DeNovoGenesDB

O. sativa

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.

Visible columns

• CDS
• Phylostratum
• Rank
• Protein size
• Is denovo?
• Is orphan?
• Is TRG?

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CDS	Phylostratum	Rank	Protein size	Is denovo?	Is orphan?	Is TRG?
transcript:Os01t0100100-01	cellular organisms	1	702	✘	✘	✘
transcript:Os01t0100200-01	Oryza	20	142	✘	✘	✔
transcript:Os01t0100300-00	cellular organisms	1	269	✘	✘	✘
transcript:Os01t0100400-01	cellular organisms	1	593	✘	✘	✘
transcript:Os01t0100466-00	Oryza sativa Japonica Group	22	77	✔	✔	✔
transcript:Os01t0100500-01	Streptophyta	4	524	✘	✘	✘
transcript:Os01t0100600-01	Streptophyta	4	355	✘	✘	✘
transcript:Os01t0100650-00	Oryza sativa Japonica Group	22	127	✔	✔	✔
transcript:Os01t0100700-01	cellular organisms	1	200	✘	✘	✘
transcript:Os01t0100800-01	Eukaryota	2	356	✘	✘	✘
transcript:Os01t0100900-01	cellular organisms	1	539	✘	✘	✘
transcript:Os01t0101150-00	cellular organisms	1	810	✘	✘	✘
transcript:Os01t0101200-01	cellular organisms	1	309	✘	✘	✘
transcript:Os01t0101200-02	cellular organisms	1	306	✘	✘	✘
transcript:Os01t0101300-01	Eukaryota	2	407	✘	✘	✘

Total number of records: 42355

Records per page: 10 | 20 | 50 | 100

Rules ^†

Hit in NCR*

Hit in NCR* and valid synteny

Hit in NCR* in outgroup

Hit in NCR* in outgroup and valid synteny

*NCR: Non-Coding Regions Apply

Output

Search entry by name

Select de novo status

All

Yes

No

Select orphan status

All

Yes

No

Select phylostratum 1 - cellular organisms 2 - Eukaryota 3 - Viridiplantae 4 - Streptophyta 5 - Streptophytina 6 - Embryophyta 7 - Tracheophyta 8 - Euphyllophyta 9 - Spermatophyta 10 - Magnoliopsida 11 - Mesangiospermae 12 - Liliopsida 13 - Petrosaviidae 14 - commelinids 15 - Poales 16 - Poaceae 17 - BOP clade 18 - Oryzeae 19 - Oryzinae 20 - Oryza 21 - Oryza sativa 22 - Oryza sativa Japonica Group X - Possible contamination or HGT X - Unknown

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Phylogeny

__ O. sativa __| | |__ O. rufipogon __| | | __ O. nivara | |__| __| |__ O. indica | | | | _____ O. glaberrima __| |__| | | |_____ O. barthii __| | | | |___________ O. glumipatula __| | | | |______________ O. meridionalis __| | | | |_________________ O. punctata _| | | |____________________ O. brachyantha | |_______________________ L. perrieri