hsa-mir-96-3p _HNSC.png
SLC25A13 _HNSC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS20004088
Fusion event
HPV-SLC25A13 integration
Validated
No
Detection method
RNA-Seq
Data source
Curated
Sample type
Tumor
Disease
Head and neck squamous cell carcinoma (HNSCC)
Quality evaluation
Normal
Reported year
2018
PubMed ID
28928286
Virus Sequence
Virus name
HPV
Subtype
HPV33
Reference genome
Not given
Gene
E7
Start
3377
Host Sequence
Chromosome
chr7
Cytoband
q21.3
Reference genome
GRCh37/hg19
Start
95783230/96153918 (Hg38)
End
95783230/96153918 (Hg38)
Location type
Intron13
Target gene
SLC25A13
miRNAs that regulate target gene
hsa-let-7b-5p ; hsa-mir-98-5p ; hsa-mir-186-5p ; hsa-mir-10a-5p ; hsa-mir-3591-5p ; hsa-mir-142-3p ; hsa-mir-96-3p ; hsa-mir-4255 ; hsa-mir-605-5p
Nearest miRNA
hsa-mir-10525/Upstream/2436913; hsa-mir-10399/Downstream/65744;
Nearest TSS
ENST00000635602/Upstream/31920; ENST00000555308/Downstream/30656;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/380798, chr7-CpG: 75/Downstream/167549
Upstream sequence
ACTACTATGATAGACAGCAAAAATTTCGCAGAATAATGAGGACAATTATCTTTAAAATAATAAACCATCTATAGTTCTTTTATGGATTAATTATCAACAT
Downstream sequence
AAATGTATTGTTTTAAAGGCACATAAACATTTGAATGAAAGAGAAATAAGTATCATTAGATTCAATGTTGCAAATACGTCACTTGGGCTATAAATTTAAA
Reference
Koneva, L. A., et al. HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers. Mol Cancer Res ,2018,16(1): 90-102.
Curate