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Summary
Sequence- Protein Information
- Genetic Variation
- External References
- ID History
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Transcript: ENST00000303395.9SCN1A-201
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sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
FEB3, GEFSP2, HBSCI, NAC1, NAV1.1, SCN1, SMEI
Chromosome 2: 165,985,813-166,128,020 reverse strand.
This transcript has28 exons, is annotated with75 domains and features, is associated with62225 variant alleles and maps to801 oligo probes.
This transcript is a product of geneENSG00000144285.24Show transcript tableHide transcript table
| Transcript ID | Name | bp | Protein | Translation ID | Biotype | CCDS | UniProt Match | RefSeq Match | Flags |
|---|---|---|---|---|---|---|---|---|---|
| ENST00000674923.1 | SCN1A-224 | 11940 | 2009aa | ENSP00000501589.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS54413 | P35498-1 | NM_001165963.4 | The Matched Annotation from NCBI and EMBL-EBI is a collaboration between Ensembl/GENCODE and RefSeq. The MANE Select is a default transcript per human gene that is representative of biology, well-supported, expressed and highly-conserved. This transcript set matches GRCh38 and is 100% identical between RefSeq and Ensembl/GENCODE for 5' UTR, CDS, splicing and 3'UTR.MANE Select,A single transcript chosen for a gene which is the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt. This is defined in detail on http://www.ensembl.org/info/genome/genebuild/canonical.htmlEnsembl Canonical,GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS ALT1: For genes in which the APPRIS core modules are unable to choose a clear principal isoform, the ALT1 is the candidate transcript(s) models that is conserved in at least three tested species. APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene. APPRIS ALT1, |
| ENST00000641575.1 | SCN1A-218 | 12874 | 1997aa | ENSP00000492917.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS86891 | A0A286YF26 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS ALT1: For genes in which the APPRIS core modules are unable to choose a clear principal isoform, the ALT1 is the candidate transcript(s) models that is conserved in at least three tested species. APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene. APPRIS ALT1, |
| ENST00000641603.1 | SCN1A-219 | 12506 | 1915aa | ENSP00000492945.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A286YEQ8 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, | |
| ENST00000303395.9 | SCN1A-201 | 11853 | 2009aa | ENSP00000303540.4 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS54413 | P35498-1 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS ALT1: For genes in which the APPRIS core modules are unable to choose a clear principal isoform, the ALT1 is the candidate transcript(s) models that is conserved in at least three tested species. APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene. APPRIS ALT1,TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, |
| ENST00000635776.1 | SCN1A-209 | 10107 | 1618aa | ENSP00000490692.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A1B0GVX7 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000637988.1 | SCN1A-216 | 8562 | 1998aa | ENSP00000490780.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS33316 | P35498-2 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P4: Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with a distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene. APPRIS P4,TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, |
| ENST00000635750.1 | SCN1A-208 | 8299 | 1998aa | ENSP00000490799.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS33316 | P35498-2 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P4: Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with a distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene. APPRIS P4,TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, |
| ENST00000640036.1 | SCN1A-217 | 8131 | 1998aa | ENSP00000491573.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A1W2PPJ3 | - | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000375405.7 | SCN1A-202 | 8097 | 1998aa | ENSP00000364554.3 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS33316 | P35498-2 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P4: Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with a distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant. APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene. APPRIS P4,TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, |
| ENST00000713692.1 | SCN1A-226 | 7757 | 1927aa | ENSP00000518996.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, | |
| ENST00000409050.2 | SCN1A-203 | 7376 | 1981aa | ENSP00000386312.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS54414 | P35498-3 | - | GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE Primary,A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, |
| ENST00000637285.2 | SCN1A-214 | 133 | 3aa | ENSP00000490612.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5,3' truncation in transcript evidence prevents annotation of the end of the CDS.CDS 3' incomplete, | |
| ENST00000641996.1 | SCN1A-220 | 12903 | 149aa | ENSP00000493054.1 | Nonsense mediated decay | A0A286YFA8 | - | - | |
| ENST00000636194.1 | SCN1A-211 | 8508 | 829aa | ENSP00000490288.1 | Nonsense mediated decay | A0A1B0GUX7 | - | TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000637038.2 | SCN1A-213 | 8426 | 1387aa | ENSP00000490184.2 | Nonsense mediated decay | A0A1B0GUN7 | - | TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000671940.1 | SCN1A-222 | 8315 | 629aa | ENSP00000500336.1 | Nonsense mediated decay | A0A5F9ZHI6 | - | - | |
| ENST00000689288.1 | SCN1A-225 | 8258 | 685aa | ENSP00000509637.1 | Nonsense mediated decay | A0A8I5KYC1 | - | - | |
| ENST00000636759.1 | SCN1A-212 | 3606 | 145aa | ENSP00000490895.1 | Nonsense mediated decay | A0A1B0GWE6 | - | TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000714447.1 | SCN1A-227 | 3020 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000642141.1 | SCN1A-221 | 921 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000714450.1 | SCN1A-230 | 587 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000714449.1 | SCN1A-229 | 456 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000714448.1 | SCN1A-228 | 348 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000635893.1 | SCN1A-210 | 168 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000673490.1 | SCN1A-223 | 10569 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | - | |
| ENST00000637968.1 | SCN1A-215 | 4614 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | TSL 5: A transcript where no single transcript supports the model structure. The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:5, | |
| ENST00000507401.2 | SCN1A-206 | 711 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | TSL 3: A transcript where the only support is from a single EST The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:3, | |
| ENST00000625916.1 | SCN1A-207 | 560 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | TSL 4: A transcript where the best supporting EST is flagged as suspect The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:4, | |
| ENST00000473295.2 | SCN1A-204 | 544 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | TSL 4: A transcript where the best supporting EST is flagged as suspect The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:4, | |
| ENST00000491429.1 | SCN1A-205 | 542 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | TSL 4: A transcript where the best supporting EST is flagged as suspect The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL:4, |
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