Transcript 16257 | MetamORF

Transcript

ID CARD

MetamORF ID

16257

ENSMUST00000017153

Name

Sdc4-201

Strand

Biotype

protein_coding

Start-end positions

164424247-164443186

CDS Start-stop positions

164426086-164443164

CDS Relative positions

Sequences

Transcript sequence

ACT ...

Genome browsers

UCSC

Gene

NCBI:20971

Aliases

AA959608,
AW108331, ENSMUSG00000017009, MGI:1349164,
NCBI:20971, OFF:Sdc4, ryudocan,
S4, Sdc4, Synd4,
syndecan-4

Chr 2

ORFs

22 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.
51407	63	TTG ...	LSS ...	Ribo-seq	TTG		14	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, Liver, MEF, NSC, R1E, Spleen_B_cell, Testis
970475	45	AGG ...	RAA ...	Ribo-seq	AGG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC
500499	246	TTG ...	LKP ...	Ribo-seq	TTG		9	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	3T3, B_cell, Brain, Liver, MEF, R1E, Spleen_B_cell
970441	120	AGG ...	RSF ...	Ribo-seq	AGG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC
49855	84	ATG ...	MLA ...	Ribo-seq	ATG		19	sORFs_org_Mouse Johnstone2016	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, C2C12, E14, Glioma, Liver, MEF, MESC, NSC, R1E, Spleen_B_cell, Testis
51491	69	ATG ...	MTL ...	Ribo-seq	ATG		16	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, Liver, MEF, NSC, R1E, Spleen_B_cell, Testis
46202	36	ATG ...	MTR ...	Ribo-seq	ATG	weak	9	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, Brain, Liver, MEF, Spleen_B_cell, Testis
16256	81	CTG ...	LAA ...	Ribo-seq	CTG		15	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, Brain, Liver, MEF, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis
50138	48	CTG ...	LEI ...	Ribo-seq	CTG		12	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, Liver, MEF, R1E, Spleen_B_cell, Testis
1213145	129	ATG ...	MLA ...	Ribo-seq	ATG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	E14
16576	51	CTG ...	LPR ...	Ribo-seq	CTG		16	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, E14, Liver, MEF, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis, v6-5
50314	189	CTG ...	LFE ...	Ribo-seq	CTG		14	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, Brain, E14, Liver, MEF, R1E, Spleen_B_cell, Testis
16293	84	ATG ...	MTC ...	Ribo-seq	ATG		17	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, E14, Liver, MEF, NSC, Skin_tumor, Spleen_B_cell, Testis, v6-5
970542	42	ATC ...	IWM ...	Ribo-seq	ATC		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	BMDC
501634	249	CTG ...	LLK ...	Ribo-seq	CTG		9	sORFs_org_Mouse	Alternative Overlapping sORF Upstream	3T3, B_cell, Brain, Liver, MEF, R1E, Spleen_B_cell
968343	222	CTG ...	LPA ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	E14
16455	30	TTG ...	LRE ...	Ribo-seq	TTG		16	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, E14, Liver, MEF, NSC, R1E, Skin_tumor, Spleen_B_cell, Testis, v6-5
1637840	153	CTG ...	LEP ...	Ribo-seq	CTG		2	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	MEF
50921	219	TTG ...	LRR ...	Ribo-seq	TTG		18	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, E14, Liver, MEF, NSC, R1E, Spleen_B_cell, Testis
50240	231	CTG ...	LPA ...	Ribo-seq	CTG		15	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, BMDC, Brain, E14, Liver, MEF, NSC, R1E, Spleen_B_cell, Testis
49946	108	CTG ...	LEP ...	Ribo-seq	CTG		14	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	3T3, B_cell, Brain, E14, Liver, MEF, R1E, Spleen_B_cell, Testis
966347	210	TTG ...	LRR ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	E14

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