RNAStructuromeDB
NEW: ScanFold results for the COVID-19 strain (SARS-CoV-2) can now be found on the RNAStructuromeDB: here
Browse all the genomes which have been scanned here: https://structurome.bb.iastate.edu/jbrowse/
View the results from a new ScanFold herpesvirus analysis here: https://structurome.bb.iastate.edu/herpesvirus/
About RNAStructuromeDB Gene Search:
Find RNA folding metrics which have been calculated for ~156,000,000 scanning windows canvassing the entire human reference genome (hg38) and linked to annotations for specific gene loci (described within the Gencode comprehensive gene annotation set Version 26): search for one gene at a time (by using the "Is equal to" filter and inputting a single entry), or a list of genes (by using the "Contains any word" filter and inputting a space-separated list of gene symbols or Ensemble IDs).
Description of RNAStructuromeDB folding metrics
RNAStructuromeDB JBrowse tutorial
Not sure what your gene symbol or Ensemble gene ID is?
Search for the official gene symbol at HGNC or Ensemble ID at Ensembl (should be in the format of ENSG00000##.#). To find data outside of gene regions use our Data Search tool.
If you find the RNAStructuromeDB helpful, please consider citing the corresponding manuscript: RNAStructuromeDB: A genome-wide database for RNA structural inference
Results:
To download the complete dataset for VEGFA, click CSV button at bottom of page.
View gene on Ensembl:ENSG00000112715.21
View gene on GeneCards:VEGFA
View VEGFA on JBrowse
Windows with interesting structures (z-score < -1; ranked from most negative to least negative) are displayed below.
Pages
Welcome to RNAStructuromeDB! Here you can find RNA folding metrics which have been predicted for 156 million windows canvassing the entire human reference sequence (hg38). We have some helpful materials about folding metrics and a tutorial for using the RNAStructuromeDB JBrowse genome browser below.
Description of RNAStructuromeDB folding metrics.
RNAStructuromeDB JBrowse tutorial.
Have a question that needs to be answered? Ask it.
Yes! You can input a comma-separated list of gene names or ensemble IDs and download all results.
From the "Gene Search" tab change the filter for Gene Name (or...
You can read about the RNA Structurome DB here: Andrews RJ, Baber L, and Moss W. Sci Rep. 2017.
The RNAStructuromeDB is a repository of RNA folding metrics describing...
We do! Here is a user guide specifically for RNAStructuromeDB: jbrowse.pdf
JBrowse is freely available as part of the generic model organism database...
