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

Links

Download data
Species Reference genome circRNAs in BED format circRNA sequences
Human   GRCh38/hg38
  human_bed_v3.0.zip
  human_sequence_v3.0.zip
Macaque   BCM Mmul_8.0.1/rheMac8
  macaca_bed_v3.0.zip
  macaca_sequence_v3.0.zip
Mouse  GRCm38/mm10
  mouse_bed_v3.0.zip
  mouse_sequence_v3.0.zip
Rat  RGSC 6.0/rn6
  rat_bed_v3.0.zip
  rat_sequence_v3.0.zip
Rabbit   Oryctolagus_cuniculus.OryCun2.0
  rabbit_bed_v3.0.zip
  rabbit_sequence_v3.0.zip
Cat   Felis_catus.Felis_catus_9.0
  cat_bed_v3.0.zip
  cat_sequence_v3.0.zip
Dog  Broad CanFam3.1/canFam3
  dog_bed_v3.0.zip
  dog_sequence_v3.0.zip
Pig  SGSC Sscrofa11.1/susScr11
  pig_bed_v3.0.zip
  pig_sequence_v3.0.zip
Sheep   Ovis_aries.Oar_v3.1
  sheep_bed_v3.0.zip
  sheep_sequence_v3.0.zip
Chicken   ICGSC Gallus_gallus-4.0/galGal4
  chicken_bed_v3.0.zip
  chicken_sequence_v3.0.zip
CircRNA softwares
Tools Description Version PMID
CIRI2 Circular RNA identification based on multiple seed matching v2.0.6 28334140
CIRI-AS Comprehensive identification of internal structure and alternative splicing events in circular RNAs. v1.2 27350239
CIRI-full Reconstruction of full-length circular RNAs enables isoform-level quantification. v2.1.1 30660194
CIRIquant Accurate quantification of circular RNAs identifies extensive circular isoform switching events. v1.1 31900416
CIRI-vis Visualization of circular RNAs and their internal splicing events from transcriptomic data. v1.4 31950978
CIRI-long Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. v1.1.0 33707777
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
POSTAR3  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.
MiOncoCirc  A compendium of circular RNAs compiled from cancer clinical samples.
CSCD2  An integrated interactional database of cancer-specific circular RNAs.