000473358/Upstream/34126; ENST00000424451/Downstream/5521;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/92307, chr1-CpG: 104/Downstream/248902
Upstream sequence
GAAGCAATTTAATAAGAATAATAAATCAAAAACTTTGTAAAACAATTGAAAGGCAAATGACATTAATTCAAATAAATAAATGAGAAAAGCAGTCACTATC
Downstream sequence
ATTGTTCTTGAGAAACTTAAGAGATTCATTAATTACTTTTTAAAGAGTGATTATTTTTCCTTTTCCTAAAGGAACGAAACACAATTCACATACTGTGCCC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate