DeNovoGenesDB

M. musculus

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 Murinae 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?

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CDS	Code	Gene	Phylostratum	Rank	Protein size	Is denovo?	Is orphan?	Is TRG?
rna-NM_025319.2	NM_025319.2	0610009B22Rik	cellular organisms	1	140	✘	✘	✘
rna-XM_006533917.5	XM_006533917.5	0610009B22Rik	cellular organisms	1	140	✘	✘	✘
rna-XM_006533918.3	XM_006533918.3	0610009B22Rik	cellular organisms	1	140	✘	✘	✘
rna-XM_006533919.3	XM_006533919.3	0610009B22Rik	cellular organisms	1	140	✘	✘	✘
rna-NM_001177601.1	NM_001177601.1	0610010K14Rik	Eumetazoa	5	191	✘	✘	✘
rna-NM_001177603.1	NM_001177603.1	0610010K14Rik	Eumetazoa	5	156	✘	✘	✘
rna-NM_001177606.1	NM_001177606.1	0610010K14Rik	Eumetazoa	5	122	✘	✘	✘
rna-NM_001177607.1	NM_001177607.1	0610010K14Rik	Eumetazoa	5	109	✘	✘	✘
rna-NM_026757.2	NM_026757.2	0610010K14Rik	Eumetazoa	5	137	✘	✘	✘
rna-NM_145758.1	NM_145758.1	0610010K14Rik	Eumetazoa	5	171	✘	✘	✘
rna-XM_017314213.3	XM_017314213.3	0610010K14Rik	Eumetazoa	5	157	✘	✘	✘
rna-XM_030245456.2	XM_030245456.2	0610010K14Rik	Eumetazoa	5	109	✘	✘	✘
rna-NM_001370862.1	NM_001370862.1	1110002E22Rik	Gnathostomata	10	1786	✘	✘	✘
rna-XM_030252339.2	XM_030252339.2	1110002E22Rik	Gnathostomata	10	1786	✘	✘	✘
rna-NM_001048005.1	NM_001048005.1	1110017D15Rik	Tetrapoda	14	260	✘	✘	✘
rna-NM_001253777.1	NM_001253777.1	1110017D15Rik	Tetrapoda	14	296	✘	✘	✘
rna-NM_001253778.1	NM_001253778.1	1110017D15Rik	Tetrapoda	14	162	✘	✘	✘
rna-NM_001253780.1	NM_001253780.1	1110017D15Rik	Euarchontoglires	20	68	✘	✘	✘
rna-NM_001253788.1	NM_001253788.1	1110017D15Rik	Tetrapoda	14	202	✘	✘	✘
rna-NM_028624.1	NM_028624.1	1110017D15Rik	Tetrapoda	14	126	✘	✘	✘
rna-XM_006538307.5	XM_006538307.5	1110017D15Rik	Tetrapoda	14	246	✘	✘	✘
rna-XM_006538308.4	XM_006538308.4	1110017D15Rik	Tetrapoda	14	240	✘	✘	✘
rna-XM_030253836.1	XM_030253836.1	1110017D15Rik	Tetrapoda	14	210	✘	✘	✘
rna-XM_030253837.2	XM_030253837.2	1110017D15Rik	Tetrapoda	14	204	✘	✘	✘
rna-NM_001276278.1	NM_001276278.1	1110025L11Rik	Glires	21	78	✘	✘	✘
rna-XM_036159678.1	XM_036159678.1	1110025M09Rik	Mus musculus	29	147	✘	✔	✔
rna-NM_001167996.1	NM_001167996.1	1110032F04Rik	Gnathostomata	10	247	✘	✘	✘
rna-NM_001311144.1	NM_001311144.1	1110051M20Rik	Eukaryota	2	326	✘	✘	✘
rna-NM_175123.5	NM_175123.5	1110051M20Rik	Eukaryota	2	331	✘	✘	✘
rna-XM_036161262.1	XM_036161262.1	1110051M20Rik	Eumetazoa	5	269	✘	✘	✘
rna-NM_025423.2	NM_025423.2	1110059E24Rik	cellular organisms	1	155	✘	✘	✘
rna-NM_025419.4	NM_025419.4	1110059G10Rik	Eumetazoa	5	155	✘	✘	✘
rna-NM_027918.2	NM_027918.2	1300017J02Rik	cellular organisms	1	700	✘	✘	✘
rna-XM_006511835.4	XM_006511835.4	1300017J02Rik	cellular organisms	1	468	✘	✘	✘
rna-XM_017317746.2	XM_017317746.2	1520401A03Rik	Theria	17	687	✘	✘	✘
rna-XM_017317747.2	XM_017317747.2	1520401A03Rik	Theria	17	677	✘	✘	✘
rna-XM_017317748.2	XM_017317748.2	1520401A03Rik	Theria	17	676	✘	✘	✘
rna-XM_017317749.2	XM_017317749.2	1520401A03Rik	Eutheria	18	669	✘	✘	✘
rna-XM_017317750.2	XM_017317750.2	1520401A03Rik	Theria	17	666	✘	✘	✘
rna-XM_017317751.2	XM_017317751.2	1520401A03Rik	Theria	17	654	✘	✘	✘
rna-XM_017317752.2	XM_017317752.2	1520401A03Rik	Theria	17	623	✘	✘	✘
rna-XM_017317753.3	XM_017317753.3	1520401A03Rik	Theria	17	618	✘	✘	✘
rna-XM_017317755.3	XM_017317755.3	1520401A03Rik	Theria	17	618	✘	✘	✘
rna-XM_017317756.2	XM_017317756.2	1520401A03Rik	Theria	17	611	✘	✘	✘
rna-XM_017317757.2	XM_017317757.2	1520401A03Rik	Theria	17	591	✘	✘	✘
rna-XM_017317758.2	XM_017317758.2	1520401A03Rik	Theria	17	579	✘	✘	✘
rna-NM_001083880.1	NM_001083880.1	1600012H06Rik	Eumetazoa	5	185	✘	✘	✘
rna-NM_001083881.1	NM_001083881.1	1600012H06Rik	Eumetazoa	5	185	✘	✘	✘
rna-NM_001083882.1	NM_001083882.1	1600012H06Rik	Eumetazoa	5	185	✘	✘	✘
rna-NM_026451.2	NM_026451.2	1600012H06Rik	Eumetazoa	5	185	✘	✘	✘
rna-NM_001085385.1	NM_001085385.1	1600014C10Rik	Eumetazoa	5	141	✘	✘	✘
rna-NM_028166.3	NM_028166.3	1600014C10Rik	Eumetazoa	5	141	✘	✘	✘
rna-NM_028164.1	NM_028164.1	1600014C23Rik	Mus musculus	29	101	✘	✔	✔
rna-XM_006524968.4	XM_006524968.4	1600014C23Rik	Mus musculus	29	101	✘	✔	✔
rna-NM_001172091.1	NM_001172091.1	1700001C19Rik	Metazoa	4	115	✘	✘	✘
rna-NM_001347584.1	NM_001347584.1	1700001C19Rik	Metazoa	4	113	✘	✘	✘
rna-NM_029296.2	NM_029296.2	1700001C19Rik	Eumetazoa	5	210	✘	✘	✘
rna-XM_030250126.1	XM_030250126.1	1700001C19Rik	Eumetazoa	5	212	✘	✘	✘
rna-XM_030250127.1	XM_030250127.1	1700001C19Rik	Eumetazoa	5	208	✘	✘	✘
rna-NM_001008547.1	NM_001008547.1	1700001J03Rik	Euteleostomi	11	219	✘	✘	✘
rna-XM_030254790.2	XM_030254790.2	1700001J03Rik	Euteleostomi	11	229	✘	✘	✘
rna-XM_030254791.2	XM_030254791.2	1700001J03Rik	Euteleostomi	11	219	✘	✘	✘
rna-NM_198000.3	NM_198000.3	1700001O22Rik	Theria	17	375	✘	✘	✘
rna-XM_006498375.4	XM_006498375.4	1700001O22Rik	Theria	17	387	✘	✘	✘
rna-XM_006498376.4	XM_006498376.4	1700001O22Rik	Theria	17	363	✘	✘	✘
rna-XM_011239195.4	XM_011239195.4	1700001O22Rik	Theria	17	403	✘	✘	✘
rna-XM_011239196.4	XM_011239196.4	1700001O22Rik	Theria	17	391	✘	✘	✘
rna-XM_011239197.4	XM_011239197.4	1700001O22Rik	Theria	17	379	✘	✘	✘
rna-XM_011239198.3	XM_011239198.3	1700001O22Rik	Theria	17	307	✘	✘	✘
rna-XM_011239199.3	XM_011239199.3	1700001O22Rik	Theria	17	295	✘	✘	✘
rna-XM_011239200.3	XM_011239200.3	1700001O22Rik	Theria	17	260	✘	✘	✘
rna-XM_030252119.2	XM_030252119.2	1700001O22Rik	Theria	17	248	✘	✘	✘
rna-XM_030252120.2	XM_030252120.2	1700001O22Rik	Theria	17	224	✘	✘	✘
rna-XM_036162617.1	XM_036162617.1	1700001O22Rik	Theria	17	260	✘	✘	✘
rna-NM_029305.2	NM_029305.2	1700003F12Rik	Theria	17	197	✘	✘	✘
rna-XM_017319305.3	XM_017319305.3	1700003F12Rik	Theria	17	210	✘	✘	✘
rna-NM_001368235.1	NM_001368235.1	1700003H04Rik	Eumetazoa	5	99	✘	✘	✘
rna-NM_001357195.1	NM_001357195.1	1700006A11Rik	cellular organisms	1	472	✘	✘	✘
rna-NM_027939.2	NM_027939.2	1700006A11Rik	cellular organisms	1	544	✘	✘	✘
rna-NM_027040.1	NM_027040.1	1700007K13Rik	Opisthokonta	3	167	✘	✘	✘
rna-NM_027049.1	NM_027049.1	1700008O03Rik	Bilateria	6	196	✘	✘	✘
rna-XM_006541171.2	XM_006541171.2	1700008O03Rik	Chordata	8	264	✘	✘	✘
rna-XM_006541172.5	XM_006541172.5	1700008O03Rik	Bilateria	6	165	✘	✘	✘
rna-XM_011250899.4	XM_011250899.4	1700008O03Rik	Bilateria	6	165	✘	✘	✘
rna-XM_011250900.4	XM_011250900.4	1700008O03Rik	Deuterostomia	7	113	✘	✘	✘
rna-XM_017312286.1	XM_017312286.1	1700008O03Rik	Bilateria	6	328	✘	✘	✘
rna-XM_030242968.1	XM_030242968.1	1700008O03Rik	Deuterostomia	7	113	✘	✘	✘
rna-XM_030242969.2	XM_030242969.2	1700008O03Rik	Deuterostomia	7	113	✘	✘	✘
rna-NM_001081095.1	NM_001081095.1	1700009N14Rik	cellular organisms	1	216	✘	✘	✘
rna-NM_026315.1	NM_026315.1	1700011L22Rik	Amniota	15	208	✘	✘	✘
rna-XM_011248492.3	XM_011248492.3	1700011L22Rik	Amniota	15	157	✘	✘	✘
rna-NM_029306.3	NM_029306.3	1700012B09Rik	Sarcopterygii	12	121	✘	✘	✘
rna-NM_027063.2	NM_027063.2	1700013G24Rik	Theria	17	286	✘	✘	✘
rna-NM_001200013.1	NM_001200013.1	1700013H16Rik	Metazoa	4	291	✘	✘	✘
rna-XM_006535361.4	XM_006535361.4	1700013H16Rik	Metazoa	4	153	✘	✘	✘
rna-XM_017315672.3	XM_017315672.3	1700014D04Rik	cellular organisms	1	983	✘	✘	✘
rna-NM_001368200.1	NM_001368200.1	1700019A02Rik	Boreoeutheria	19	146	✘	✘	✘
rna-NM_027070.2	NM_027070.2	1700019A02Rik	Boreoeutheria	19	146	✘	✘	✘
rna-XM_006496255.3	XM_006496255.3	1700019A02Rik	Tetrapoda	14	168	✘	✘	✘
rna-XM_036153462.1	XM_036153462.1	1700019A02Rik	Boreoeutheria	19	219	✘	✘	✘

Total number of records: 40867

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

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Select phylostratum 1 - cellular organisms 2 - Eukaryota 3 - Opisthokonta 4 - Metazoa 5 - Eumetazoa 6 - Bilateria 7 - Deuterostomia 8 - Chordata 9 - Vertebrata 10 - Gnathostomata 11 - Euteleostomi 12 - Sarcopterygii 13 - Dipnotetrapodomorpha 14 - Tetrapoda 15 - Amniota 16 - Mammalia 17 - Theria 18 - Eutheria 19 - Boreoeutheria 20 - Euarchontoglires 21 - Glires 22 - Rodentia 23 - Myomorpha 24 - Muroidea 25 - Muridae 26 - Murinae 27 - Mus 28 - Mus 29 - Mus musculus X - Unknown X - Possible contamination or HGT

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Phylogeny

____ M. musculus __| __| |____ M. caroli | | __| |_______ M. pahari | | | | _______ A. niloticus | |__| | |_______ G. surdaster | _| __ R. rattus |__________| | |__ R. norvegicus | |_____________ M. coucha