Herein we provide a step-by-step instruction on how to easily use the riboCIRC database.
Overview of riboCIRC
riboCIRC is a comprehensive database of computationally predicted ribo-circRNAs and experimentally verified translated circRNAs. The main sections of this website have Home, Computationally predicted ribo-circRNAs, Experimentally validated translated circRNAs, cross-species conserved ribo-circRNAs, Circ-peptide, Visualization, Statistics, Download, Tutorial and Feedback. The latest version, updated on 25, December, 2020, contains 2,247 translatable circRNAs from 3,168 unique ribo-seq samples involving 314 studies spanning 6 different species (Human, Mouse, Rat, C.elegans, Drosophila and Zebrafish). Please check this website often as we will frequently add newly published studies.
The Home page provides a brief introduction to riboCIRC, a descriptive statistics on ribo-circRNAs, quick Start module, a brief history of the website, a guide to the database citation, and contacts for website questions and database comments. Welcome to the online tour for our riboCIRC database using A GuidedTour button. More...
(I) Computationally predicted ribo-circRNAs are presented in two different levels: ① Condition-independent ribo-circRNAs predicted by
previously documented circRNAs and Ribo-seq data and ② Condition-dependent ribo-circRNAs predicted by public RNA-seq and matched Ribo-seq data.
Meta-information of the characterized ribo-circRNAs are given, including riboCIRC_ID (self-named according to
"a guide to naming human non-coding RNA genes"),
circRNA_coordinates (chr:start-end), Host_gene (Ensembl_ID, Symbol, and Transcript), circRNA length(nt), derived-database/algorithm.
Moreover, when the riboCIRC_ID is clicked on, the detailed translation information will be displayed, including translatable conditions and Number
of junction-spanning footprints.
A built-in search box in these two pages can help to further narrow down the results of interest. More...
(II) The Experimentally validated translated circRNAs page provides a manually curated encyclopedia of circRNAs validated by different experiments to be able to generate peptides. Detailed meta-information of these translated circRNAs are also given, including documented circRNA_Name, Mapped CircBase_ID, circRNA_coordinates (chr:start-end), Strand, Host_gene (Transcript), circRNA derived ORF (Length(aa) and peptide sequence), Experimental evidence (MS data supporting,Exogenous expression, and Antibody detection of endogenous peptide), and related reference (PubMed_ID, Paper, Journal and Release year)
(III) The 'cross-species conserved ribo-circRNAs' provides translatable circRNA conserved among different species. Each row represents the circRNAs conserved in various species and if you would like to view the detail information of them then just clicking on the interested circRNA id.
The Circ-peptide page provides a systematic de novo sequence, structural, and functional annotation on
circRNA-encoded peptides based on bioinformatics prediction. When clicking on the items enclosed in the container
box to select one from the dropdown list, more information about circRNA-encoded peptides will be returned, including
circRNA-derived ORF annotation (cORF_coordinates (chr:start-end), cORF length(aa) and cORF_seq), cORF conservation (phastCons score),
predicted peptide characteristics (signal cleavage site (SignalP), N-terminal presequences (TargetP), transmembrane domain prediction
(TMHMM and Phobius), and localization (DeepLoc)), and protein structure prediction (I-TASSER). These results provide a foundation for
circRNA translation studies, serving as a starting point for further investigation into their biological significance of circRNA-encoded
The visualization page provides intuitive visualization-oriented information about circRNA translation, including view of junction-spanning ribosome footprints, view of designed circRNA primer sets, and graphical representation of circRNA structure. The context-specific selection for translatabe circRNAs and ribosome profiling data tracks are accessible in the left side bar of JBrowse. When selecting one circRNA in JBrowse, circRNA structure plots and designed circRNA primer sets will be returned simultaneously. The graphical representation of circRNA structure panel shows the results from circView, allowing users to view the regulatory elements, such as microRNA response elements and RNA-binding protein binding sites. The circRNA primer panel shows the results from CircPrimer, helping users to design primers for circRNAs and to determine the specificity of the circRNA primers. More...
The feedback page provides a feedback form, allowing users to provide feedback about published ribo-circRNAs or ribosome prifling data. In addition,if you have any specific and helpful suggestions, please don't hesitate to contact us. More...
Detection of transcribed and ribosome-associated circRNAs
We combined three different detection tools to identify transcribed circRNAs in each RNA-seq dataset, namely, CIRCexplorer2 (CE2), CIRI2, and DCC. The full-length sequence of each identified circRNA was assembled by the CIRI-full pipeline or extracted from the circAtlas database when the RNA-seq data were unavailable. Taking advantaging of these full sequences, we generated a pseudo circRNA reference for each species by initial extraction of the 23-base pair (bp) sequences on either side of the backsplice junction (BSJ) site of each transcribed circRNA with subsequent concatenation of the two-sided sequences. To identify ribosome-associated circRNAs (ribo-circRNAs), we first eliminated sequence reads corresponding to nonribosomal RNA-protein complexes in each Ribo-seq dataset using Rfoot (version 1.0), considering that ribosomes are not specifically selected during the biochemical isolation procedure of ribosome profiling experiment. After removal of footprints from nonribosomal complexes, all the ribosome-protected footprints were then mapped with Tophat2 to the corresponding linear reference genome, and further the resulting unmapped.bam files were remapped to the pseudo circRNA reference using Tophat2 (version 2.1.1), with default parameters except N, which was set to 0 (the default is 2). Finally, a circRNAs was defined to be associated with translating ribosomes only when it met all of the following three criteria simultaneously: (1) at least two unique backsplice junction-spanning Ribo-seq reads, (2) a minimum read-junction overlap of three nucleotides (nt) on either side of the backsplice junction site, and (3) a typical range of read lengths of 25-35 nt. Two different strategies were here used to characterize ribo-circRNAs: (1) condition-dependent detection for Ribo-seq and perfectly matched RNA-seq datasets and (2) condition-independent detection for previously reported circRNAs and Ribo-seq datasets.