Basic Information
VIS ID
TVIS30010707
Fusion event
HIV-RBM39 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
chr20
Cytoband
q11.22
Reference genome
GRCh37/hg19
Start
34323107/35735185 (Hg38)
End
34323107/35735185 (Hg38)
Orient
+
Location type
Intronic
Target gene
RBM39
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-484 ; hsa-mir-221-3p ; hsa-mir-26a-5p ; hsa-mir-22-3p ; hsa-mir-369-5p ; hsa-mir-382-5p
Nearest miRNA
hsa-mir-103a-2/Upstream/281088; hsa-mir-1-1/Downstream/2781378;
Nearest TSS
ENST00000382410/Upstream/2379; ENST00000617560/Downstream/1456;
Nearest CpG islands
None/Target, chr20-CpG: 39/Upstream/35406, chr20-CpG: 81/Downstream/6383
Upstream sequence
AAAATAAGAAAAAAAATAGAAAAGTCATTTATTCCAAAATTTATAGATAATCCACACCACAGTAGCCAATATATTTCAACTGTGTCATTTTAATGTTATC
Downstream sequence
TTTTATTGAGTAATTCTCTAAAGAGCTTAACGGAATGGACGCTGATTTAGACTTTGCAAAACTGGTTACTTTAACAAATAATATTCCCATGAGGGCAAGC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
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