Transcript 56419 | MetamORF

Transcript

ID CARD

MetamORF ID

56419

ENSMUST00000123244

Name

Sycp3-202

Strand

Biotype

nonsense_mediated_decay

Start-end positions

88459664-88473236

CDS Start-stop positions

88459666-88467320

CDS Relative positions

Sequences

Transcript sequence

AGA ...

Genome browsers

UCSC

Gene

NCBI:20962

Aliases

Cor1,
ENSMUSG00000020059, MGI:109542, NCBI:20962,
OFF:Sycp3, Scp3, Sycp3

Chr 10

ORFs

29 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.
72475	114	GTG ...	VLQ ...	Ribo-seq	GTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
63337	111	TTG ...	LQQ ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
77453	63	TTG ...	LQK ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
69803	114	TTG ...	LIS ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
58821	51	TTG ...	LRN ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
65171	108	TTG ...	LYF ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Downstream NMD sORF	Testis
75252	117	GTG ...	VAF ...	Ribo-seq	GTG		1	sORFs_org_Mouse	Downstream NMD sORF	Testis
58708	96	CTG ...	LDI ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
69478	93	CTG ...	LSF ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
76433	36	TTG ...	LEN ...	Ribo-seq	TTG		1	sORFs_org_Mouse	InCDS NMD Overlapping sORF	Testis
77711	93	TTG ...	LTL ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
80244	156	GTG ...	VEE ...	Ribo-seq	GTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
61258	78	ATG ...	MIK ...	Ribo-seq	ATG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
57091	132	CTG ...	LGS ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
83058	42	CTG ...	LTS ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
67576	159	CTG ...	LVE ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
76118	87	ATG ...	MWK ...	Ribo-seq	ATG	moderate	2	sORFs_org_Mouse Johnstone2016	Downstream NMD sORF	Glioma, Liver, MEF, MESC, Testis
61839	141	CTG ...	LGN ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
57796	51	ATG ...	MFI ...	Ribo-seq	ATG		1	sORFs_org_Mouse	Downstream NMD sORF	Testis
90067	126	ATG ...	MCC ...	Ribo-seq	ATG		1	Johnstone2016	Alternative Downstream NMD sORF	Glioma, Liver, MEF, MESC
86511	138	TTG ...	LED ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
58162	87	TTG ...	LRK ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
75741	87	ATG ...	MCC ...	Ribo-seq	ATG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
85598	129	GTG ...	VEK ...	Ribo-seq	GTG		1	sORFs_org_Mouse	Alternative Downstream NMD sORF	Testis
82799	96	TTG ...	LLS ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
81865	45	GTG ...	VNL ...	Ribo-seq	GTG	moderate	1	sORFs_org_Mouse	Downstream NMD sORF	Testis
71876	39	CTG ...	LEK ...	Ribo-seq	CTG		1	sORFs_org_Mouse	Alternative InCDS NMD Overlapping sORF	Testis
85631	57	TTG ...	LFL ...	Ribo-seq	TTG		1	sORFs_org_Mouse	Alternative CDS NMD sORF	Testis
56418	72	ATG ...	MII ...	Ribo-seq	ATG	moderate	1	sORFs_org_Mouse	Downstream NMD sORF	Testis

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