Basic Information
VIS ID
TVIS30010497
Fusion event
HIV-CDK12 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
chr17
Cytoband
q12
Reference genome
GRCh37/hg19
Start
37689239/39532986 (Hg38)
End
37689239/39532986 (Hg38)
Orient
-
Location type
UTR3
Target gene
CDK12
miRNAs that regulate target gene
hsa-mir-744-5p ; hsa-mir-503-5p ; hsa-mir-193b-3p ; hsa-mir-193a-3p ; hsa-mir-10b-5p ; hsa-mir-4443 ; hsa-mir-6515-5p ; hsa-mir-9-5p ; hsa-mir-130b-5p ; hsa-mir-4762-5p ; hsa-mir-216b-5p ; hsa-mir-548t-3p ; hsa-mir-548ap-3p ; hsa-mir-548aa ; hsa-mir-4753-3p ; hsa-mir-6894-5p ; hsa-mir-765 ; hsa-mir-7154-3p ; hsa-mir-766-5p ; hsa-mir-3613-3p ; hsa-mir-3617-3p ; hsa-mir-4311 ; hsa-mir-4524a-3p ; hsa-mir-545-3p ; hsa-mir-548p
Nearest miRNA
hsa-mir-1180/Upstream/235477; hsa-mir-10226/Downstream/193509;
Nearest TSS
ENST00000595228/Upstream/3104; ENST00000581963/Downstream/11005;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/71194, chr17-CpG: 51/Downstream/40472
Upstream sequence
ATGTCATATAATTTATCTGCACAGACTTAGACCTTCAGGAAACATAGGTTAAGCCCCCTTTTACAAAGAAAAAGTAAACATACTTCAGCATCTTGGAGGG
Downstream sequence
TAGTTTTCAAAACTCAAGTTTCATGTTTCAATGCCAAGTTCTTATTTTAAAAAATAAAATCTACTTATAAGAGAAAGGTGCATTACTTAAAAAAAAAAAA
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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