Basic Information
VIS ID
TVIS30009298
Fusion event
HIV-NUDCD3 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
chr7
Cytoband
p13
Reference genome
GRCh37/hg19
Start
44475904/44436305 (Hg38)
End
44475904/44436305 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA7D
Target gene
NUDCD3
miRNAs that regulate target gene
hsa-mir-7-5p ; hsa-mir-324-3p ; hsa-mir-149-5p ; hsa-mir-92a-3p ; hsa-mir-1225-3p ; hsa-mir-5695 ; hsa-mir-3943 ; hsa-mir-6888-3p ; hsa-mir-3120-5p ; hsa-mir-371a-5p ; hsa-mir-3613-3p ; hsa-mir-3664-5p ; hsa-mir-5582-3p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p ; hsa-mir-3662 ; hsa-mir-1251-3p ; hsa-mir-208a-5p ; hsa-mir-208b-5p ; hsa-mir-28-5p ; hsa-mir-3139 ; hsa-mir-4487 ; hsa-mir-6128 ; hsa-mir-6505-5p ; hsa-mir-6516-5p ; hsa-mir-708-5p
Nearest miRNA
hsa-mir-1183/Upstream/325393; hsa-mir-10399/Downstream/445443;
Nearest TSS
ENST00000635602/Upstream/8664; ENST00000419661/Downstream/35655;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/110587, chr7-CpG: 73/Downstream/53806
Upstream sequence
taaatttaagtccttatttcttattgaagtatttacgggtgaaattacatgatgtctgggatttgttctatcaaaaacaaaaccaaaagtctgagagtag
Downstream sequence
ggagaaagatgaaacaacaaccatgtcgtgttgctaagtgatgaagcagggtgaaagtttcgtgggcgttcattatgctattccctcctttttgtgtact
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate