Gene NCBI:93711 | MetamORF

Gene

ID CARD

NCBI:93711

Aliases

ENSMUSG00000104346
MGI:1935215, NCBI:93711, OFF:Pcdhga3
Pcdhga3

Chromosome

Transcripts

7 ORFs
1 known transcript
7 ORF to known transcript associations

MetamORF
transcript ID

The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.

Transcript ID

The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).

Transcript name

The transcript name (e.g. MDK-202).

Transcript biotype

The biotype of the transcript (as defined by Ensembl).

ORFs

Display all the transcripts related to the entry.

393140

ENSMUST00000073447

Pcdhga3-201

protein_coding

MetamORF ORF ID The MetamORF ID of the ORF. This is an unique ID referring to the ORF.	ORF length 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.
393237	156	CTG ...	LTR ...	Ribo-seq	CTG	moderate	1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	Brain
394852	123	CTG ...	LRT ...	Ribo-seq	CTG	weak	1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	Brain
393416	102	ATG ...	MPL ...	Ribo-seq	ATG	weak	1	Johnstone2016	Alternative Downstream Overlapping sORF	Glioma, Liver, MEF, MESC
393440	204	ATG ...	MLG ...	Ribo-seq	ATG	moderate	1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	Brain
398030	45	ATG ...	MGA ...	Ribo-seq	ATG	moderate	1	Johnstone2016	Alternative InCDS Overlapping sORF	Glioma, Liver, MEF, MESC
393139	276	ATG ...	MCQ ...	Ribo-seq	ATG	weak	1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	Brain
397424	147	ATG ...	MHK ...	Ribo-seq	ATG	moderate	1	sORFs_org_Mouse	Alternative InCDS Overlapping sORF	Brain

ORFs

7 ORFs
1 known transcript
7 ORF to known transcript associations

MetamORF
ORF ID

The MetamORF ID of the ORF. This is an unique ID referring to the ORF.

ORF Length

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.

Start codon

The start codon sequence of the ORF.

ORF annotations

A comma-separated list of all the annotations computed by our algorithm for the ORF. This list includes the annotations computed for the ORF for all transcripts. 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 all the cell types in which the ORF has already been identified.

Transcripts

Display all the transcripts related to the entry.

393416

102

ATG...

MPL...

ATG

Alternative
Downstream
Overlapping
sORF
NMD

Glioma, Liver, MEF,
MESC, Brain,
NSC, 3T3

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
1719393	ENSMUST00000192511	Pcdhga7-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
1196335	ENSMUST00000195239	Pcdhgc4-203	protein_coding	Ribo-seq	weak	1	Johnstone2016
392627	ENSMUST00000192931	Pcdhgb1-201	protein_coding	Ribo-seq	weak	2	sORFs_org_Mouse Johnstone2016
2475058	ENSMUST00000193404	Pcdhga10-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2475124	ENSMUST00000194928	Pcdhgb7-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2474771	ENSMUST00000195363	Pcdhgb4-202	protein_coding	Ribo-seq	weak	1	Johnstone2016
2474893	ENSMUST00000192535	Pcdhgb5-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
3171959	UNKNOWN_TRANSCRIPT			Predicted		1	Samandi2017
1005901	ENSMUST00000195823	Pcdhga6-201	protein_coding	Ribo-seq	weak	2	sORFs_org_Mouse Johnstone2016
2474232	ENSMUST00000115661	Gm42416-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
1154393	ENSMUST00000192103	Pcdhgc3-202	nonsense_mediated_decay	Ribo-seq	weak	2	sORFs_org_Mouse Johnstone2016
1630293	ENSMUST00000193869	Pcdhga2-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
396740	ENSMUST00000194190	Pcdhga1-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
713989	ENSMUST00000091935	Pcdhga9-201	protein_coding	Ribo-seq	weak	2	sORFs_org_Mouse Johnstone2016
411428	ENSMUST00000195764	Pcdhgb8-201	polymorphic_pseudogene	Ribo-seq	weak	1	sORFs_org_Mouse
2475172	ENSMUST00000061279	Pcdhga11-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2474484	ENSMUST00000194418	Pcdhga4-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2474584	ENSMUST00000193414	Pcdhga5-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2475008	ENSMUST00000003599	Pcdhgb6-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2475298	ENSMUST00000193941	Pcdhgc5-204	protein_coding	Ribo-seq	weak	1	Johnstone2016
2475230	ENSMUST00000044851	Pcdhga12-201	protein_coding	Ribo-seq	weak	1	Johnstone2016
2474542	ENSMUST00000195112	Pcdhgb2-202	protein_coding	Ribo-seq	weak	1	Johnstone2016
714198	ENSMUST00000066149	Pcdhga8-201	protein_coding	Ribo-seq	weak	1	Johnstone2016

398030

ATG...

MGA...

ATG

InCDS
Overlapping
sORF
Alternative
Downstream
NMD

3T3, Glioma, Liver,
MEF, MESC, Brain,
E14, R1E

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
713989	ENSMUST00000091935	Pcdhga9-201	protein_coding	Ribo-seq	moderate	2	sORFs_org_Mouse Johnstone2016
2474542	ENSMUST00000195112	Pcdhgb2-202	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2475058	ENSMUST00000193404	Pcdhga10-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2475230	ENSMUST00000044851	Pcdhga12-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2475298	ENSMUST00000193941	Pcdhgc5-204	protein_coding	Ribo-seq	moderate	1	Johnstone2016
714198	ENSMUST00000066149	Pcdhga8-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
1630293	ENSMUST00000193869	Pcdhga2-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
1154393	ENSMUST00000192103	Pcdhgc3-202	nonsense_mediated_decay	Ribo-seq	moderate	1	Johnstone2016
411428	ENSMUST00000195764	Pcdhgb8-201	polymorphic_pseudogene	Ribo-seq	moderate	1	sORFs_org_Mouse
2474584	ENSMUST00000193414	Pcdhga5-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
1196335	ENSMUST00000195239	Pcdhgc4-203	protein_coding	Ribo-seq	moderate	2	sORFs_org_Mouse Johnstone2016
2474484	ENSMUST00000194418	Pcdhga4-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2474893	ENSMUST00000192535	Pcdhgb5-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2475172	ENSMUST00000061279	Pcdhga11-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
392627	ENSMUST00000192931	Pcdhgb1-201	protein_coding	Ribo-seq	moderate	2	sORFs_org_Mouse Johnstone2016
396740	ENSMUST00000194190	Pcdhga1-201	protein_coding	Ribo-seq	moderate	2	sORFs_org_Mouse Johnstone2016
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2474232	ENSMUST00000115661	Gm42416-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
1005901	ENSMUST00000195823	Pcdhga6-201	protein_coding	Ribo-seq	moderate	2	sORFs_org_Mouse Johnstone2016
1719393	ENSMUST00000192511	Pcdhga7-201	protein_coding	Ribo-seq	moderate	2	sORFs_org_Mouse Johnstone2016
2475008	ENSMUST00000003599	Pcdhgb6-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2474771	ENSMUST00000195363	Pcdhgb4-202	protein_coding	Ribo-seq	moderate	1	Johnstone2016
2475124	ENSMUST00000194928	Pcdhgb7-201	protein_coding	Ribo-seq	moderate	1	Johnstone2016

393237

156

CTG...

LTR...

CTG

Alternative
InCDS
Overlapping
sORF

Brain

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	moderate	1	sORFs_org_Mouse

394852

123

CTG...

LRT...

CTG

Alternative
InCDS
Overlapping
sORF

Brain

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	weak	1	sORFs_org_Mouse

393440

204

ATG...

MLG...

ATG

Alternative
InCDS
Overlapping
sORF

Brain

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	moderate	1	sORFs_org_Mouse

393139

276

ATG...

MCQ...

ATG

Alternative
InCDS
Overlapping
sORF

Brain

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	weak	1	sORFs_org_Mouse

397424

147

ATG...

MHK...

ATG

Alternative
InCDS
Overlapping
sORF

Brain

MetamORF transcript ID The MetamORF ID of the transcript. This is an arbitrary ID that does not correspond to any official (Ensembl, NCBI...) transcript ID or external reference.	Transcript ID The official transcript ID (usually an Ensembl ID, e.g. ENST00000395565).	Transcript name The transcript name (e.g. MDK-202).	Transcript biotype The biotype of the transcript (as defined by Ensembl).	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.	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.
393140	ENSMUST00000073447	Pcdhga3-201	protein_coding	Ribo-seq	moderate	1	sORFs_org_Mouse

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