Basic Information
VIS ID
TVIS30006955
Fusion event
HIV-SMYD4 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
p13.3
Reference genome
GRCh37/hg19
Start
1700665/1797371 (Hg38)
End
1700665/1797371 (Hg38)
Orient
-
Location type
Intronic
Target gene
SMYD4
miRNAs that regulate target gene
hsa-mir-744-5p ; hsa-mir-6749-3p ; hsa-mir-6792-3p ; hsa-mir-4691-5p ; hsa-mir-4284 ; hsa-mir-4634 ; hsa-mir-2276-3p ; hsa-mir-1236-3p ; hsa-mir-4638-5p ; hsa-mir-1307-3p ; hsa-mir-1304-3p ; hsa-mir-6741-3p ; hsa-mir-6890-3p ; hsa-mir-6796-3p ; hsa-mir-122-5p ; hsa-mir-143-5p ; hsa-mir-199a-3p ; hsa-mir-199b-3p ; hsa-mir-215-3p ; hsa-mir-24-3p ; hsa-mir-3129-5p ; hsa-mir-3135b ; hsa-mir-3652 ; hsa-mir-3664-5p ; hsa-mir-4430 ; hsa-mir-4714-5p ; hsa-mir-500b-3p ; hsa-mir-504-3p ; hsa-mir-514a-5p ; hsa-mir-550b-3p ; hsa-mir-6773-3p ; hsa-mir-6879-3p ; hsa-mir-8057
Nearest miRNA
hsa-mir-22/Upstream/83384; hsa-mir-10226/Downstream/252537;
Nearest TSS
ENST00000595228/Upstream/13508; ENST00000571725/Downstream/3434;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/42988, chr17-CpG: 75/Downstream/32220
Nearest cancer related gene
SMYD4(TSG, No orient, 0)
Upstream sequence
CTCAAGAGAGTTAATTGAAAAAATTAAGAAAAGTATAATGAACGGATTGAGTCAAAAAACATTTTCTGCTAAAATGAAGATCATAAAATAGAAAGACTAC
Downstream sequence
AAATGCCACTTTTCTAATAATAGTTGTATCTGTTGTCAGCACAGTCACACTGGAGATGTCAAGCTGGATCATGATTCTCGGCACATCCAACCTTCCCATC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate