Basic Information
VIS ID
TVIS30007040
Fusion event
HIV-EFCAB5 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
q11.2
Reference genome
GRCh37/hg19
Start
28323743/29996725 (Hg38)
End
28323743/29996725 (Hg38)
Orient
+
Location type
Intronic
Target gene
EFCAB5
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-1273e ; hsa-mir-6807-5p ; hsa-mir-561-5p ; hsa-mir-6894-5p ; hsa-mir-7106-5p ; hsa-mir-1233-3p ; hsa-mir-3922-5p ; hsa-mir-1225-3p
Nearest miRNA
hsa-mir-1180/Upstream/605995; hsa-mir-10226/Downstream/120354;
Nearest TSS
ENST00000595228/Upstream/27519; ENST00000584826/Downstream/35038;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/66335, chr17-CpG: 27/Downstream/120003
Upstream sequence
cttacatacatagaattttaaaagaaagatatgatgtcataactgtgatgtaaacgagaaataaaagtaaagGCATAAGAAAACTATATGCACTGGCTAG
Downstream sequence
GCATGGTGGCTCACGCTAATATTTACCAGAGTTGAACACTGCCTCCGTAAATTCCTTAGTTTGAATTTCCTTGACTCTACCCAGTCTTATATCCTACACC
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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