circAtlas 3.0 a gateway to 3 million standardized named vertebrate circular RNAs
Welcome to circAtlas 3.0 (a gateway to consistently curated vertebrate circular RNAs).
circAtlas 3.0 contains a compendium of 2,674 RNA-seq libraries from 33 normal tissues from human, macaque, mouse, rat, rabbit, cat, dog, pig, sheep and chicken.
Main characteristics of circAtlas include:
circAtlas uses the standardized nomenclature scheme proposed by the circRNA community.
circAtlas integrates Illumina and Nanopore circRNA sequencing datasets, providing the full-length sequences and downstream functional analysis results of over 2.5 million circRNAs.
Convert the circRNA ID among different circRNA databases.
Search and find conserved circRNAs across human, macaque, mouse, rat, rabbit, cat, dog, pig, sheep and chicken.
Predict second structure of circRNAs.
Predict potential peptide-encoding circRNAs. e.g: ORF, IRES.
Predict regulation elements of circRNAs. e.g: miRNA, RBP.
circAtlas uses three types of networks including gene co-expression, miRNA regulation and RBP regulation to infer circRNA functions.
circAtlas 3.0 comprises a comprehensive compendium of 2,609 Illumina and 65 nanopore RNA-seq datasets from 33 diverse tissues within 10 distinct species. More details are show in index page.
Users can select one of the ten species to search for circRNAs.
Users can get the detailed information of each circRNA by clicking the circAltas ID.
1. Users can search the circRNA known in circAtlas by circAtlas ID, chromosome position, host gene and name in other circRNA databases.
2. Users can search the circRNA by expressed species and tissues.
3. Users can search for the circRNAs that are known in the circAtlas and have a potential function, such as:
circAltas provides two types of names for each circRNA:
For Illumina RNA-seq data, the cleaned reads were aligned to the reference genome using bwa (v0.7.17), and circRNAs were subsequently identified and quantified using the CIRI2 (v2.0.6) and CIRIquant (v1.1.2) pipeline. To reconstruct the full-length sequence of circRNA isoforms, CIRI-full (v2.1.1) and CIRI-vis (v1.4.1) were employed to assemble full-length circRNAs using the reverse overlap feature. To further reduce the number of false positives , three other software, CIRCexplorer2 (v2.3.8), DCC (v0.5.0) and find_circ (v1.2), were also used to identify circRNAs, and circRNAs that are supported by at least one of the other tools were retained for further analysis.
For long-read sequencing data, the raw sequencing data from the CIRI-long protocol were trimmed using Porechop, and CIRI-long (v1.1.0) was performed to identify circRNAs from nanopore sequencing reads. For other long-read circRNA sequencing protocols including isoCirc, circFL-seq and an adapted version of CIRI-long, the processed data were obtained from their original manuscripts. Finally, the reconstructed full-length sequences were used to annotate the spliced isoforms of the identified circRNAs.
Based on the assembled full-length circRNA sequences, the secondary structure was predicted using the RNAfold algorithm of the Vienna RNA 2.0 package.
circAltas provides the expression of circRNAs across normal and cancer tissues(human only). circAltas integrates the expression landscape of human circRNAs in clinical samples across 36 cancer types from the MiOncoCirc and CSCD2 databases.
Users can search for circRNAs in different databases and liftover circRNA position from different assemblies.
Users can search predicted IREs on currently available circRNAs or predict IREs on given circRNAs from a corresponding input.
User can search predicted IREs on currently available circRNAs or predict IREs on given circRNAs from a corresponding input.
User can search predicted RBP binding on currently available circRNAs or predict RBP binding sites on given circRNAs from corresponding input.
User can search predicted miRNA binding on currently available circRNAs or predict miRNA binding sites on given circRNAs from acorresponding input.
User can search functional annotation of currently available circRNAs or annotate given circRNAs by constructing network.
The page provides disease related circRNA by integrating three databases: circad, CircR2Disease and circRNADisease. Users can search and query target circRNAs using this module. Users can also submit new records by providing your work email address, where you will receive the confirmation request. If there are any problems with your future submissions, the circAtlas curators will contact you at this email address. Please note that your email address will be presented on the web in a way that should protect it from spammers.