Basic Information
VIS ID
TVIS30011184
Fusion event
HIV-KDM1A 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
chr1
Cytoband
p36.12
Reference genome
GRCh37/hg19
Start
23369721/23043228 (Hg38)
End
23369721/23043228 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
KDM1A
miRNAs that regulate target gene
hsa-mir-137 ; hsa-mir-155-5p ; hsa-mir-500a-5p ; hsa-mir-23b-3p ; hsa-mir-329-3p ; hsa-mir-708-5p
Nearest miRNA
hsa-mir-12136/Upstream/180002; hsa-mir-101-1/Downstream/1077;
Nearest TSS
ENST00000473358/Upstream/23735; ENST00000481879/Downstream/7197;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/23044, chr1-CpG: 92/Downstream/124518
Upstream sequence
AATGTAGGACCTATATTTTCAAGATAAGTTTGCAGATTGGATTTAGTAACCCGATCGTCTCTTCATGATTGTATGCCTTTTTCCAAGGGCTGTAAATAGG
Downstream sequence
TATACCTTGGGCCTTGTCTGAGAAGCATAACCTTCTTGAACCTAAAGGACCCTTCAGACGAGAGCTTAGTAAAATAAGTTTAGAATGAGATTCTATTCTA
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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