Protein:MTMR1 |
Protein Summary |
 Gene summary |
| Gene name: MTMR1 | ASpdb.0 ID: 8776 | Gene | Gene symbol | MTMR1 | Gene ID | 8776 |
| Gene name | myotubularin related protein 1 |
| Synonyms | - |
| Cytomap | Xq28 |
| Type of gene | protein-coding |
| Description | myotubularin-related protein 1phosphatidylinositol-3,5-bisphosphate 3-phosphatasephosphatidylinositol-3-phosphate phosphatase |
| Modification date | 20240305 |
| UniProtAcc | Q13613 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | MTMR1 | GO:0004438 | phosphatidylinositol-3-phosphate phosphatase activity | 11733541|27018598 |
| Gene | MTMR1 | GO:0005737 | cytoplasm | 16787938 |
| Gene | MTMR1 | GO:0046856 | phosphatidylinositol dephosphorylation | 11733541|27018598 |
| Gene | MTMR1 | GO:0052629 | phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity | 27018598 |
| Gene | MTMR1 | GO:0060304 | regulation of phosphatidylinositol dephosphorylation | 16787938 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| Q13613-1 | Q13613-1_5c16_A.pdb | 5C16 | X-ray | 2.07 | A | 98 | 605 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| Q13613 | MTMR1 | Q13613-1 | Q13613-2 | 665 | 568 | 553 | 568 | Substitution | DVYTKTISLWSYINSQ | AWGAGTQRARGSLRSR | 553 | 568 |
| Q13613 | MTMR1 | Q13613-1 | Q13613-2 | 665 | 568 | 569 | 665 | Deletion | none | none | 568 | 568 |
| Multiple sequence alignment of our canonical and alternatively spliced MTMR1 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of MTMR1 |
| UniProt-id | ENSG | ENST | ENSP |
| Q13613-1 | ENSG00000063601.17 | ENST00000370390.7 | ENSP00000359417.3 |
| Q13613-2 | ENSG00000063601.17 | ENST00000485376.5 | ENSP00000434105.1 |
| UniProt-id | NM ID | NP ID |
| Q13613-1 | NM_003828.3 | NP_003819.1 |
| Q13613-1 | XM_006724855.3 | XP_006724918.1 |
| Amino acid sequences of our canonical and alternatively spliced MTMR1 |
| accession_id | Protein sequence |
| Q13613-1 | MDRPAAAAAAGCEGGGGPNPGPAGGRRPPRAAGGATAGSRQPSVETLDSPTGSHVEWCKQLIAATISSQISGSVTSENVSRDYKALRDGN KLAQMEEAPLFPGESIKAIVKDVMYICPFMGAVSGTLTVTDFKLYFKNVERDPHFILDVPLGVISRVEKIGAQSHGDNSCGIEIVCKDMR NLRLAYKQEEQSKLGIFENLNKHAFPLSNGQALFAFSYKEKFPINGWKVYDPVSEYKRQGLPNESWKISKINSNYEFCDTYPAIIVVPTS VKDDDLSKVAAFRAKGRVPVLSWIHPESQATITRCSQPLVGPNDKRCKEDEKYLQTIMDANAQSHKLIIFDARQNSVADTNKTKGGGYES ESAYPNAELVFLEIHNIHVMRESLRKLKEIVYPSIDEARWLSNVDGTHWLEYIRMLLAGAVRIADKIESGKTSVVVHCSDGWDRTAQLTS LAMLMLDSYYRTIKGFETLVEKEWISFGHRFALRVGHGNDNHADADRSPIFLQFVDCVWQMTRQFPSAFEFNELFLITILDHLYSCLFGT FLCNCEQQRFKEDVYTKTISLWSYINSQLDEFSNPFFVNYENHVLYPVASLSHLELWVNYYVRWNPRMRPQMPIHQNLKELLAVRAELQK |
| Q13613-2 | MDRPAAAAAAGCEGGGGPNPGPAGGRRPPRAAGGATAGSRQPSVETLDSPTGSHVEWCKQLIAATISSQISGSVTSENVSRDYKALRDGN KLAQMEEAPLFPGESIKAIVKDVMYICPFMGAVSGTLTVTDFKLYFKNVERDPHFILDVPLGVISRVEKIGAQSHGDNSCGIEIVCKDMR NLRLAYKQEEQSKLGIFENLNKHAFPLSNGQALFAFSYKEKFPINGWKVYDPVSEYKRQGLPNESWKISKINSNYEFCDTYPAIIVVPTS VKDDDLSKVAAFRAKGRVPVLSWIHPESQATITRCSQPLVGPNDKRCKEDEKYLQTIMDANAQSHKLIIFDARQNSVADTNKTKGGGYES ESAYPNAELVFLEIHNIHVMRESLRKLKEIVYPSIDEARWLSNVDGTHWLEYIRMLLAGAVRIADKIESGKTSVVVHCSDGWDRTAQLTS LAMLMLDSYYRTIKGFETLVEKEWISFGHRFALRVGHGNDNHADADRSPIFLQFVDCVWQMTRQFPSAFEFNELFLITILDHLYSCLFGT |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| MTMR1 (go to UniProt):Q13613 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q13613 | Domain | 226 | 601 | Note=Myotubularin phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00669 | Type=Substitution;Start=553;End=568 |
| Q13613 | Domain | 226 | 601 | Note=Myotubularin phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00669 | Type=Deletion;Start=569;End=665 |
| Q13613 | Region | 608 | 665 | Note=Required for dimerization;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27018598;Dbxref=PMID:27018598 | Type=Deletion;Start=569;End=665 |
| Q13613 | Region | 642 | 665 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=569;End=665 |
Gene Isoform Structures and Expression Levels for MTMR1 |
| Gene structures of our canonical and alternative spliced genes of MTMR1 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of Q13613-1 |
| 3D view using mol* of Q13613-2 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of Q13613-1 |
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| pLDDT distribution across the protein length of Q13613-2 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of Q13613-1 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q13613-1 | 1.109 | 158 | 1.156 | 413.658 | 0.461 | 0.789 | 1.018 | 1.485 | 0.789 | 1.882 | 0.79 | 116,118,155,156,173,175,176,177,179,181,183,381,38 4,385,388,389,392,393,479,481,484,485,492,493,494, 497,498,499,500,501,502,533,534 |
| Q13613-2 | 1.052 | 205 | 1.098 | 542.283 | 0.548 | 0.716 | 0.951 | 1.111 | 0.834 | 1.333 | 0.923 | 114,116,118,155,156,160,161,162,164,165,167,168,16 9,170,171,175,176,177,179,181,183,185,187,381,384, 385,388,389,392,393,479,481,484,485,492,497,498,49 9,500,501,502,533,534 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of Q13613-1_Q13613-1_5c16_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q13613-1_5c16_A_Q13613-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q13613-1_Q13613-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q13613-1_vs_Q13613-2.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q13613-1_vs_Q13613-2.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to MTMR1 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to MTMR1 |
| Previous studies relating to the alternative splicing of MTMR1 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| MTMR1 | 12217958 | Muscle-specific alternative splicing of myotubularin-related 1 gene is impaired in DM1 muscle cells. | The myotubularin-related 1 (MTMR1) gene belongs to a highly conserved family of eucaryotic phosphatases, with at least 11 members in humans. The founder member of this gene family, MTM1, is mutated in X-linked myotubular myopathy, a severe congenital disorder that affects skeletal muscle, and codes for myotubularin, a specific phosphatidylinositol 3-phosphate [PI(3)P] phosphatase. MTM1 and MTMR1 are adjacent on the X chromosome, and the corresponding proteins share 59% sequence identity. In the present study, we investigated the putative role of MTMR1 in myogenesis by analysing its expression pattern in muscle cells during differentiation and in skeletal muscle throughout development. We have identified three novel coding exons in the MTMR1 intron 2 that are conserved between mouse and human, are alternatively spliced, and give rise to six mRNA isoforms. One of the transcripts is muscle-specific and is induced during myogenesis both in vitro and in vivo, and represents the major isoform in adult skeletal muscle. We show that the two main MTMR1 protein muscular isoforms, like myotubularin, efficiently dephosphorylate PI(3)P in vitro. We have also analysed whether MTMR1 alternative splicing is affected in skeletal muscle cells derived from patients with congenital myotonic dystrophy (cDM1), in which mRNA splicing disturbances of specific genes are thought to constitute an important pathogenic mechanism. We found a striking reduction in the level of the muscle-specific isoform and the appearance of an abnormal MTMR1 transcript in differentiated cDM1 muscle cells in culture and in skeletal muscle from cDM1 patients. Our results suggest that MTMR1 plays a role in muscle formation and represents a novel target for abnormal mRNA splicing in myotonic dystrophy. | D009223 | Myotonic Dystrophy |
| MTMR1 | 20685272 | Analysis of MTMR1 expression and correlation with muscle pathological features in juvenile/adult onset myotonic dystrophy type 1 (DM1) and in myotonic dystrophy type 2 (DM2). | Among genes abnormally expressed in myotonic dystrophy type1 (DM1), the myotubularin-related 1 gene (MTMR1) was related to impaired muscle differentiation. Therefore, we analyzed MTMR1 expression in correlation with CUG-binding protein1 (CUG-BP1) and muscleblind-like1 protein (MBNL1) steady-state levels and with morphological features in muscle tissues from DM1 and myotonic dystrophy type 2 (DM2) patients. Semi-quantitative RT-PCR for MTMR1 was done on muscle biopsies and primary muscle cultures. The presence of impaired muscle fiber maturation was evaluated using immunochemistry for neural cell adhesion molecule (NCAM), Vimentin and neonatal myosin heavy chain. CUG-BP1 and MBNL1 steady-state levels were estimated by Western blot. RNA-fluorescence in situ hybridization combined with immunochemistry for CUG-BP1, MBNL1 and NCAM were performed on serial muscle sections. An aberrant splicing of MTMR1 and a significant amount of NCAM-positive myofibers were detected in DM1 and DM2 muscle biopsies; these alterations correlated with DNA repeat expansion size only in DM1. CUG-BP1 levels were increased only in DM1 muscles, while MBNL1 levels were similar among DM1, DM2 and controls. Normal and NCAM-positive myofibers displayed no differences either in the amount of ribonuclear foci and the intracellular distribution of MBNL1 and CUG-BP1. In conclusion, an aberrant MTMR1 expression and signs of altered myofiber maturation were documented in both DM1 and in DM2 muscle tissues. The more severe dysregulation of MTMR1 expression in DM1 versus DM2, along with increased CUG-BP1 levels only in DM1 tissues, suggests that the mutual antagonism between MBNL1 and CUG-BP1 on alternative splicing is more unbalanced in DM1. | D009223 | Myotonic Dystrophy |
Clinically important variants in MTMR1 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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