HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 [Source:MGI Symbol;Acc:MGI:2177742]
2010205O06Rik, BLOC-3, C130020P05Rik, Hermansky-Pudlak syndrome 4
Chromosome 5: 112,490,614-112,526,289 forward strand.
GRCm39:CM000998.3
This gene has 34 transcripts (splice variants), 204 orthologues and is associated with 15 phenotypes.
| Transcript ID | Name | bp | Protein | Translation ID | Biotype | CCDS | UniProt Match | Flags |
|---|---|---|---|---|---|---|---|---|
| ENSMUST00000112359.10 | Hps4-202 | 3369 | 671aa | ENSMUSP00000107978.3 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 Q99KG7 | 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 P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2,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, |
| ENSMUST00000522381.1 | Hps4-230 | 5331 | 123aa | ENSMUSP00000300744.1 | 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 ALT2: 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 appear to be conserved in fewer than 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 ALT2, | |
| ENSMUST00000565725.1 | Hps4-232 | 3950 | 671aa | ENSMUSP00000344088.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522378.1 | Hps4-227 | 3875 | 671aa | ENSMUSP00000300741.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000565726.1 | Hps4-233 | 3745 | 671aa | ENSMUSP00000344089.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522361.1 | Hps4-210 | 3671 | 671aa | ENSMUSP00000300724.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522375.1 | Hps4-224 | 3648 | 671aa | ENSMUSP00000300738.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522376.1 | Hps4-225 | 3560 | 671aa | ENSMUSP00000300739.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522368.1 | Hps4-217 | 3354 | 666aa | ENSMUSP00000300731.1 | 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, APPRIS ALT2: 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 appear to be conserved in fewer than 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 ALT2, | |
| ENSMUST00000522359.1 | Hps4-208 | 3151 | 671aa | ENSMUSP00000300722.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522370.1 | Hps4-219 | 3151 | 671aa | ENSMUSP00000300733.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522373.1 | Hps4-222 | 3136 | 666aa | ENSMUSP00000300736.1 | 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, APPRIS ALT2: 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 appear to be conserved in fewer than 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 ALT2, | |
| ENSMUST00000565727.1 | Hps4-234 | 3018 | 671aa | ENSMUSP00000344090.1 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2, |
| ENSMUST00000522372.1 | Hps4-221 | 2920 | 687aa | ENSMUSP00000300735.1 | 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 ALT2: 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 appear to be conserved in fewer than 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 ALT2, | |
| ENSMUST00000035279.5 | Hps4-201 | 2872 | 671aa | ENSMUSP00000047920.4 | Gene/transcipt that contains an open reading frame (ORF).Protein coding | CCDS19540 | Q541V2 Q99KG7 | A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic, APPRIS P2: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be 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 P2,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, |
| ENSMUST00000522366.1 | Hps4-215 | 2866 | 669aa | ENSMUSP00000300729.1 | 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, APPRIS ALT2: 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 appear to be conserved in fewer than 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 ALT2, | |
| ENSMUST00000522371.1 | Hps4-220 | 2843 | 679aa | ENSMUSP00000300734.1 | 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, APPRIS ALT2: 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 appear to be conserved in fewer than 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 ALT2, | |
| ENSMUST00000522364.1 | Hps4-213 | 3361 | 205aa | ENSMUSP00000300727.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522379.1 | Hps4-228 | 3356 | 230aa | ENSMUSP00000300742.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522363.1 | Hps4-212 | 3314 | 242aa | ENSMUSP00000300726.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522380.1 | Hps4-229 | 3120 | 150aa | ENSMUSP00000300743.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522365.1 | Hps4-214 | 3068 | 123aa | ENSMUSP00000300728.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522374.1 | Hps4-223 | 3066 | 205aa | ENSMUSP00000300737.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522360.1 | Hps4-209 | 2982 | 237aa | ENSMUSP00000300723.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000565724.1 | Hps4-231 | 2972 | 280aa | ENSMUSP00000344087.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522362.1 | Hps4-211 | 2872 | 205aa | ENSMUSP00000300725.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522377.1 | Hps4-226 | 2799 | 237aa | ENSMUSP00000300740.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522367.1 | Hps4-216 | 2795 | 242aa | ENSMUSP00000300730.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000522369.1 | Hps4-218 | 2672 | 257aa | ENSMUSP00000300732.1 | Nonsense mediated decay | - | - | |
| ENSMUST00000175718.2 | Hps4-205 | 820 | 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, | |
| ENSMUST00000176737.2 | Hps4-206 | 734 | 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, | |
| ENSMUST00000133708.2 | Hps4-204 | 3189 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | 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, | |
| ENSMUST00000177121.2 | Hps4-207 | 570 | No protein | - | An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron | - | 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, | |
| ENSMUST00000129839.2 | Hps4-203 | 548 | 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, |
