CATdb

Help & Documentation

Get help using CATdb and learn about its features to explore non-canonical circular RNAs effectively

Contents

play_circle_outline Getting Started with CATdb

CATdb (CircRNA All Type Database) is a comprehensive database specifically focused on non-canonical circular RNAs. This database provides detailed annotations, analysis tools, and experimental design features to help researchers explore and understand circular RNA data.

CATdb offers the following core functionalities:

  • search Search: Look up specific circRNAs by ID, gene name, or other attributes
  • view_list Browse: Explore circRNA data organized by species, source, or ID
  • medical_services Disease Association: Discover disease-associated circRNAs
  • analytics Conservation: Explore conservation between human and mouse circRNAs
  • biotech ORF Prediction: Predict open reading frames in circRNA sequences
  • science miRNA & RBP Analysis: Analyze miRNA targets and RNA-binding protein sites
  • compare_arrows BLAST Search: Search for sequence similarity using BLAST
  • science Experimental Design: Design divergent primers and siRNAs

featured_play_list Features Overview

Browse & Search

The Browse and Search features allow you to explore circRNA information:

  • Browse by species, source, or ID
  • Advanced search with filters for gene type, source, and species
  • Autocomplete suggestions for circRNA IDs and gene names
  • Download search results in CSV format
Disease Association

Explore disease-associated circRNAs and their potential roles in various pathological conditions.

Conservation Analysis

Study conservation patterns between human and mouse circRNAs to identify evolutionarily conserved elements.

Sequence Analysis Tools
  • ORF Prediction: Identify potential coding regions in circRNA sequences
  • BLAST Search: Compare sequences against our database or NCBI
  • miRNA Target Analysis: Predict miRNA binding sites
  • RBP Site Analysis: Identify RNA-binding protein interaction sites
Experimental Design Tools
  • Divergent Primers Design: Design primers for circRNA validation
  • siRNA Design: Design siRNAs for circRNA knockdown experiments

school Tutorials

How to Search for a Specific circRNA
1
Navigate to the Search Page

Click on the "Search" link in the navigation menu.

2
Enter Search Criteria

Enter a circRNA ID or gene name. Use the autocomplete feature for suggestions. Apply filters for gene type, tissue, or species if needed.

3
View Results

Browse the paginated results table. Click on any circRNA ID for detailed information.

4
Download Results

Use the "Download Results" button to export your search results in CSV format.

Using the BLAST Search
1
Access BLAST Search

Navigate to the BLAST search page from the tools menu.

2
Input Sequence

Enter your sequence in FASTA format or plain text.

3
Choose Search Options

Select whether to search against CATdb or NCBI database.

4
Analyze Results

View alignment results and sequence similarities.

Designing Divergent Primers
1
Navigate to Primer Design Tool

Go to the "Tools" section and select "Divergent Primers Design".

2
Select Target circRNA

Enter the circRNA ID or search by gene name. You can also directly input a custom sequence.

3
Adjust Design Parameters

Modify primer length, GC content, melting temperature, and other parameters as needed for your specific experimental conditions.

4
Generate and Evaluate Primers

Click "Design Primers" to generate candidate primer pairs. Review the results table showing primer properties, specificity scores, and potential secondary structures.

5
Export Results

Download the primer sequences and detailed information in CSV format for ordering and experimental documentation.

build Tools

Experimental Design Tools
science Divergent Primers Design
Design specific primers for circRNA validation experiments. The tool considers sequence specificity, optimal amplification conditions, and junction-spanning requirements. Primers are evaluated for GC content, melting temperature, and potential secondary structures to ensure reliable amplification of circular transcripts.
science siRNA Design
Design effective siRNAs for circRNA knockdown experiments, considering sequence specificity, potential off-target effects, and junction-targeting strategies. The tool evaluates siRNA candidates based on thermodynamic properties, seed region analysis, and specificity scoring to maximize knockdown efficiency while minimizing off-target effects.
science Probe Design
Create custom probes for northern blot, FISH, or other hybridization-based detection methods. The tool optimizes probe sequences for specificity to circular junction regions while considering hybridization kinetics and experimental conditions.
Sequence Analysis Tools
biotech ORF Prediction
Identify potential open reading frames in circRNA sequences, with scoring for likelihood of translation. The tool analyzes all possible reading frames across the circular junction, identifies start and stop codons, and evaluates sequence features associated with translation initiation. Results include ORF length, amino acid sequence, and translation potential scores.
compare_arrows BLAST Search
Search for sequence similarities against CATdb or NCBI databases using BLAST algorithm. The tool supports nucleotide and protein sequence queries, with customizable parameters for match/mismatch scores, gap penalties, and E-value thresholds. Results are displayed with alignment details and downloadable in standard formats.
hub miRNA Target Prediction
Predict potential miRNA binding sites within circRNA sequences using advanced algorithms that consider seed matching, site accessibility, and evolutionary conservation. Results include binding site locations, interaction energies, and confidence scores to help prioritize experimental validation targets.
analytics Motif Analysis
Identify and analyze sequence motifs within circRNAs that may be associated with biogenesis, regulation, or function. The tool searches for known regulatory elements and discovers novel motifs using statistical approaches, with results visualized through sequence logos and positional distribution plots.

help_outline Frequently Asked Questions

question_answer What is a non-canonical circular RNA?
Non-canonical circular RNAs (nc-circRNAs) are RNA molecules that form circular structures through mechanisms other than the traditional back-splicing process. They represent a diverse group with increasingly recognized biological importance.
question_answer How is the data in CATdb collected?
CATdb data is collected through systematic analysis of RNA sequencing data from multiple sources. We use specialized bioinformatics pipelines to identify and catalog putative nc-circRNAs across various species, tissues, and cell lines.
question_answer What experimental validation tools are available?
CATdb provides tools for designing divergent primers for PCR validation and siRNAs for functional studies. These tools are optimized for circRNA-specific applications.
question_answer How can I analyze potential interactions?
CATdb offers tools for analyzing miRNA binding sites and RNA-binding protein interactions. You can also use the BLAST search to find sequence similarities.
question_answer What does the TPM value represent?
TPM (Transcripts Per Million) represents the normalized expression level of a circRNA, accounting for both sequencing depth and transcript length. Higher TPM values indicate higher expression levels.
question_answer How can I download bulk data from CATdb?
CATdb allows bulk data download from the "Download" section. You can select specific datasets based on species, tissue type, or experimental condition. Data is available in standard formats (CSV, FASTA, BED) for easy integration with other analysis tools.

menu_book Glossary

circRNA
Circular RNA (circRNA) is a type of RNA molecule that forms a covalently closed continuous loop.
nc-circRNA
Non-canonical circular RNA (nc-circRNA) refers to circular RNAs formed through alternative mechanisms.
TPM
Transcripts Per Million, a normalization method for RNA-seq data.
ORF
Open Reading Frame, a sequence that could potentially be translated into a protein.
miRNA
MicroRNA, a small non-coding RNA molecule involved in gene regulation.
RBP
RNA-Binding Protein, proteins that interact with RNA molecules.
siRNA
Small interfering RNA, used for specific gene silencing in experimental studies.
Back-splicing
A process where a downstream 5' splice site joins to an upstream 3' splice site, resulting in a circular RNA molecule.
BSJ
Back-Splice Junction, the junction point where the ends of a linear RNA are joined to form a circular RNA.
IRES
Internal Ribosome Entry Site, a sequence that allows for cap-independent translation initiation in some circRNAs.
m6A
N6-methyladenosine, a common RNA modification that can affect circRNA biogenesis, stability, and function.
circRNome
The complete set of circular RNAs expressed in a specific cell, tissue, or organism.
Exonic circRNA
Circular RNAs composed exclusively of exonic sequences.
Intronic circRNA
Circular RNAs derived from intronic sequences, often formed through lariat intermediates.
EIciRNA
Exon-Intron circRNA, containing both exonic and intronic sequences.
ciRNA
Circular Intronic RNA, formed from intron lariats that escape debranching.
circQTL
Circular RNA Quantitative Trait Loci, genetic variants associated with circRNA expression levels.

contact_support Contact & Support

If you have any questions, suggestions, or encounter any issues while using CATdb, please don't hesitate to contact us:

email Email: [email protected]
language Website: https://genomics-in-healthcare.github.io/