Basic Information
VIS ID
TVIS30001846
Fusion event
HIV-BDNF-AS 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
chr11
Cytoband
p14.1
Reference genome
GRCh37/hg19
Start
27544590/27523043 (Hg38)
End
27544590/27523043 (Hg38)
Orient
+
Location type
ncRNA_intronic
Target gene
BDNF-AS
miRNAs that regulate target gene
hsa-mir-3942-3p ; hsa-mir-27b-3p ; hsa-mir-27a-3p ; hsa-mir-513a-5p ; hsa-mir-589-3p ; hsa-mir-6500-3p ; hsa-mir-3614-5p ; hsa-mir-205-3p ; hsa-mir-4519 ; hsa-mir-6887-5p ; hsa-mir-6795-5p ; hsa-mir-6870-5p ; hsa-mir-7111-5p ; hsa-mir-5698 ; hsa-mir-4723-5p ; hsa-mir-625-5p ; hsa-mir-6825-5p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-6739-5p ; hsa-mir-3153 ; hsa-mir-6733-5p ; hsa-mir-4784 ; hsa-mir-3150b-3p ; hsa-mir-4786-5p ; hsa-mir-6794-5p ; hsa-mir-4716-3p ; hsa-mir-186-5p
Nearest miRNA
hsa-mir-210/Upstream/7996; hsa-let-7a-2/Downstream/533772;
Nearest TSS
ENST00000527297/Upstream/16191; ENST00000530313/Downstream/111479;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/16073, chr11-CpG: 80/Downstream/177071
Upstream sequence
ttttcttatcttctttataacaaaacttcttcaaagtattgttcatacttgtagtatccatttctgctctcttactctctcttcaataactctaagtaga
Downstream sequence
cttttatctacaccactccaccaaaacaaccccgtcagcatctccagtgacttccacgttgtcaaagcgaattgtcagttttcagtccttatctcactcg
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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