Basic Information
VIS ID
TVIS30003818
Fusion event
HIV-HMGN4 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
chr6
Cytoband
p22.2
Reference genome
GRCh37/hg19
Start
26540153/26539925 (Hg38)
End
26540153/26539925 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA6C
Target gene
HMGN4
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-7-5p ; hsa-mir-615-3p ; hsa-mir-505-3p ; hsa-mir-6830-5p ; hsa-mir-340-5p ; hsa-mir-3163 ; hsa-mir-5582-3p ; hsa-mir-548f-3p ; hsa-mir-548e-3p ; hsa-mir-548az-3p ; hsa-mir-548ar-3p ; hsa-mir-548a-3p ; hsa-mir-2113 ; hsa-mir-5010-3p ; hsa-mir-5695 ; hsa-mir-3654 ; hsa-mir-1243 ; hsa-mir-3145-5p
Nearest miRNA
hsa-mir-3691/Upstream/7968045; hsa-mir-10398/Downstream/607701;
Nearest TSS
ENST00000381078/Upstream/1487; ENST00000641660/Downstream/29399;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/1138, chr6-CpG: 31/Downstream/10629
Upstream sequence
CAATAAACTTGGGCATGTGCTCAACAGCAACCTGTCTAATACATTTTCATTTAAAATCCCCTCTGTACTACTCAGAAATATAAGCAAGTTATTATGGTGC
Downstream sequence
CCAGAAAGGGGGCAAAGGTTCCAGGGTCCTAGGAGATGACAAGGATTTATCCTCTTCATCTTTCTCCGATCCCAGTTAGCAGGAATACTTTAGCCTGGAA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate