serine palmitoyltransferase long chain base subunit 1 [Source:HGNC Symbol;Acc:HGNC:11277]
HLCB1, HSAN1, HSN1, LCB1, SPTI
Chromosome 9: 92,000,087-92,115,433 reverse strand.
GRCh38:CM000671.2
This gene has 41 transcripts (splice variants), 206 orthologues, 5 paralogues and is associated with 4 phenotypes.
| Transcript ID | Name | bp | Protein | Translation ID | Biotype | CCDS | UniProt Match | RefSeq Match | Flags |
|---|---|---|---|---|---|---|---|---|---|
| ENST00000262554.7 | SPTLC1-201 | 2783 | 473aa | ENSP00000262554.2 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS6692 | O15269-1 | NM_006415.4 | 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 P3: Where the APPRIS core modules are unable to choose a clear principal variant and there more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated. 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 P3,TSL 1: A transcript where all splice junctions are supported by at least one non-suspect mRNA. 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:1, |
| ENST00000953500.1 | SPTLC1-238 | 2972 | 543aa | ENSP00000623559.1 | 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, | |
| ENST00000686600.1 | SPTLC1-213 | 2968 | 504aa | ENSP00000509268.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A8I5KUM4 | - | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, | |
| ENST00000953498.1 | SPTLC1-236 | 2809 | 488aa | ENSP00000623557.1 | 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, | |
| ENST00000687972.1 | SPTLC1-217 | 2807 | 493aa | ENSP00000509208.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A8I5QKQ8 | - | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, | |
| ENST00000884974.1 | SPTLC1-227 | 2803 | 482aa | ENSP00000555033.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | 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, | |
| ENST00000953503.1 | SPTLC1-241 | 2793 | 486aa | ENSP00000623562.1 | 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, | |
| ENST00000953501.1 | SPTLC1-239 | 2778 | 480aa | ENSP00000623560.1 | 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, | |
| ENST00000913243.1 | SPTLC1-233 | 2777 | 471aa | ENSP00000583302.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | 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, | |
| ENST00000913242.1 | SPTLC1-232 | 2774 | 469aa | ENSP00000583301.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | 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, | |
| ENST00000884977.1 | SPTLC1-230 | 2772 | 481aa | ENSP00000555036.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | 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, | |
| ENST00000953502.1 | SPTLC1-240 | 2737 | 467aa | ENSP00000623561.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | - | - | 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, | |
| ENST00000884973.1 | SPTLC1-226 | 2714 | 443aa | ENSP00000555032.1 | 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, | |
| ENST00000884976.1 | SPTLC1-229 | 2658 | 437aa | ENSP00000555035.1 | 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, | |
| ENST00000913245.1 | SPTLC1-235 | 2628 | 430aa | ENSP00000583304.1 | 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, | |
| ENST00000953499.1 | SPTLC1-237 | 2571 | 409aa | ENSP00000623558.1 | 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, | |
| ENST00000884975.1 | SPTLC1-228 | 2476 | 373aa | ENSP00000555034.1 | 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, | |
| ENST00000913244.1 | SPTLC1-234 | 2193 | 285aa | ENSP00000583303.1 | 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, | |
| ENST00000884978.1 | SPTLC1-231 | 1970 | 534aa | ENSP00000555037.1 | 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, | |
| ENST00000461132.2 | SPTLC1-203 | 1842 | 87aa | ENSP00000509096.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A8I5KWE0 | - | 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 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs 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:2, | |
| ENST00000692363.1 | SPTLC1-223 | 1197 | 87aa | ENSP00000509481.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | A0A8I5KWE0 | - | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, | |
| ENST00000337841.4 | SPTLC1-202 | 946 | 143aa | ENSP00000337635.4 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS6693 | O15269-2 | - | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, TSL 1: A transcript where all splice junctions are supported by at least one non-suspect mRNA. 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:1, |
| ENST00000687817.1 | SPTLC1-216 | 4920 | 144aa | ENSP00000508926.1 | Nonsense mediated decay | A0A2R8Y6A2 | - | - | |
| ENST00000689401.1 | SPTLC1-219 | 3110 | 42aa | ENSP00000510251.1 | Nonsense mediated decay | A0A8I5QJP4 | - | - | |
| ENST00000687427.1 | SPTLC1-215 | 3022 | 504aa | ENSP00000509426.1 | Nonsense mediated decay | A0A8I5KUM4 | - | - | |
| ENST00000646534.1 | SPTLC1-212 | 2982 | 144aa | ENSP00000495388.1 | Nonsense mediated decay | A0A2R8Y6A2 | - | - | |
| ENST00000690139.1 | SPTLC1-222 | 2892 | 143aa | ENSP00000510483.1 | Nonsense mediated decay | CCDS6693 | O15269-2 | - | - |
| ENST00000644140.1 | SPTLC1-210 | 2792 | 143aa | ENSP00000493933.1 | Nonsense mediated decay | A0A2R8Y4S0 | - | - | |
| ENST00000642671.1 | SPTLC1-208 | 2289 | 22aa | ENSP00000495764.1 | Nonsense mediated decay | A0A2R8Y763 | - | 5' truncation in transcript evidence prevents annotation of the start of the CDS.CDS 5' incomplete, | |
| ENST00000643599.1 | SPTLC1-209 | 2042 | 22aa | ENSP00000494770.1 | Nonsense mediated decay | A0A2R8Y763 | - | 5' truncation in transcript evidence prevents annotation of the start of the CDS.CDS 5' incomplete, | |
| ENST00000646481.1 | SPTLC1-211 | 1727 | 22aa | ENSP00000496627.1 | Nonsense mediated decay | A0A2R8Y763 | - | 5' truncation in transcript evidence prevents annotation of the start of the CDS.CDS 5' incomplete, | |
| ENST00000689423.1 | SPTLC1-220 | 1721 | 42aa | ENSP00000508519.1 | Nonsense mediated decay | A0A8I5QJP4 | - | - | |
| ENST00000693147.1 | SPTLC1-225 | 1511 | 42aa | ENSP00000510358.1 | Nonsense mediated decay | A0A8I5QJP4 | - | - | |
| ENST00000488921.6 | SPTLC1-207 | 1311 | 42aa | ENSP00000510034.1 | Nonsense mediated decay | A0A8I5QJP4 | - | 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, | |
| ENST00000690095.1 | SPTLC1-221 | 3132 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000686799.1 | SPTLC1-214 | 3043 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000689261.1 | SPTLC1-218 | 2651 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | - | |
| ENST00000469778.1 | SPTLC1-204 | 490 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | - | TSL 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs 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:2, | |
| ENST00000477888.1 | SPTLC1-205 | 359 | 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, | |
| ENST00000692458.1 | SPTLC1-224 | 2810 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | - | - | |
| ENST00000482632.6 | SPTLC1-206 | 1738 | 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, |
