Transcript 1632 | MetamORF

Transcript

ID CARD

MetamORF ID

1632

ENSMUST00000170181

Name

Sema3c-204

Strand

Biotype

nonsense_mediated_decay

Start-end positions

17574649-17682083

CDS Start-stop positions

17576868-17670475

CDS Relative positions

Sequences

Transcript sequence

AGC ...

Genome browsers

UCSC

Gene

NCBI:20348

Aliases

1110036B02Rik,
ENSMUSG00000028780, MGI:107557, NCBI:20348,
OFF:Sema3c, Sema3c, Semae,
SemE

Chr 5

ORFs

30 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.
1660350	60	TTG ...	LYL ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Downstream NMD sORF	MEF
181218	57	TTG ...	LNI ...	Ribo-seq	TTG		1	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Brain
182572	36	CTG ...	LAK ...	Ribo-seq	CTG	strong	1	sORFs_org_Mouse	Alternative Downstream NMD sORF	MEF
1660409	33	CTG ...	LST ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	MEF
168851	63	CTG ...	LSL ...	Ribo-seq	CTG		1	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Brain
1661880	51	ATG ...	MTL ...	Ribo-seq	ATG	weak	2	sORFs_org_Mouse Johnstone2016	Downstream NMD sORF	Glioma, Liver, MEF, MESC
1665261	171	ATG ...	MSF ...	Ribo-seq	ATG		1	Johnstone2016	Alternative Downstream NMD sORF	Glioma, Liver, MEF, MESC
184970	54	ATG ...	MKI ...	Ribo-seq	ATG		2	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Brain, MEF
184251	48	GTG ...	VDH ...	Ribo-seq	GTG	moderate	1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Brain
1663907	33	ATG ...	MWG ...	Ribo-seq	ATG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	MEF
61893	141	GTG ...	VIP ...	Ribo-seq	GTG		4	sORFs_org_Mouse	Alternative Downstream NMD sORF	Brain, E14, MEF, Testis
175126	48	ATG ...	MLF ...	Ribo-seq	ATG		3	sORFs_org_Mouse	Alternative Downstream NMD sORF	E14, MEF
1663222	33	TTG ...	LYR ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Downstream NMD sORF	MEF
61453	30	GTG ...	VYG ...	Ribo-seq	GTG		2	sORFs_org_Mouse	Alternative Downstream NMD sORF	E14, Testis
1631	39	TTG ...	LKS ...	Ribo-seq	TTG		3	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Brain, MEF, Skin_tumor
65418	33	GTG ...	VNT ...	Ribo-seq	GTG		3	sORFs_org_Mouse	Downstream NMD sORF	Brain, MEF, Testis
169809	114	CTG ...	LMD ...	Ribo-seq	CTG		1	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Brain
61696	117	TTG ...	LLM ...	Ribo-seq	TTG		2	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Brain, Testis
1663295	45	ATG ...	MSV ...	Ribo-seq	ATG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	MEF
189339	48	ATG ...	MLF ...	Ribo-seq	ATG		1	Johnstone2016	Alternative Downstream NMD sORF	Glioma, Liver, MEF, MESC
62427	81	CTG ...	LTD ...	Ribo-seq	CTG		3	sORFs_org_Mouse	Alternative Downstream NMD sORF	Brain, MEF, Testis
1664643	42	GTG ...	VNL ...	Ribo-seq	GTG	moderate	1	sORFs_org_Mouse	Alternative Downstream NMD sORF	MEF
1660806	39	ATG ...	MQF ...	Ribo-seq	ATG	moderate	3	sORFs_org_Mouse Johnstone2016	Alternative Downstream NMD sORF	Glioma, Liver, MEF, MESC
63481	60	CTG ...	LET ...	Ribo-seq	CTG		3	sORFs_org_Mouse	Alternative Downstream NMD sORF	E14, MEF, Testis
63062	63	CTG ...	LLE ...	Ribo-seq	CTG		4	sORFs_org_Mouse	Alternative Downstream NMD sORF	Brain, E14, MEF, Testis
66143	153	GTG ...	VDA ...	Ribo-seq	GTG		3	sORFs_org_Mouse	Alternative Downstream NMD sORF	Brain, E14, Testis
63384	147	CTG ...	LSH ...	Ribo-seq	CTG		4	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Brain, E14, MEF, Testis
1660277	45	CTG ...	LVD ...	Ribo-seq	CTG	strong	1	sORFs_org_Mouse	Downstream NMD sORF	MEF
1661938	36	GTG ...	VQN ...	Ribo-seq	GTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	MEF
181587	84	GTG ...	VGS ...	Ribo-seq	GTG		1	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Brain

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