Basic Information
VIS ID
TVIS30009682
Fusion event
HIV-RFX3 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
chr9
Cytoband
p24.2
Reference genome
GRCh37/hg19
Start
3367838/3367838 (Hg38)
End
3367838/3367838 (Hg38)
Orient
+
Location type
Intronic
Target gene
RFX3
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-148b-3p ; hsa-mir-128-3p ; hsa-mir-615-3p ; hsa-mir-342-3p ; hsa-mir-4698 ; hsa-mir-892c-5p ; hsa-mir-4428 ; hsa-mir-3646 ; hsa-mir-3662 ; hsa-mir-1264 ; hsa-mir-4668-5p ; hsa-mir-6738-3p ; hsa-mir-544a ; hsa-mir-3977 ; hsa-mir-6071 ; hsa-mir-6828-3p ; hsa-mir-222-5p
Nearest miRNA
hsa-mir-1302-9/Upstream/3337557; hsa-let-7a-1/Downstream/1482459;
Nearest TSS
ENST00000422679/Upstream/21074; ENST00000430387/Downstream/27750;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/185971, chr9-CpG: 89/Downstream/158183
Upstream sequence
ACCTAAATCCTTAATTTCCTGCTAAATGTTAAGGCTTTGGTGAAATACAAGGATAATTCTTCCTCAAAAAGTTCGAATAGTTAAGTTACAAGCAAATTGA
Downstream sequence
AAACTAAAAATATCAAAGGACAAGACGAAATCTCAAAGTCAATGAGTAAAGTATCACATGAAAATTTAGGAGAATGCTATCATCAATCCCTAGAATTGAA
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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