Transcript 2786 | MetamORF

Transcript

ID CARD

MetamORF ID

2786

ENSMUST00000041111

Name

Sem1-201

Strand

Biotype

protein_coding

Start-end positions

6557294-6578658

CDS Start-stop positions

6558449-6578554

CDS Relative positions

Sequences

Transcript sequence

TCG ...

Genome browsers

UCSC

Gene

NCBI:20422

Aliases

DSS1,
ENSMUSG00000042541, MGI:109238, NCBI:20422,
OFF:Sem1, Sem1, Shfdg1,
Shfg, Shfm1

Chr 6

ORFs

26 ORFs

MetamORF ORF ID The MetamORF ID of the ORF. This is an unique ID referring to the ORF.	ORF lenght The genomic length of the ORF (in bp). This length is defined as the sum of the lengths of each exon constituting the ORF (thus excluding its eventual introns) and includes both the start and the stop codons.	Nucleic sequence The nucleic sequence of the ORF.	Amino acid sequence The amino acid sequence of the ORF.	Identification The method of identification used to identify the ORF. MetamORF currently integrates data from three main type of identification methods: bioinformatic predictions, ribosome profiling experiments and mass spectrometry experiments (either proteomics or proteogenomics). See the data sources section of the advances documentation for more information about this.	Start codon The start codon sequence of the ORF.	Kozak context The Kozak context computed by our algorithm for the ORF on the transcript. See the Kozak contexts section of the advanced documentation for more details regarding the nomenclature we use.	Exp. count The number of original datasets that identifed the ORF on the transcript.	Data sources The data sources in which the ORF has been identified. Click on the button to display all the original IDs in a pop-up. See the data sources section of the advanced documentation for more details regarding the information related to the data sources and the original ORF IDs.	ORF annotations A comma-separated list of the annotations computed by our algorithm for the ORF on the transcript. See the section dedicated to ORF annotations in the advanced documentation for more details regarding the nomenclature we use.	Cell types A comma-separated list of the cell types in which the ORF has already been identified on the transcript.
1687369	144	CTG ...	LGM ...	Ribo-seq	CTG	moderate	1	sORFs_org_Mouse	Downstream sORF	MEF
910253	57	ATC ...	IIA ...	Ribo-seq	ATC	moderate	1	sORFs_org_Mouse	Alternative Downstream Overlapping sORF	BMDC
207836	144	ATG ...	MTS ...	Ribo-seq	ATG		14	sORFs_org_Mouse Johnstone2016	Alternative Downstream Overlapping sORF	3T3, B_cell, Brain, C2C12, Glioma, Liver, MEF, MESC, Neutrophil, NSC, R1E, Spleen_B_cell, v6-5
198781	120	CTG ...	LSW ...	Ribo-seq	CTG	moderate	10	sORFs_org_Mouse	Alternative Downstream Overlapping sORF	3T3, B_cell, Brain, MEF, NSC, R1E, Spleen_B_cell, v6-5
3281	48	ATG ...	MKM ...	Ribo-seq	ATG	moderate	20	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, C2C12, E14, Liver, MEF, Neutrophil, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis, v6-5
204230	30	TTG ...	LSG ...	Ribo-seq	TTG	moderate	5	sORFs_org_Mouse	sORF Upstream	Brain, Liver, Neutrophil, NSC
1688372	138	ATG ...	MSQ ...	Ribo-seq	ATG	moderate	2	sORFs_org_Mouse Johnstone2016	Downstream sORF	Glioma, Liver, MEF, MESC
3006	36	ATG ...	MSG ...	Ribo-seq	ATG	weak	21	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, C2C12, E14, Liver, MEF, Neutrophil, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis, v6-5
69981	120	TTG ...	LRP ...	Ribo-seq	TTG		15	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	3T3, BMDC, Brain, C2C12, E14, Liver, MEF, Neutrophil, NSC, v6-5
911285	51	AAG ...	KRT ...	Ribo-seq	AAG		2	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC, MEF
69469	45	ATG ...	MVA ...	Ribo-seq	ATG	moderate	11	sORFs_org_Mouse Johnstone2016	sORF Upstream	3T3, BMDC, Brain, E14, Glioma, Liver, MEF, MESC, Neutrophil, NSC
415214	51	ATG ...	MTS ...	Ribo-seq	ATG		2	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	C2C12, MEF
2785	54	ATG ...	MKM ...	Ribo-seq	ATG	weak	22	sORFs_org_Mouse Johnstone2016	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, C2C12, E14, Glioma, Liver, MEF, MESC, Neutrophil, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis, v6-5
909539	276	AAG ...	KRT ...	Ribo-seq	AAG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC
907718	153	ATC ...	IGA ...	Ribo-seq	ATC		2	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	BMDC, E14
196143	123	GTG ...	VLS ...	Ribo-seq	GTG		7	sORFs_org_Mouse	Alternative Downstream Overlapping sORF	3T3, B_cell, Brain, MEF, NSC, v6-5
415680	33	AGG ...	RSF ...	Ribo-seq	AGG		2	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	C2C12, E14
415688	42	ACG ...	TSS ...	Ribo-seq	ACG		2	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC, C2C12
415569	267	ACG ...	TSS ...	Ribo-seq	ACG		2	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC, C2C12
2857	42	ATG ...	MHM ...	Ribo-seq	ATG	moderate	21	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, C2C12, E14, Liver, MEF, Neutrophil, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis, v6-5
415574	258	AGG ...	RSF ...	Ribo-seq	AGG		3	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC, C2C12, E14
3027	93	TTG ...	LAR ...	Ribo-seq	TTG		17	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	3T3, BMDC, Brain, C2C12, E14, Liver, MEF, Neutrophil, NSC, Skin_tumor, v6-5
415559	132	AGG ...	RLP ...	Ribo-seq	AGG		2	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	BMDC, C2C12
69858	135	CTG ...	LRL ...	Ribo-seq	CTG		14	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	3T3, BMDC, Brain, E14, Liver, MEF, Neutrophil, NSC, v6-5
1248872	45	ACG ...	TTS ...	Ribo-seq	ACG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	E14
1243997	270	ACG ...	TTS ...	Ribo-seq	ACG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	E14

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