Basic Information
VIS ID
TVIS30008611
Fusion event
HIV-FAM13A 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
chr4
Cytoband
q22.1
Reference genome
GRCh37/hg19
Start
89741779/88820628 (Hg38)
End
89741779/88820628 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA4E
Target gene
FAM13A
miRNAs that regulate target gene
hsa-mir-615-3p ; hsa-mir-10b-5p ; hsa-mir-4291 ; hsa-mir-4777-3p ; hsa-mir-558 ; hsa-mir-545-3p ; hsa-mir-3908 ; hsa-mir-4446-5p ; hsa-mir-3679-3p ; hsa-mir-302c-5p ; hsa-mir-2355-5p ; hsa-mir-3143 ; hsa-mir-4262 ; hsa-mir-181d-5p ; hsa-mir-181c-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p ; hsa-mir-543 ; hsa-mir-5047 ; hsa-mir-6721-5p ; hsa-mir-1301-3p ; hsa-mir-2115-5p ; hsa-mir-4660
Nearest miRNA
hsa-mir-12113/Upstream/1520045; hsa-mir-1243/Downstream/10176759;
Nearest TSS
ENST00000502981/Upstream/52214; ENST00000603357/Downstream/2573;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/122725, chr4-CpG: 126/Downstream/290125
Upstream sequence
TGAAAAAATCCTCACATAAGGTCAGATATTAAATATGCTATTTGGAGATGTTGAGTAGTATAATGCTAGATTCCTATATATGCCAGCTGTCACTAGCTTT
Downstream sequence
ATAAGCGCTATAATCATTAACTAGAATTTAGATCAGTGTTTCTCTACGAGTGGACCATCtgcattagatttaggaagcttgttaaaatgcagatgctctc
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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