|
Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for MYO5A |
Gene summary |
Gene information | Gene symbol | MYO5A | Gene ID | 4644 |
Gene name | myosin VA | |
Synonyms | GS1|MYH12|MYO5|MYR12 | |
Cytomap | 15q21.2 | |
Type of gene | protein-coding | |
Description | unconventional myosin-Vadilute myosin heavy chain, non-musclemyosin Vmyosin VA (heavy chain 12, myoxin)myosin, heavy polypeptide kinasemyosin-12myosin-Vamyoxin | |
Modification date | 20200313 | |
UniProtAcc | A0A087WY00, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for MYO5A |
Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
IFG | UP | ENST00000358212.10 | MYO5A-202:protein_coding:MYO5A | 1.030482e+01 | 2.160957e+01 | 8.122361e-13 | 6.682335e-09 |
CB | UP | ENST00000556196.5 | MYO5A-210:nonsense_mediated_decay:MYO5A | 1.306782e+00 | 1.362741e+00 | 2.799696e-03 | 1.218584e-02 |
CB | UP | ENST00000399229.6 | MYO5A-204:protein_coding:MYO5A | 1.028992e+00 | 2.615046e+00 | 4.111549e-03 | 1.674464e-02 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for MYO5A |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_131991 | chr15 | 52353605:52353658:52353871:52354014:52359968:52360081 | 52353871:52354014 |
exon_skip_166339 | chr15 | 52340196:52340394:52343117:52343197:52346361:52346461 | 52343117:52343197 |
exon_skip_177218 | chr15 | 52405287:52405393:52407292:52407399:52408059:52408136 | 52407292:52407399 |
exon_skip_204044 | chr15 | 52391930:52392070:52396316:52396397:52397201:52397466 | 52396316:52396397 |
exon_skip_23989 | chr15 | 52405287:52405393:52407292:52407399:52408059:52408140 | 52407292:52407399 |
exon_skip_265623 | chr15 | 52425830:52425974:52428398:52428569:52433175:52433285 | 52428398:52428569 |
exon_skip_276093 | chr15 | 52340288:52340394:52343117:52343197:52346361:52346461 | 52343117:52343197 |
exon_skip_281456 | chr15 | 52336463:52336556:52337810:52337884:52340196:52340394 | 52337810:52337884 |
exon_skip_28723 | chr15 | 52416145:52416301:52425830:52425974:52428398:52428569 | 52425830:52425974 |
exon_skip_290986 | chr15 | 52327852:52328006:52330353:52330499:52336463:52336556 | 52330353:52330499 |
exon_skip_32701 | chr15 | 52346361:52346461:52348818:52348826:52351254:52351481 | 52348818:52348826 |
exon_skip_40510 | chr15 | 52336463:52336556:52337810:52337884:52340196:52340263 | 52337810:52337884 |
exon_skip_46217 | chr15 | 52410333:52410476:52416145:52416301:52425830:52425967 | 52416145:52416301 |
exon_skip_77497 | chr15 | 52407292:52407399:52408059:52408140:52410333:52410476 | 52408059:52408140 |
exon_skip_92679 | chr15 | 52346361:52346461:52348818:52348826:52351254:52351382 | 52348818:52348826 |
exon_skip_9849 | chr15 | 52353871:52354014:52359968:52360081:52364554:52364702 | 52359968:52360081 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for MYO5A |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000399231 | 52408059 | 52408140 | Frame-shift |
ENST00000399231 | 52416145 | 52416301 | Frame-shift |
ENST00000399231 | 52425830 | 52425974 | Frame-shift |
ENST00000399231 | 52428398 | 52428569 | Frame-shift |
ENST00000399231 | 52330353 | 52330499 | In-frame |
ENST00000399231 | 52343117 | 52343197 | In-frame |
ENST00000399231 | 52348818 | 52348826 | In-frame |
ENST00000399231 | 52353871 | 52354014 | In-frame |
ENST00000399231 | 52359968 | 52360081 | In-frame |
ENST00000399231 | 52407292 | 52407399 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000399231 | 52396316 | 52396397 | Frame-shift |
ENST00000399231 | 52408059 | 52408140 | Frame-shift |
ENST00000399231 | 52425830 | 52425974 | Frame-shift |
ENST00000399231 | 52428398 | 52428569 | Frame-shift |
ENST00000399231 | 52330353 | 52330499 | In-frame |
ENST00000399231 | 52343117 | 52343197 | In-frame |
ENST00000399231 | 52348818 | 52348826 | In-frame |
ENST00000399231 | 52407292 | 52407399 | In-frame |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000399231 | 52396316 | 52396397 | Frame-shift |
ENST00000399231 | 52408059 | 52408140 | Frame-shift |
ENST00000399231 | 52416145 | 52416301 | Frame-shift |
ENST00000399231 | 52425830 | 52425974 | Frame-shift |
ENST00000399231 | 52428398 | 52428569 | Frame-shift |
ENST00000399231 | 52330353 | 52330499 | In-frame |
ENST00000399231 | 52343117 | 52343197 | In-frame |
ENST00000399231 | 52348818 | 52348826 | In-frame |
ENST00000399231 | 52353871 | 52354014 | In-frame |
ENST00000399231 | 52407292 | 52407399 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MYO5A |
p-ENSG00000197535_img4.png |
Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000399231 | 12242 | 1855 | 52407292 | 52407399 | 1083 | 1189 | 279 | 315 |
ENST00000399231 | 12242 | 1855 | 52359968 | 52360081 | 3554 | 3666 | 1103 | 1140 |
ENST00000399231 | 12242 | 1855 | 52353871 | 52354014 | 3668 | 3810 | 1141 | 1188 |
ENST00000399231 | 12242 | 1855 | 52343117 | 52343197 | 4204 | 4283 | 1320 | 1346 |
ENST00000399231 | 12242 | 1855 | 52330353 | 52330499 | 4578 | 4723 | 1444 | 1493 |
Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000399231 | 12242 | 1855 | 52407292 | 52407399 | 1083 | 1189 | 279 | 315 |
ENST00000399231 | 12242 | 1855 | 52343117 | 52343197 | 4204 | 4283 | 1320 | 1346 |
ENST00000399231 | 12242 | 1855 | 52330353 | 52330499 | 4578 | 4723 | 1444 | 1493 |
Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000399231 | 12242 | 1855 | 52407292 | 52407399 | 1083 | 1189 | 279 | 315 |
ENST00000399231 | 12242 | 1855 | 52353871 | 52354014 | 3668 | 3810 | 1141 | 1188 |
ENST00000399231 | 12242 | 1855 | 52343117 | 52343197 | 4204 | 4283 | 1320 | 1346 |
ENST00000399231 | 12242 | 1855 | 52330353 | 52330499 | 4578 | 4723 | 1444 | 1493 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
Q9Y4I1 | 279 | 315 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 279 | 315 | 69 | 763 | Domain | Note=Myosin motor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00782 |
Q9Y4I1 | 1103 | 1140 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1103 | 1140 | 914 | 1237 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1141 | 1188 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1141 | 1188 | 914 | 1237 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1141 | 1188 | 1177 | 1177 | Sequence conflict | Note=D->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1320 | 1346 | 1321 | 1347 | Alternative sequence | ID=VSP_003351;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7835087,ECO:0000303|PubMed:8188282,ECO:0000303|Ref.1;Dbxref=PMID:7835087,PMID:8188282 |
Q9Y4I1 | 1320 | 1346 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1320 | 1346 | 1338 | 1445 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1444 | 1493 | 1475 | 1478 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1444 | 1493 | 1338 | 1445 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1444 | 1493 | 1481 | 1483 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 1484 | 1491 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 1452 | 1452 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
Q9Y4I1 | 1444 | 1493 | 1465 | 1477 | Sequence conflict | Note=NIPRKEKDFQGML->SVLCACCVSVTVR;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1471 | 1471 | Sequence conflict | Note=K->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1484 | 1484 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1492 | 1494 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Lost protein functional features of individual exon skipping events in MSBB. |
UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
Q9Y4I1 | 279 | 315 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 279 | 315 | 69 | 763 | Domain | Note=Myosin motor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00782 |
Q9Y4I1 | 1320 | 1346 | 1321 | 1347 | Alternative sequence | ID=VSP_003351;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7835087,ECO:0000303|PubMed:8188282,ECO:0000303|Ref.1;Dbxref=PMID:7835087,PMID:8188282 |
Q9Y4I1 | 1320 | 1346 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1320 | 1346 | 1338 | 1445 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1444 | 1493 | 1475 | 1478 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1444 | 1493 | 1338 | 1445 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1444 | 1493 | 1481 | 1483 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 1484 | 1491 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 1452 | 1452 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
Q9Y4I1 | 1444 | 1493 | 1465 | 1477 | Sequence conflict | Note=NIPRKEKDFQGML->SVLCACCVSVTVR;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1471 | 1471 | Sequence conflict | Note=K->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1484 | 1484 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1492 | 1494 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Lost protein functional features of individual exon skipping events in Mayo. |
UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
Q9Y4I1 | 279 | 315 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 279 | 315 | 69 | 763 | Domain | Note=Myosin motor;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00782 |
Q9Y4I1 | 1141 | 1188 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1141 | 1188 | 914 | 1237 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1141 | 1188 | 1177 | 1177 | Sequence conflict | Note=D->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1320 | 1346 | 1321 | 1347 | Alternative sequence | ID=VSP_003351;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7835087,ECO:0000303|PubMed:8188282,ECO:0000303|Ref.1;Dbxref=PMID:7835087,PMID:8188282 |
Q9Y4I1 | 1320 | 1346 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1320 | 1346 | 1338 | 1445 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1444 | 1493 | 1475 | 1478 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 2 | 1855 | Chain | ID=PRO_0000123456;Note=Unconventional myosin-Va |
Q9Y4I1 | 1444 | 1493 | 1338 | 1445 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9Y4I1 | 1444 | 1493 | 1481 | 1483 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 1484 | 1491 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
Q9Y4I1 | 1444 | 1493 | 1452 | 1452 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:20068231;Dbxref=PMID:20068231 |
Q9Y4I1 | 1444 | 1493 | 1465 | 1477 | Sequence conflict | Note=NIPRKEKDFQGML->SVLCACCVSVTVR;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1471 | 1471 | Sequence conflict | Note=K->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1484 | 1484 | Sequence conflict | Note=E->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9Y4I1 | 1444 | 1493 | 1492 | 1494 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4LX2 |
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3'-UTR located exon skipping events that lost miRNA binding sites in MYO5A |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for MYO5A |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- Non-synonymous mutations located in the skipped exons in CCLE. |
Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for MYO5A |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
ADstage | MSBB | IFG | exon_skip_166339 | 5.387651e-01 | 3.096550e-03 | chr15 | - | 52340196 | 52340394 | 52343117 | 52343197 | 52346361 | 52346461 |
CDR | MSBB | IFG | exon_skip_166339 | 4.622599e-01 | 1.326291e-02 | chr15 | - | 52340196 | 52340394 | 52343117 | 52343197 | 52346361 | 52346461 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MYO5A |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
PCC | exon_skip_281456 | rs1405184 | chr15:52389180 | 8.528515e-06 | 2.211068e-03 |
PCC | exon_skip_281456 | rs3794565 | chr15:52363169 | 9.333501e-06 | 2.390721e-03 |
PCC | exon_skip_281456 | rs871488 | chr15:52417680 | 3.570650e-04 | 4.676387e-02 |
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Correlation with RNA binding proteins (RBPs) for MYO5A |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TRA2A | exon_skip_77497 | -6.343237e-01 | 1.735121e-18 |
CB | RBM4 | exon_skip_77497 | -6.031488e-01 | 1.986080e-16 |
PCC | RBMS3 | exon_skip_281456 | 4.375240e-01 | 6.698197e-11 |
PCC | SRSF11 | exon_skip_281456 | 4.025569e-01 | 2.617262e-09 |
PCC | RBM47 | exon_skip_281456 | 4.415811e-01 | 4.257796e-11 |
PG | G3BP2 | exon_skip_166339 | -5.082548e-01 | 2.858192e-14 |
TC | ELAVL1 | exon_skip_281456 | -4.318548e-01 | 1.317922e-08 |
TC | RALYL | exon_skip_281456 | -8.122544e-01 | 1.372883e-38 |
TC | NOVA1 | exon_skip_281456 | -5.771380e-01 | 1.682979e-15 |
TC | G3BP2 | exon_skip_166339 | -6.196112e-01 | 3.981633e-18 |
TC | NUP42 | exon_skip_166339 | -5.514829e-01 | 5.944265e-14 |
TC | NOVA1 | exon_skip_166339 | -4.575325e-01 | 1.505923e-09 |
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RelatedDrugs for MYO5A |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for MYO5A |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |