Proximate region of VIS (GRCh38)VISEnhancerEnhancer/PromoterPromoterGene29140547291940712963075129536933299400332950136929502138294998012949995029540290
GRIK1 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004311
Fusion event
HPV-GRIK1 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
L2
Start
4488
Integrated sequence
GGGTGTATTTTTTGGTGGGTTAGGAATTGGAACAGGGTCGGGTACAGGCGGACGCACTGGGTATATTCCATTGGGAACAAGGCCTCCCACAGCTACAGAT| |ACACTTGCTCCTGTAAGACCCCCTTTAACAGTAGATCCTGTGGGCCCTTCTGATCCTTCTATAGTTTCTTTAGTGGAAGAAACTAGTTTTATTGATGCTG
Host Sequence
Chromosome
chr21
Cytoband
q21.3
Reference genome
GRCh37/hg19
Start
30912611/29540290 (Hg38)
End
30912611/29540290 (Hg38)
Location type
Intronic
Target gene
GRIK1
Nearest miRNA
hsa-let-7c/Upstream/2586247; hsa-mir-3197/Downstream/835004;
Nearest TSS
ENST00000624081/Upstream/163951; ENST00000462262/Downstream/55750;
Nearest CpG islands
None/Target, chr21-CpG: 261/Upstream/240825, chr21-CpG: 61/Downstream/398778
Junction sequence
CAGGAGCAAGTG---CTGCTTGTGTGAGAGCAAATATAAACATAGTTTTATCAG
* 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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