Basic Information
VIS ID
TVIS30006922
Fusion event
HIV-RFWD3 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
q23.1
Reference genome
GRCh37/hg19
Start
74686158/74652260 (Hg38)
End
74686158/74652260 (Hg38)
Orient
+
Location type
Intronic
Target gene
RFWD3
miRNAs that regulate target gene
hsa-mir-340-5p ; hsa-mir-124-3p ; hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-484 ; hsa-mir-339-5p ; hsa-mir-125b-5p ; hsa-let-7c-5p ; hsa-mir-218-5p ; hsa-mir-3151-5p ; hsa-mir-4504 ; hsa-mir-6769b-5p ; hsa-mir-6769a-5p ; hsa-mir-92a-2-5p ; hsa-mir-654-5p ; hsa-mir-541-3p ; hsa-mir-486-3p ; hsa-mir-5583-3p ; hsa-mir-6881-3p ; hsa-mir-3713 ; hsa-mir-492 ; hsa-mir-877-3p ; hsa-mir-1290 ; hsa-mir-876-5p ; hsa-mir-3167 ; hsa-mir-3116 ; hsa-mir-1254 ; hsa-mir-219b-5p ; hsa-mir-6839-5p ; hsa-mir-378j ; hsa-mir-8066
Nearest miRNA
hsa-mir-1225/Upstream/4621838; hsa-mir-11401/Downstream/2216676;
Nearest TSS
ENST00000527434/Upstream/3017; ENST00000568511/Downstream/14277;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/44961, chr16-CpG: 63/Downstream/14147
Upstream sequence
AACTATCATCACAAAAACAATCTATAGTGATTTGAAGTAAATCCTATCACTTCAACCCATCTCCAGGCCATTAAATGCTGCCTTTGAAAGCTGAAGCAGG
Downstream sequence
TATAGCAGATAAGGGGGGGAGACTGGCCTCCTAGATATTATTTTTTACCACTCAACCACTGCTACATTAGCCCACAAAGGAGCTTGATCCTTCCGTTAAA
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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