structural maintenance of chromosomes 4 [Source:MGI Symbol;Acc:MGI:1917349]
2500002A22Rik, Smc4l1
Chromosome 3: 68,911,944-68,941,960 forward strand.
GRCm39:CM000996.3
This gene has 32 transcripts (splice variants), 213 orthologues and 7 paralogues.
| Transcript ID | Name | bp | Protein | Translation ID | Biotype | CCDS | UniProt Match | Flags |
|---|---|---|---|---|---|---|---|---|
| ENSMUST00000042901.16 | Smc4-201 | 4320 | 1286aa | ENSMUSP00000047872.9 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS17401 | Q8CG47 | 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, |
| ENSMUST00000394857.1 | Smc4-213 | 5317 | 1286aa | ENSMUSP00000173220.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS17401 | - | 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, |
| ENSMUST00000107803.8 | Smc4-202 | 4245 | 1261aa | ENSMUSP00000103433.2 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | E9Q2X6 | 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, | |
| ENSMUST00000394863.1 | Smc4-219 | 4235 | 1286aa | ENSMUSP00000173226.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS17401 | - | 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, |
| ENSMUST00000394865.1 | Smc4-221 | 4201 | 1286aa | ENSMUSP00000173228.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS17401 | - | 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, |
| ENSMUST00000560847.1 | Smc4-228 | 4155 | 1231aa | ENSMUSP00000339210.1 | 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, | |
| ENSMUST00000394858.1 | Smc4-214 | 4128 | 1222aa | ENSMUSP00000173221.1 | 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, | |
| ENSMUST00000136502.8 | Smc4-206 | 1163 | 337aa | ENSMUSP00000115033.2 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | Q3U763 | 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, 3' truncation in transcript evidence prevents annotation of the end of the CDS.CDS 3' incomplete, | |
| ENSMUST00000394866.1 | Smc4-222 | 4594 | 46aa | ENSMUSP00000173229.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394869.1 | Smc4-225 | 4490 | 673aa | ENSMUSP00000173232.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000560846.1 | Smc4-227 | 4439 | 195aa | ENSMUSP00000339209.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394867.1 | Smc4-223 | 4405 | 621aa | ENSMUSP00000173230.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394870.1 | Smc4-226 | 4224 | 46aa | ENSMUSP00000173233.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394864.1 | Smc4-220 | 4218 | 46aa | ENSMUSP00000173227.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394859.1 | Smc4-215 | 4194 | 372aa | ENSMUSP00000173222.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394860.1 | Smc4-216 | 4073 | 47aa | ENSMUSP00000173223.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000560851.1 | Smc4-232 | 4070 | 389aa | ENSMUSP00000339214.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000560849.1 | Smc4-230 | 4067 | 886aa | ENSMUSP00000339212.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000148385.8 | Smc4-207 | 4057 | 46aa | ENSMUSP00000123350.2 | Nonsense mediated decay | D6RCX2 | 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, | |
| ENSMUST00000394868.1 | Smc4-224 | 4019 | 45aa | ENSMUSP00000173231.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000560848.1 | Smc4-229 | 4010 | 673aa | ENSMUSP00000339211.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394862.1 | Smc4-218 | 3922 | 248aa | ENSMUSP00000173225.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000560850.1 | Smc4-231 | 3886 | 882aa | ENSMUSP00000339213.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394856.1 | Smc4-212 | 3865 | 45aa | ENSMUSP00000173219.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000394861.1 | Smc4-217 | 3279 | 45aa | ENSMUSP00000173224.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000195525.2 | Smc4-211 | 784 | 56aa | ENSMUSP00000141779.2 | Nonsense mediated decay | A0A0A6YX07 | 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, | |
| ENSMUST00000149174.3 | Smc4-208 | 557 | 109aa | ENSMUSP00000142192.2 | Nonsense mediated decay | A0A0A6YXY3 | 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, 5' truncation in transcript evidence prevents annotation of the start of the CDS.CDS 5' incomplete, | |
| ENSMUST00000124983.2 | Smc4-203 | 496 | 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, | |
| ENSMUST00000128118.2 | Smc4-204 | 756 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | 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, | |
| ENSMUST00000156354.2 | Smc4-209 | 576 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | 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, | |
| ENSMUST00000194693.2 | Smc4-210 | 549 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | 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, | |
| ENSMUST00000128134.2 | Smc4-205 | 393 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | 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, |
