CRAT _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004250
Fusion event
HPV-CRAT 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
1203
Integrated sequence
AGATGCAGTACAGGTTCTAAAACGAAAGTATTTGGGTAGTCCACTTAGTGATATTAGTGGATGTGTAGACAATAATATTAGTCCTAGATTAAAAGCTATA| |TGTATAGAAAAACAAAGTAGAGCTGCAAAAAGGAGATTATTTGAAAGCGAAGACAGCGGGTATGGCAATACTGAAGTGGAAACTCAGCAGATGTTACAGG
Host Sequence
Chromosome
chr9
Cytoband
q34.11
Reference genome
GRCh37/hg19
Start
131857931/129095652 (Hg38)
End
131857931/129095652 (Hg38)
Location type
Intronic
Target gene
CRAT
miRNAs that regulate target gene
hsa-mir-155-5p
Nearest miRNA
hsa-let-7a-1/Upstream/702938; hsa-mir-12126/Downstream/773953;
Nearest TSS
ENST00000422679/Upstream/11053; ENST00000434250/Downstream/2202;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/14183, chr9-CpG: 135/Downstream/14693
Junction sequence
AGGGACCTGGGGACGGCAGGATGAAAGCTCTCAGCTCCCCTACCTT---[TTA]---ATATAGCTTTTAATCTAGGACTAATATTATTGTCTACACATCCACTAATATC
* 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.
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