C. elegans
The Rules Panel enables users to set the desired criteria for identifying de novo emerged genes, while the Output Panel facilitates filtering and analysis of the resulting list.
The default table displayed was generated with the default parameters of the DENSE workflow:
- TRGs at genus level
- Hit in non-coding regions (NCR) of outgroup species validated
- Microsynteny validated (1 on core up- & downstream in a window of 4 genes)
However, you can try out your own combination of some of these settings using the Rules box below.
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CDS
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Code
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Gene
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Phylostratum
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Rank
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Protein size
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Is denovo?
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Is orphan?
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Is TRG?
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| CDS | Gene | Phylostratum | Protein size | Is denovo? | Is orphan? |
|---|---|---|---|---|---|
| transcript:B0001.8d.1 | B0001.8 | Caenorhabditis | 309 | ✘ | ✘ |
| transcript:B0001.8d.2 | B0001.8 | Caenorhabditis | 309 | ✘ | ✘ |
| transcript:B0001.8d.3 | B0001.8 | Caenorhabditis | 309 | ✘ | ✘ |
| transcript:B0001.8d.4 | B0001.8 | Caenorhabditis | 309 | ✘ | ✘ |
| transcript:B0019.1.1 | amx-2 | cellular organisms | 724 | ✘ | ✘ |
| transcript:B0019.2.1 | B0019.2 | Caenorhabditis | 747 | ✘ | ✘ |
| transcript:B0024.1.1 | col-149 | cellular organisms | 297 | ✘ | ✘ |
| transcript:B0024.10.1 | asps-1 | Eukaryota | 573 | ✘ | ✘ |
| transcript:B0024.11.1 | B0024.11 | cellular organisms | 577 | ✘ | ✘ |
| transcript:B0024.12.1 | gna-1 | cellular organisms | 165 | ✘ | ✘ |
| transcript:B0024.13.1 | B0024.13 | cellular organisms | 309 | ✘ | ✘ |
| transcript:B0024.14a.1 | crm-1 | Metazoa | 900 | ✘ | ✘ |
| transcript:B0024.14b.1 | crm-1 | Metazoa | 966 | ✘ | ✘ |
| transcript:B0024.14d.1 | crm-1 | Metazoa | 904 | ✘ | ✘ |
| transcript:B0024.14f.1 | crm-1 | Metazoa | 875 | ✘ | ✘ |
Total number of records: 31755
Records per page: 10 | 20 | 50 | 100
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Phylogeny
______________ C. elegans __| | |______________ C. inopinata | | ________ C. brenneri | __| __| | |________ C. doughertyi | | __| | | | | ________ C. tropicalis | | | |__| | | | |________ C. wallacei | |__| | | ________ C. remanei | | __| __| | | |________ C. latens | | | | | | |__| _____ C. nigoni | | | __| | | | | |_____ C. briggsae | | |__| | | | _____ C. sinica | | |__| __| | | __ C. zanzibari | | | |__| | | | |__ C. tribulationis | | | | | |____________________ C. kamaaina | | | | ____________________ C. japonica | | | | |__| ______________ C. afra | | __| | | | |______________ C. sulstoni __| |__| | | | ______________ C. macrosperma | | | | | | |__| ________ C. becei | | | __| | | | | |________ C. nouraguensis _| | |__| | | | ________ C. waitukubuli | | |__| | | |________ C. panamensis | | | |__________________________ C. uteleia | | __________________________ C. monodelphis | | |__| _______________________ C. parvicauda | | |__| _________________ C. bovis | __| | | |_________________ C. plicata |__| | _________________ C. virilis |__| | ______________ C. quiockensis |__| | ___________ C. angaria |__| |___________ C. castelli
†: Switching between rules will not affect the number of records in the table. It will, however, affect the definition of the "Is denovo?" column.