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 will 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, ZIF3, ZIF4, 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
- 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.
- Page not loading: Check your internet connection or try refreshing the page
📧 Need More Help?
Contact: liucf [at] issas.ac.cn