retinoic acid receptor, alpha [Source:MGI Symbol;Acc:MGI:97856]
RAR alpha 1, RARalpha1
Chromosome 11: 98,818,612-98,865,768 forward strand.
GRCm39:CM001004.3
This gene has 20 transcripts (splice variants), 330 orthologues, 19 paralogues and is associated with 32 phenotypes.
| Transcript ID | Name | bp | Protein | Translation ID | Biotype | CCDS | UniProt Match | Flags |
|---|---|---|---|---|---|---|---|---|
| ENSMUST00000107475.10 | Rara-204 | 3339 | 462aa | ENSMUSP00000103099.3 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | P11416-1 | 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 P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1,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, |
| ENSMUST00000557567.1 | Rara-215 | 3511 | 462aa | ENSMUSP00000335930.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | Q3U3R3 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1, |
| ENSMUST00000068133.11 | Rara-201 | 3494 | 462aa | ENSMUSP00000069744.4 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | P11416-1 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1,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, |
| ENSMUST00000450324.1 | Rara-210 | 3433 | 462aa | ENSMUSP00000228687.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | Q3U3R3 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1, |
| ENSMUST00000450326.1 | Rara-212 | 3372 | 462aa | ENSMUSP00000228689.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | Q3U3R3 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1, |
| ENSMUST00000557569.1 | Rara-217 | 3331 | 389aa | ENSMUSP00000335932.1 | 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, | |
| ENSMUST00000107473.3 | Rara-202 | 3238 | 459aa | ENSMUSP00000103097.3 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS48905 | P11416-2 | 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, |
| ENSMUST00000450327.1 | Rara-213 | 3200 | 462aa | ENSMUSP00000228690.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | Q3U3R3 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1, |
| ENSMUST00000107474.9 | Rara-203 | 3192 | 462aa | ENSMUSP00000103098.2 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | P11416-1 | 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 P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1,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, |
| ENSMUST00000450322.1 | Rara-208 | 3184 | 389aa | ENSMUSP00000228685.1 | 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, | |
| ENSMUST00000450323.1 | Rara-209 | 3182 | 462aa | ENSMUSP00000228686.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | Q3U3R3 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1, |
| ENSMUST00000557571.1 | Rara-219 | 3178 | 462aa | ENSMUSP00000335934.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | Q3U3R3 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1, |
| ENSMUST00000164748.8 | Rara-207 | 3129 | 462aa | ENSMUSP00000129791.2 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS36304 | P11416-1 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P1: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS. 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 P1,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, |
| ENSMUST00000450328.1 | Rara-214 | 1121 | 92aa | ENSMUSP00000228691.1 | 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, | |
| ENSMUST00000585807.1 | Rara-220 | 879 | 92aa | ENSMUSP00000364172.1 | 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, | |
| ENSMUST00000557568.1 | Rara-216 | 3424 | 68aa | ENSMUSP00000335931.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000557570.1 | Rara-218 | 3255 | 217aa | ENSMUSP00000335933.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000450325.1 | Rara-211 | 2337 | 132aa | ENSMUSP00000228688.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000139399.2 | Rara-205 | 356 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | 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, | |
| ENSMUST00000147985.2 | Rara-206 | 307 | No protein | - | Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.Protein coding CDS not defined | - | 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, |
