User Guide
This is the main tutorial and help file for CropCircDB:
CropCircDB is a dedicated database and comprehensive system for crop circular RNAs. Currently, the database is developed to host 38,785 circular RNAs for maize and 63,048 circular RNAs for rice. The collected information can be used to help biologists to study this enigmatic molecule in crops.
The search option includes following information,
Column name Example Description circName ath-circ59801-AT4G24020 A unique identifier describing the circular RNA. This is a novel naming design with hosting gene information circID ath-circ59801-AT4G24020 A unique identifier used in the system that describing the circular RNA, including chromosome, start, end, and strand information gene OS12T0123100 gene name hosting the circRNAs isoform OS12T0123100-01 isoform name hosting the circRNAs
In the web page, the users can have the columns as follows,
Options Example Description circName osa-circ43878-OS12T0123100 A unique identifier describing the circular RNA. This is a novel naming design with hosting gene information circID 12:1096458-1096549_- A unique identifier used in the system that describing the circular RNA, including chromosome, start, end, and strand information detection_score 0.33 a metric to measure the robustness of circRNAs in the sample. It is calculated by the number of samples containing this circRNAs / total number of samples. A rule of thumb is to use 1 as the cutoff value. stress_detection_score 1.818 the environmental effect on the sample stress cold a metric to measure the robustness of circRNAs in the stressed sample. It is calculated by the number of cold-stressed samples containing this circRNAs / total number of cold-stressed samples genome_view link web link to JBrowser of the genome circRNA_view link web link to circRNA structure expression_view link web link to circRNA expression profile gene OS12T0123100 the gene containing this circRNA isoform OS12T0123100-01 the isoform containing this circRNA tissue multipleTissue tissue information for this circRNA chr 12 chromosome information for this circRNA width 92 the length of this circRNA start_anno exon,CDS the start position overlaps not only the boundary of exon, but also that of CDS end_anno exon the end position overlaps the boundary of exon antisense this circRNA are NOT antisense to existing gene algorithm CIRCexplorer2 this circRNA are detected by CIRCexplorer2 software splicedSeq GGGAGCCCTTCCGCCGCCGCCGCCGCCCCGATGTTGGGACACCTCCGGCGATCCTCCCAACGACTGCCCGTAGCCAACCTCGCCGTATACT the spliced sequence without intron sequence predAA MLGHLRRSSQRLPVANLAVYWEPFRRRRRP the spliced sequence does NOT have stop-codon, and has potential to produce amino acid sequence miRNA - there is NO miRNA candidate that interacts with the circular RNA (the results are predicted from psRNATarget) superCircRNARegion 12:1094820-1096549_- super enriched region that hosts the circular RNA crop rice crop species containing this circRNA strand - strand information of this circRNA start 1096458 start information of this circRNA end 1096549 end information of this circRNA seq GGGAGCCCTTCCGCCGCCGCCGCCGCCCCGATGTTGGGACACCTCCGGCGATCCTCCCAACGACTGCCCGTAGCCAACCTCGCCGTATACT full sequences of this circRNA from the start to the end position
Please feel free to send validated circular RNAs to johnsunx1@126.com or johnsunx1@yahoo.com. All new circular RNAs will be deposited into the database in 24 hours.
Any users can freely access and use CropCircDB for academic or industrial purpose without registrations and charge.
