Basic Information
VIS ID
TVIS30006877
Fusion event
HIV-NLRC5 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
chr16
Cytoband
q13
Reference genome
GRCh37/hg19
Start
57042433/57008521 (Hg38)
End
57042433/57008521 (Hg38)
Orient
+
Location type
Intronic
Target gene
NLRC5
miRNAs that regulate target gene
hsa-mir-218-5p ; hsa-mir-216b-5p ; hsa-mir-6811-5p ; hsa-mir-6511b-5p ; hsa-mir-452-3p ; hsa-mir-6504-5p ; hsa-mir-4736 ; hsa-mir-3064-5p ; hsa-mir-664a-5p ; hsa-mir-4794 ; hsa-mir-17-3p ; hsa-mir-1205 ; hsa-mir-1184 ; hsa-mir-3158-5p ; hsa-mir-4692 ; hsa-mir-4514 ; hsa-mir-3126-3p ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-149-5p ; hsa-mir-34a-5p
Nearest miRNA
hsa-mir-1225/Upstream/104168; hsa-mir-11401/Downstream/763768;
Nearest TSS
ENST00000527434/Upstream/4035; ENST00000536231/Downstream/8553;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/18665, chr16-CpG: 133/Downstream/83611
Nearby gene
NLRC5(No orient, 8553)
Upstream sequence
tcatctagactttattttgatataattgtgaaatagaaatccatttttattctAAAAGAACActttttaaatgttcatgaaatgttttaaaatttattat
Downstream sequence
ataccaagcaagaaaaaatctcaacatagtcctcaaagcagaaattgcacaggacttattctttgtacagtgtaatgcacaaaaactaataagaaaGCCT
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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