circAtlas

circAtlas 3.0 a gateway to 3 million standardized named vertebrate circular RNAs

Links

Download data

Species	Reference genome	circRNAs in BED format	Liftover	circRNA sequences
Human	GRCh38/hg38	human_bed_v2.0.zip	hg38_hg19_v2.0.zip	human_sequence_v2.0.zip
Macaca	BCM Mmul_8.0.1/rheMac8	macaca_bed_v2.0.zip	rheMac8_rheMac3_v2.0.zip	macaca_sequence_v2.0.zip
Mouse	GRCm38/mm10	mouse_bed_v2.0.zip	mm10_mm9_v2.0.zip	mouse_sequence_v2.0.zip
Rat	RGSC 6.0/rn6	rat_bed_v2.0.zip	rn6_rn5_v2.0.zip	rat_sequence_v2.0.zip
Pig	SGSC Sscrofa11.1/susScr11	pig_bed_v2.0.zip	susScr11_susScr10_v2.0.zip	pig_sequence_v2.0.zip
Chicken	ICGSC Gallus_gallus-4.0/galGal4	chicken_bed_v2.0.zip	galGal4_galGal5_v2.0.zip	chicken_sequence_v2.0.zip
Dog	Broad CanFam3.1/canFam3	dog_bed_v2.0.zip	canFam3_canFam2_v2.0.zip	dog_sequence_v2.0.zip

CircRNA softwares

Tools	Description	Link	Version	PMID
CIRI	CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.	CIRI_v1.2.zip	v1.2	25583365
CIRI2	Circular RNA identification based on multiple seed matching.	CIRI_v2.0.6.zip	v2.0.6	28334140
CIRI-AS	Comprehensive identification of internal structure and alternative splicing events in circular RNAs.	CIRI_AS_v1.2.zip	v1.2	27350239
CIRI-full	Reconstruction of full-length circular RNAs enables isoform-level quantification.	CIRI_full_v2.0.zip	v2.0	30660194
CIRIquant	Accurate quantification of circular RNAs identifies extensive circular isoform switching events.	CIRIquant_v1.0.tar.gz	v1.0	31900416
CIRI-vis	Visualization of circular RNAs and their internal splicing events from transcriptomic data.	CIRI-vis_v1.4.jar	v1.4	31950978

Annotation Tools

Tools	Description
clusterProfiler	R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
miRanda	Predicted microRNA targets and target down regulation scores.
Pita	PITA starts by scanning the UTR for potential microRNA targets and then scores each site.
RNAhybird	Fast and effective prediction of microRNA/target duplexes RNA.
RNA22	A pattern-based method for the identification of MicroRNA binding sites.

Related Databases

Database	Descriptions
POSTAR	A comprehensive database for exploring post-transcriptional regulation based on CLIP-seq data, Ribo-seq data, RNA-seq data and other high-throughput sequencing data from 6 species, including human, mouse, fly, worm, Arabidopsis, and yeast.
miRBase	A searchable database of published miRNA sequences and annotation.
GENCODE	GENCODE reference annotation for the human and mouse genomes.
Ensembl	A database produces genome databases for vertebrates and other eukaryotic species.
OMA	A method and database for the inference of orthologs among complete genomes.
UCSC	A broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.
starBase	An integrated platform that can be use for decoding miRNA-mRNA, miRNA-lncRNA, miRNA-circRNA, miRNA-pseudogene, ceRNA-ceRNA and protein-RNA interaction maps from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data.
ENCODE	Encyclopedia of DNA Elements.
circad	A manually curated database of circular RNAs associated with diseases.
circR2Disease	A manually curated database for experimentally supported circular RNAs associated with various diseases.
circRNADisease	A manually curated database of experimentally supported circRNA-disease associations.