DeNovoDB

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	Code	Gene	Phylostratum	Rank	Protein size	Is denovo?	Is orphan?	Is TRG?
transcript:2L52.1a.1	WBGene00007063	2L52.1	Chromadorea	10	427	✘	✘	✘
transcript:2L52.1b.1	WBGene00007063	2L52.1	Caenorhabditis	14	220	✘	✘	✘
transcript:2RSSE.1a.1	WBGene00007064	rga-9	Eukaryota	2	343	✘	✘	✘
transcript:2RSSE.1b.1	WBGene00007064	rga-9	Eukaryota	2	478	✘	✘	✘
transcript:2RSSE.1c.1	WBGene00007064	rga-9	Eukaryota	2	258	✘	✘	✘
transcript:3R5.1a.1	WBGene00007065	pot-3	Caenorhabditis	14	215	✘	✘	✔
transcript:3R5.1b.1	WBGene00007065	pot-3	Caenorhabditis	14	211	✘	✘	✔
transcript:4R79.1a.1	WBGene00003525	nas-6	cellular organisms	1	344	✘	✘	✘
transcript:4R79.1b.1	WBGene00003525	nas-6	cellular organisms	1	180	✘	✘	✘
transcript:4R79.2a.1	WBGene00007067	4R79.2	cellular organisms	1	395	✘	✘	✘
transcript:4R79.2b.1	WBGene00007067	4R79.2	cellular organisms	1	311	✘	✘	✘
transcript:AC3.10.1	WBGene00004964	spe-10	cellular organisms	1	351	✘	✘	✘
transcript:AC3.10.2	WBGene00004964	spe-10	cellular organisms	1	351	✘	✘	✘
transcript:AC3.12.1	WBGene00077503	AC3.12	Chromadorea	10	94	✘	✘	✘
transcript:AC3.1a.1	WBGene00005532	sri-20	Rhabditida	11	355	✘	✘	✘

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Total number of records: 31755

Records per page: 10 | 20 | 50 | 100

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.

DeNovoGenesDB

C. elegans

Rules ^†

Output

Phylogeny

C. elegans

Rules †

Output

Phylogeny

Rules ^†