Help - How to Use This Database
🔍 Search by Gene ID
Enter a valid gene ID in the search box. Examples:
Supported ID Types:
• Gene Symbol: ARV1, CIPK11, CYP85A1, bZIP1
• TAIR ID (Arabidopsis): AT1G01020, AT2G48020
• NCBI Gene ID: 543618, 107275263
• LOC ID: LOC123183847, LOC4326813
• Ensembl ID: TraesCS3B03G0843100
• Maize GRMZM ID: GRMZM2G059865
🎯 Filter by Species
Use the dropdown menu to restrict your search to a specific species. If no species is selected, the database will search across all species.
🔤 Case-Insensitive Search
Search is case-insensitive. Entering arv1, ARV1, or Arv1 all return the same results across species.
🔎 Prefix Search
If an exact match is not found, the database automatically tries prefix matching. For example, searching ZIF will find ZIF1, ZIF2, ZIFL1, and other genes starting with "ZIF".
📋 Multiple Transcripts
When a gene has multiple transcript variants, all are listed. Click "View" to see uORF details for each transcript.
📊 Understanding Results
- Species: Scientific name of the source organism
- Gene ID: Unique identifier in the source database
- Transcript ID: Specific mRNA isoform identifier
- 5' UTR Length: Length of the 5' untranslated region in base pairs
- uORF Count: Number of upstream open reading frames identified
- uORF Sequences: Nucleotide sequences of all identified uORFs
- uORF Peptides: Amino acid sequences encoded by uORFs
- 🌍 Conservation Score: Shown as "cross-species, within-species" (e.g., "2,1" = 2 other species + 1 paralog). Based on DIAMOND comparisons across 10 plant species. Higher cross-species values suggest functional importance.
- ⭐ Novel Candidates: The Candidates page lists 5,185 conserved unannotated uORF peptides (≥10 aa) from a total of 6,628 candidates. Filter by species and length, and click Gene ID to search.
- 🔬 Ribo-seq Validated: green badge indicates the gene has translation evidence from public Ribo-seq data. Available for Arabidopsis, Maize, Tomato, Medicago, Rice, and Sorghum. See About page for details.
📥 Data Download
Complete datasets for each species are available in the Download section. Files are in TSV format and can be opened with spreadsheet software or analyzed with custom scripts.
❓ Troubleshooting
- Too many results: Try selecting a specific species or using a more precise gene ID to narrow down results
- No results found: Check the gene ID format and try a different species or use prefix search
- Gene not found: The gene exists in our database, but its 5' UTR contains no uORF meeting our criteria (AUG start, in-frame stop, ≥6 aa). Alternatively, the gene ID may not be in our database. This does NOT mean the gene is absent from the genome—only that no canonical uORF was identified.
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📧 Need More Help?
Contact: liucf [at] issas.ac.cn