Basic Information
VIS ID
TVIS30013822
Fusion event
HIV-SHROOM4 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
chrX
Cytoband
p11.22
Reference genome
GRCh37/hg19
Start
50547980/50804980 (Hg38)
End
50547980/50804980 (Hg38)
Orient
-
Location type
Intronic
Target gene
SHROOM4
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-5096 ; hsa-mir-4662a-5p ; hsa-mir-3152-3p ; hsa-mir-6832-5p ; hsa-mir-296-3p ; hsa-mir-2392 ; hsa-mir-4676-5p ; hsa-mir-575 ; hsa-mir-6858-3p ; hsa-mir-6778-3p ; hsa-mir-4661-5p ; hsa-mir-122-3p ; hsa-mir-1976 ; hsa-mir-3653-5p ; hsa-mir-4722-3p ; hsa-mir-6727-3p ; hsa-mir-6747-3p ; hsa-mir-6783-3p ; hsa-mir-1343-3p ; hsa-mir-23b-5p ; hsa-mir-23a-5p ; hsa-mir-6742-3p ; hsa-mir-6852-5p ; hsa-mir-939-3p ; hsa-mir-660-3p ; hsa-mir-4279 ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-6875-3p ; hsa-mir-6891-3p ; hsa-mir-6072 ; hsa-mir-5196-3p ; hsa-mir-6729-3p ; hsa-mir-1306-5p
Nearest miRNA
hsa-mir-1587/Upstream/790297; hsa-let-7f-2/Downstream/1531577;
Nearest TSS
ENST00000429181/Upstream/109043; ENST00000252677/Downstream/9064;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/333996, chrX-CpG: 65/Downstream/8279
Upstream sequence
CTTTTGCTTGTTGTCTTGATCCTTCCTGATCGCCAATTTAAGTTAATACAGAGCTCCAAACTCTTGTCAAATCCTCTACAGAATGTGAGAGTCAAGCCTG
Downstream sequence
ATACTTACCCCCTGAAGCTTCAAGATGTCATCACTCACACTCTCAGTCAGAGTAAGATGCCATCCAAAGCTGCCTACCTGTAGAATTTTTCAGGGTGGCT
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate