DeNovoGenesDB

A. thaliana

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
• Code
• Gene
• Phylostratum
• Rank
• Protein size
• Is denovo?
• Is orphan?
• Is TRG?

Table content is loading...

CDS	Code	Gene	Phylostratum	Rank	Protein size	Is denovo?	Is orphan?	Is TRG?
rna-NM_203102.2	NM_203102.2	—	cellular organisms	1	352	✘	✘	✘
rna-NM_203103.3	NM_203103.3	—	cellular organisms	1	520	✘	✘	✘
rna-NM_203104.2	NM_203104.2	—	Eukaryota	2	997	✘	✘	✘
rna-NM_203105.2	NM_203105.2	—	Tracheophyta	7	99	✘	✘	✘
rna-NM_203106.3	NM_203106.3	—	cellular organisms	1	418	✘	✘	✘
rna-NM_203107.3	NM_203107.3	—	cellular organisms	1	422	✘	✘	✘
rna-NM_203108.2	NM_203108.2	—	cellular organisms	1	298	✘	✘	✘
rna-NM_203109.2	NM_203109.2	—	cellular organisms	1	475	✘	✘	✘
rna-NM_203110.2	NM_203110.2	—	Eukaryota	2	735	✘	✘	✘
rna-NM_203111.2	NM_203111.2	—	Embryophyta	6	335	✘	✘	✘
rna-NM_203112.1	NM_203112.1	—	Mesangiospermae	11	156	✘	✘	✘
rna-NM_203113.3	NM_203113.3	DPD1	cellular organisms	1	316	✘	✘	✘
rna-NM_203114.2	NM_203114.2	DES1	cellular organisms	1	323	✘	✘	✘
rna-NM_203115.2	NM_203115.2	—	cellular organisms	1	465	✘	✘	✘
rna-NM_203117.2	NM_203117.2	—	cellular organisms	1	1087	✘	✘	✘

Total number of records: 48224

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 - Pentapetalae 13 - rosids 14 - malvids 15 - Brassicales 16 - Brassicaceae 17 - Camelineae 18 - Arabidopsis 19 - Arabidopsis thaliana X - Possible contamination or HGT X - Unknown

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Phylogeny

__ A. thaliana __| __| |__ A. suecica | | | | __ A. lyrata | |__| _| |__ A. halleri | |________ C. rubella