SERPINB4 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004236
Fusion event
HPV-SERPINB4 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
L1
Start
5746
Integrated sequence
TTGGCTGCCTAGTGAGGCCACTGTCTACTTGCCTCCTGTCCCAGTATCTAAGGTTGTAAGCACGGATGAATATGTTGCACGCACAAACATATATTATCAT| |GCAGGAACATCCAGACTACTTGCAGTTGGACATCCCTATTTTCCTATTAAAAAACCTAACAATAACAAAATATTAGTTCCTAAAGTATCAGGATTACAAT
Host Sequence
Chromosome
chr18
Cytoband
q21.33
Reference genome
GRCh37/hg19
Start
61317176/63649942 (Hg38)
End
61317176/63649942 (Hg38)
Location type
Intronic
Target gene
SERPINB4
miRNAs that regulate target gene
hsa-mir-6807-5p ; hsa-mir-556-5p ; hsa-mir-3123 ; hsa-mir-4517
Nearest miRNA
hsa-mir-1-2/Upstream/5198784; hsa-mir-5011/Downstream/3431642;
Nearest TSS
ENST00000575820/Upstream/2363; ENST00000613567/Downstream/11942;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/226818, chr18-CpG: 63/Downstream/286224
Junction sequence
TTGTTTACTGCACAGGAAGCACGGATGAATATGTTGCACGCACAAACATATATTATCATG---GCTAAATTAAGCTAATTAGCATATCCATTACCTCATATAAT
* 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