This is the main tutorial and help file for AtCircDB: a tissue-specific database for Arabidopsis
AtCircDB is a dedicated database and comprehensive system for tissue-specific circular RNAs. The database is developed to host 69,707 circular RNAs, 25,715 tissue-specific circular RNAs and 1180 miRNA-circular RNA interactions. The collected information can be used to help biologists to study this enigmatic molecule in Arabidopsis.
Any users can freely access and use AtCircDB for academic or industrial purpose without registrations and charge.
In the search page, the users can have seven options as follows,
Options Example Description circID ath-circ12-AT1G01050 A unique identifier describing the circular RNA genome locus chr1:31521-31602 the back splicing sites for the circular RNA tissue mixedTissue tissue information for the circular RNA miRNA ath-miR859 the miRNA candidate that interacts with the circular RNA (the results are predicted from psRNATarget and TAPIR) super enriched region chr5:553944-556442_- super enriched region that hosts the circular RNA TAIR ID AT1G01160 TAIR ID that hosts the circular RNA antisense yes antisense transcript
The output includes following information,
Column name Example Description circID ath-circ59801-AT4G24020 A unique identifier describing the circular RNA. This is a novel naming design with hosting gene information. chr chr4 The chromosome information for the circular RNA start 12480682 the start site of the back-splicing sites end 12481259 the end site of the back-splicing sites strand + the strand information for the circular RNA TAIR ID AT4G24020 gene ID that hosts the circular RNA genome_locus chr4:12480682-12481259 genome locus for the circular RNA. It can be easily used in genome visualization software, such as IGV. genomic_length 578 the distance between two back splicing sites detection_score 3.7 the detection score is between 0 and 100. The higher the detection score, the higher probability that this circular RNA will be detected in the RNA-Seq data set. If the detection score is 100, it represents this circular RNA has been detected in all previous samples; if the detection score is 0, it suggests that this circular RNA has never been found before start_annotation intron the annotation for the starting position. It could be exon, exonBoundary, intron, CDS, or intergenic. end_annotation exonBoundary,CDS the annotation for the ending position. It could be exon, exonBoundary, intron, CDS, or intergenic. antisense yes or no whether or not the circular RNA is an antisense transcript. detection_algorithm CIRCexplorer2 the algorithm used to detect circular RNAs. Two algorithms were utilized, including CIRCexplorer2 and CIRI2. exp_evidence 0 or 1 0: there is NO experimental evidence for the circular RNA; 1: there is experimental evidence for the circular RNA tissue leaf tissue information for the circular RNA. Currently the database includes 9 tissues: leaf, hypocotyl, cotyledon, root, endosperm, flower, embryo, pollen, and shoot miRNA ath-miR859(1) or ath-miR860(2) the miRNA candidate that interacts with the circular RNA (the results are predicted from psRNATarget and TAPIR). (1) is predicted from psRNATarget, (2) is predicted from TAPIR SuperCircRegion chr1:28895699-28896371 the regions with enriched circular RNAs. More details are available at the paper.
Please feel free to send validated circular RNAs to email@example.com or firstname.lastname@example.org. All new circular RNAs will be deposited into the database in 24 hours.