Information of circRNAs
1. Quick search
The search in the PanCircBase database works as a simple quick search by querying the circRNA host gene symbol.
Users can easily search pancreatic circRNA directly on the Home page of the PanCircBase database. Users can search all the related circRNAs in the database by gene symbol (e.g., Hipk3). Search results will be displayed in a new page.
2. Search results
Results for circRNA search
Results for a quick search will be listed on a new page, sorted by the PanCircBase ID. The default search result will show all the records on a single page with a number of circRNAs found on top. Each circRNA record will show a set of PanCircBase ID, mm39_Chr. Position ID, Gene name, CircRNA type, Splice length under the list.
To get more details about specific circRNA, users can click on the “Quick view ” button, and basic information about selected circRNA will be shown in a pop-up window. Alternatively, users can click the “ Full details” button, and detailed information related to selected circRNA will be shown on a new page.
3. Information on circRNAs
There is a complete detailed information page for each selected circRNA displayed using “ Full details” option in search results. In this page, information about each circRNA is divided into many sections to provide extensive information.
The basic annotation information for selected circRNA is shown including PanCircBase ID, mm39_Chr. Position ID, Gene name, Transcript, CircRNA type, Exon/Intron count, Exon/intron indexes, Exon/intron sizes, Exon/intron offsets, Flanking exon/introns, Genomic length and Splice length. Minimal basic information can also be seen using “Quick view” option in search results.
Mature spliced sequence: The complete spliced sequence of each circRNA is given. Users can directly copy the sequence for downstream analysis.
Other database IDs: The unique IDs for each known PanCircBase circRNA from different databases – circBase, CIRCpedia, circAtlas are shown for reference.
Human Ortholog IDs: The human ortholog IDs from other databases for each conserved PanCircBase circRNA are listed. Users can find more information using given ortholog IDs.
It is recommended that for the experimental validation and functional analysis of circRNAs users can utilize the advanced information provided for each circRNA, including the following sections:
Divergent primers for circRNA PCR
Two sets of divergent primers targeting circRNA junction sequence are provided for each circRNA. Related details such as Tm and expected PCR product size are also shown. Primers were designed using primer3-py program. Users can choose any of the given primer sets for carrying out PCR amplification of circRNA of interest.
Information of miRNAs related to circRNA
Users can find circRNA associated miRNAs by going through the list of miRNA IDs predicted to interact with selected circRNA including number of binding site positions (predicted by miRanda v3.3a) per miRNA. The total number of different miRNAs related to a given circRNA is also shown. Such information will enable the users to study miRNA-circRNA interaction and its biological implication in pancreas.
Information of siRNAs for circRNA silencing
Users can find 1-3 siRNA sequences designed (using RNAxs tool) to specifically target the circRNA junction site and downregulate circRNA related functions in cell. Users can use the provided siRNA sequences for silencing circRNA of interest and study its biological role. The circRNA junction sequence predicted to be silenced by given siRNAs is also shown.
Information about coding abilty of circRNA
CPAT results: Coding potential assessment tool (CPAT) analysis gave the coding probability, Fickett score (measures bias between coding and non-coding sequences) and Hexamer score (measures hexamer usage differences between coding and non-coding sequences) for junction spanning ORF present in each circRNA sequences. The ORF ID, ORF length, ORF sequence and resultant Peptide sequence for selected coding circRNA is also shown under CPAT analysis.
IRESfinder results: IRESfinder was used to classify circRNA spliced sequences into IRES and non-IRES depending on IRESfinder scoring.
RiboCIRC information: The corresponding riboCIRC ID, Evidence supporting coding ability and peptide sequence reported in riboCIRC database for selected circRNA is shown.
4. UCSC Genome Browser trackhub
PanCircBase provides a user-friendly UCSC Genome Browser track link to directly visualize circRNAs in PanCircBase and known circRNAs reported by circBase in UCSC Genome Browser.
Users can download the data used in making PanCircBase database from the resource page. Data accessible as excel files include circRNA annotation, divergent primers for circRNAs, siRNAs for circRNA silencing, miRNAs interacting with circRNA and protein coding circRNAs.
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