IFT140 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004239
Fusion event
HPV-IFT140 integration
Validated
Yes
Detection method
WGS, RNA-seq, Whole-Exome sequencing, PCR
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Perfect
Reported year
2014
PubMed ID
25313082
Virus Sequence
Virus name
HPV
Subtype
HPV16
Reference genome
AY686584
Gene
E1
Start
2421
Integrated sequence
TGGTATGAGTTTAATGAAATTTCTGCAAGGGTCTGTAATATGTTTTGTAAATTCTAAAAGCCATTTTTGGTTACAACCATTAGCAGATGCCAAAATAGGT| |ATGTTAGATGATGCTACAGTGCCCTGTTGGAACTACATAGATGACAATTTAAGAAATGCATTGGATGGAAATTTAGTTTCTATGGATGTAAAGCATAGAC
Host Sequence
Chromosome
chr16
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
1611951/1561950 (Hg38)
End
1611951/1561950 (Hg38)
Location type
Intronic
Target gene
IFT140
miRNAs that regulate target gene
hsa-mir-93-3p ; hsa-mir-6874-5p ; hsa-mir-6500-5p ; hsa-mir-4633-3p ; hsa-mir-6080 ; hsa-mir-558 ; hsa-mir-6849-5p ; hsa-mir-3681-5p ; hsa-mir-22-3p
Nearest miRNA
hsa-mir-3176/Upstream/791673; hsa-mir-11401/Downstream/173035;
Nearest TSS
ENST00000527434/Upstream/28377; ENST00000563162/Downstream/2160;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/6606, chr16-CpG: 424/Downstream/48103
Junction sequence
AAAAGCCATTTTTGGTTACAACCATTAGCAGATGCCAAAATAGGTA---[GTA]---CAGAAGACACCTGTGCGGATGTCGTGGCTTCGTACCTTTCTTGTGAAGTAGTCG
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Parfenov, M., et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A,2014,111(43): 15544-15549.
Curate