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Navigating the viewer
Select using the brush tool to select a region. Double click to zoom out.
5' UTR Architechure
VuTR is able to visualise the various different uORFs and oORFs within a 5' UTR. This is done by scanning through from 5' to 3' end of the UTR and identifying all ATGs with an in-frame stop codon. These are then characterized whether they are (a) uORF (b) in-frame oORFs causing a N-terminal extension or (c) an out-of-frame oORF. These ORFs are separately viewed on different tracks on the viewer. They are color coded with their match to Kozak Consensus Sequence (5'-(gcc)gccRccAUGG-3') and categorized as either (a) Strong, (b) Moderate or (c) Weak. Where RiboSeq data is available, VuTR is able to plot smORF data from Chothani, Sonia P., et al. "A high-resolution map of human RNA translation." Molecular Cell 82.15 (2022): 2885-2899.
Users are able to view additional contextual detail such as the sequence, frame, context and transcript positions by clicking on the ORF of their choice.
ClinVar and gnomAD variants
VuTR uses gnomAD (version 3.1.2) to access population variants within 5' UTR exons. ClinVar variants are placed in separate tracks, one for each variant with a 5' UTR consequence.
Finding the impact your variant
Users are available to input their favorite variant in the box user-supplied variant section in the following format CHROM-POS-REF-ALT (e.g. 5-88823796-G-A). Only variants with a 5' UTR impact are searchable all other SNV variants in 5' UTR regions are assumed to have no 5' UTR consequence. Clicking on the ORF that is either created or gain will allow users to view the consequences provided from VEP's UTR annotator.
Gene detail card
The gene detail card contains information about the gene chosen including alternate identifiers and links to external sources for that gene. We include the following information:
- HGNC Symbol: The gene's HGNC symbol
- Gene Name: The gene's common name
- Ensembl Gene ID: Ensembl's gene identifier (e.g. ENSG000001000)
- Ensembl Transcript ID: The Ensembl transcript of that gene according to MANE Select 1.0
- RefSeq Match: The RefSeq transcript identifier according to MANE Select 1.0
- 5' UTR exon count:The number of exons in the 5' UTR
- 5' UTR length: The length of the 5' UTR (in bps)
- ClinGen Scores:Both Haploinsufficiency and Triplosensitivity scores from ClinGen
- Gene LOEUF: Constraint scores according to gnomAD v.2.1.1
- External Resources See this gene in other resources such as gnomAD, ClinVar, OMIM, and DECIPHER.