Basic Information
VIS ID
TVIS30006174
Fusion event
HIV-chr12 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
chr12
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
56411713/56017929 (Hg38)
End
56411713/56017929 (Hg38)
Orient
+
Location type
Intronic
Target gene
IKZF4 ; LOC105369781
miRNAs that regulate target gene
hsa-mir-130b-3p ; hsa-mir-93-5p ; hsa-mir-30b-5p ; hsa-mir-30c-5p ; hsa-mir-32-5p ; hsa-mir-16-5p ; hsa-mir-125b-5p ; hsa-mir-190a-3p ; hsa-mir-656-3p ; hsa-mir-3924 ; hsa-mir-5011-5p ; hsa-mir-1277-5p ; hsa-mir-548c-3p ; hsa-mir-3920 ; hsa-mir-4801 ; hsa-mir-4731-3p ; hsa-mir-4762-3p ; hsa-mir-3192-3p ; hsa-mir-29a-5p
Nearest miRNA
hsa-mir-1244-3/Upstream/1680615; hsa-let-7i/Downstream/1176575;
Nearest TSS
ENST00000382841/Upstream/6371; ENST00000547668/Downstream/1391;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/9893, chr12-CpG: 58/Downstream/23860
Nearby gene
IKZF4(No orient, 2976)
Upstream sequence
caggcacatgccacgatgcctaatttatttttatattttgtagagatgggatctccctatattgcccaggctggtctcaaactcctgggctcgagtgatc
Downstream sequence
ctcccaccttctttccaaagcactaggattacaggtgttgagccacagtgcctggcTAAGGTTTTTCTTCTTTAGGATAGTATCAGACCATGCTTAAGTG
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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