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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for MSH3 |
 Gene summary |
| Gene information | Gene symbol | MSH3 | Gene ID | 4437 |
| Gene name | mutS homolog 3 | |
| Synonyms | DUP|FAP4|MRP1 | |
| Cytomap | 5q14.1 | |
| Type of gene | protein-coding | |
| Description | DNA mismatch repair protein Msh3divergent upstream proteinhMSH3mismatch repair protein 1 | |
| Modification date | 20180523 | |
| UniProtAcc | P20585 | |
| Context | PubMed: MSH3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| MSH3 | GO:0006281 | DNA repair | 8942985 |
| MSH3 | GO:0045910 | negative regulation of DNA recombination | 17715146 |
| MSH3 | GO:0051096 | positive regulation of helicase activity | 17715146 |
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Exon skipping events across known transcript of Ensembl for MSH3 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
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Gene isoform structures and expression levels for MSH3 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for MSH3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_436164 | 5 | 79960961:79961182:79965915:79966128:79968062:79968179 | 79965915:79966128 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436165 | 5 | 79965915:79966128:79968062:79968179:79968559:79968677 | 79968062:79968179 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436168 | 5 | 80024669:80024784:80037282:80037367:80040324:80040434 | 80037282:80037367 | ENSG00000113318.9 | ENST00000512258.1,ENST00000265081.6 |
| exon_skip_436171 | 5 | 80037282:80037367:80040324:80040434:80057364:80057429 | 80040324:80040434 | ENSG00000113318.9 | ENST00000512258.1,ENST00000265081.6 |
| exon_skip_436173 | 5 | 80040324:80040434:80057364:80057497:80063751:80063939 | 80057364:80057497 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436176 | 5 | 80063751:80063939:80064653:80064822:80071512:80071577 | 80064653:80064822 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436178 | 5 | 80064653:80064822:80071512:80071577:80074538:80074655 | 80071512:80071577 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436179 | 5 | 80071512:80071577:80074538:80074655:80083383:80083491 | 80074538:80074655 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436184 | 5 | 80149948:80150135:80160631:80160761:80168934:80169106 | 80160631:80160761 | ENSG00000113318.9 | ENST00000265081.6 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for MSH3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_436164 | 5 | 79960961:79961182:79965915:79966128:79968062:79968179 | 79965915:79966128 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436165 | 5 | 79965915:79966128:79968062:79968179:79968559:79968677 | 79968062:79968179 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436168 | 5 | 80024669:80024784:80037282:80037367:80040324:80040434 | 80037282:80037367 | ENSG00000113318.9 | ENST00000265081.6,ENST00000512258.1 |
| exon_skip_436171 | 5 | 80037282:80037367:80040324:80040434:80057364:80057429 | 80040324:80040434 | ENSG00000113318.9 | ENST00000265081.6,ENST00000512258.1 |
| exon_skip_436173 | 5 | 80040324:80040434:80057364:80057497:80063751:80063939 | 80057364:80057497 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436176 | 5 | 80063751:80063939:80064653:80064822:80071512:80071577 | 80064653:80064822 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436178 | 5 | 80064653:80064822:80071512:80071577:80074538:80074655 | 80071512:80071577 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436179 | 5 | 80071512:80071577:80074538:80074655:80083383:80083491 | 80074538:80074655 | ENSG00000113318.9 | ENST00000265081.6 |
| exon_skip_436184 | 5 | 80149948:80150135:80160631:80160761:80168934:80169106 | 80160631:80160761 | ENSG00000113318.9 | ENST00000265081.6 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for MSH3 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000265081 | 80037282 | 80037367 | Frame-shift |
| ENST00000265081 | 80040324 | 80040434 | Frame-shift |
| ENST00000265081 | 80057364 | 80057497 | Frame-shift |
| ENST00000265081 | 80064653 | 80064822 | Frame-shift |
| ENST00000265081 | 80071512 | 80071577 | Frame-shift |
| ENST00000265081 | 80160631 | 80160761 | Frame-shift |
| ENST00000265081 | 79965915 | 79966128 | In-frame |
| ENST00000265081 | 79968062 | 79968179 | In-frame |
| ENST00000265081 | 80074538 | 80074655 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000265081 | 80037282 | 80037367 | Frame-shift |
| ENST00000265081 | 80040324 | 80040434 | Frame-shift |
| ENST00000265081 | 80057364 | 80057497 | Frame-shift |
| ENST00000265081 | 80064653 | 80064822 | Frame-shift |
| ENST00000265081 | 80071512 | 80071577 | Frame-shift |
| ENST00000265081 | 80160631 | 80160761 | Frame-shift |
| ENST00000265081 | 79965915 | 79966128 | In-frame |
| ENST00000265081 | 79968062 | 79968179 | In-frame |
| ENST00000265081 | 80074538 | 80074655 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MSH3 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000265081 | 4109 | 1137 | 79965915 | 79966128 | 660 | 872 | 193 | 264 |
| ENST00000265081 | 4109 | 1137 | 79968062 | 79968179 | 873 | 989 | 264 | 303 |
| ENST00000265081 | 4109 | 1137 | 80074538 | 80074655 | 2399 | 2515 | 773 | 811 |
| Loci of skipped exons in GTEx 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 |
| ENST00000265081 | 4109 | 1137 | 79965915 | 79966128 | 660 | 872 | 193 | 264 |
| ENST00000265081 | 4109 | 1137 | 79968062 | 79968179 | 873 | 989 | 264 | 303 |
| ENST00000265081 | 4109 | 1137 | 80074538 | 80074655 | 2399 | 2515 | 773 | 811 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| P20585 | 193 | 264 | 246 | 251 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 253 | 259 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 1 | 1137 | Chain | ID=PRO_0000115192;Note=DNA mismatch repair protein Msh3 |
| P20585 | 193 | 264 | 231 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 260 | 270 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 75 | 297 | Region | Note=Interaction with EXO1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11427529;Dbxref=PMID:11427529 |
| P20585 | 193 | 264 | 241 | 245 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 275 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 280 | 286 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 1 | 1137 | Chain | ID=PRO_0000115192;Note=DNA mismatch repair protein Msh3 |
| P20585 | 264 | 303 | 260 | 270 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 287 | 289 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 290 | 300 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 75 | 297 | Region | Note=Interaction with EXO1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11427529;Dbxref=PMID:11427529 |
| P20585 | 773 | 811 | 769 | 773 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 773 | 811 | 775 | 781 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 773 | 811 | 1 | 1137 | Chain | ID=PRO_0000115192;Note=DNA mismatch repair protein Msh3 |
| P20585 | 773 | 811 | 783 | 814 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 773 | 811 | 789 | 789 | Natural variant | ID=VAR_055251;Note=Y->F;Dbxref=dbSNP:rs10067975 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| P20585 | 193 | 264 | 246 | 251 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 253 | 259 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 1 | 1137 | Chain | ID=PRO_0000115192;Note=DNA mismatch repair protein Msh3 |
| P20585 | 193 | 264 | 231 | 240 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 260 | 270 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 193 | 264 | 75 | 297 | Region | Note=Interaction with EXO1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11427529;Dbxref=PMID:11427529 |
| P20585 | 193 | 264 | 241 | 245 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 275 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 280 | 286 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 1 | 1137 | Chain | ID=PRO_0000115192;Note=DNA mismatch repair protein Msh3 |
| P20585 | 264 | 303 | 260 | 270 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 287 | 289 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 290 | 300 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 264 | 303 | 75 | 297 | Region | Note=Interaction with EXO1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11427529;Dbxref=PMID:11427529 |
| P20585 | 773 | 811 | 769 | 773 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 773 | 811 | 775 | 781 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 773 | 811 | 1 | 1137 | Chain | ID=PRO_0000115192;Note=DNA mismatch repair protein Msh3 |
| P20585 | 773 | 811 | 783 | 814 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3THX |
| P20585 | 773 | 811 | 789 | 789 | Natural variant | ID=VAR_055251;Note=Y->F;Dbxref=dbSNP:rs10067975 |
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SNVs in the skipped exons for MSH3 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_436173 | 80057365 | 80057497 | 80057492 | 80057492 | Frame_Shift_Del | A | - | p.K632fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_436176 | 80064654 | 80064822 | 80064705 | 80064705 | Frame_Shift_Del | A | - | p.I712fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_436176 | 80064654 | 80064822 | 80064771 | 80064771 | Frame_Shift_Del | A | - | p.R734fs |
| COAD | TCGA-AA-3663-01 | exon_skip_436184 | 80160632 | 80160761 | 80160684 | 80160684 | Frame_Shift_Del | A | - | p.E1018fs |
| KIRC | TCGA-A3-3374-01 | exon_skip_436179 | 80074539 | 80074655 | 80074560 | 80074561 | Frame_Shift_Ins | - | A | p.L781fs |
| KIRP | TCGA-A4-8098-01 | exon_skip_436184 | 80160632 | 80160761 | 80160742 | 80160743 | Frame_Shift_Ins | - | GAAA | p.-1038fs |
| KIRP | TCGA-A4-8098-01 | exon_skip_436184 | 80160632 | 80160761 | 80160742 | 80160743 | Frame_Shift_Ins | - | GAAA | p.D1037fs |
| HNSC | TCGA-HD-A633-01 | exon_skip_436164 | 79965916 | 79966128 | 79965953 | 79965953 | Nonsense_Mutation | C | G | p.S206* |
| BLCA | TCGA-G2-A3IE-01 | exon_skip_436164 | 79965916 | 79966128 | 79965995 | 79965995 | Nonsense_Mutation | C | A | p.S220* |
| LUSC | TCGA-43-3394-01 | exon_skip_436165 | 79968063 | 79968179 | 79968171 | 79968171 | Nonsense_Mutation | G | T | p.G301* |
| PAAD | TCGA-IB-7651-01 | exon_skip_436176 | 80064654 | 80064822 | 80064769 | 80064769 | Nonsense_Mutation | C | T | p.R734* |
| PAAD | TCGA-IB-7651-01 | exon_skip_436176 | 80064654 | 80064822 | 80064769 | 80064769 | Nonsense_Mutation | C | T | p.R734X |
| LUAD | TCGA-55-8092-01 | exon_skip_436179 | 80074539 | 80074655 | 80074609 | 80074609 | Nonsense_Mutation | G | T | p.E797* |
| STAD | TCGA-BR-4361-01 | exon_skip_436179 | 80074539 | 80074655 | 80074641 | 80074641 | Nonsense_Mutation | G | A | p.W807* |
| STAD | TCGA-BR-4361-01 | exon_skip_436179 | 80074539 | 80074655 | 80074641 | 80074641 | Nonsense_Mutation | G | A | p.W807X |
| KIRP | TCGA-HE-A5NI-01 | exon_skip_436168 | 80037283 | 80037367 | 80037368 | 80037368 | Splice_Site | G | C | . |
| KIRP | TCGA-HE-A5NI-01 | exon_skip_436168 | 80037283 | 80037367 | 80037368 | 80037368 | Splice_Site | G | C | p.Q551_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| CAL33_UPPER_AERODIGESTIVE_TRACT | 80160632 | 80160761 | 80160647 | 80160648 | Frame_Shift_Del | CT | - | p.L1006fs |
| EN_ENDOMETRIUM | 79965916 | 79966128 | 79965925 | 79965926 | Frame_Shift_Ins | - | T | p.L197fs |
| EN_ENDOMETRIUM | 79965916 | 79966128 | 79965935 | 79965935 | Missense_Mutation | T | C | p.L200P |
| KATOIII_STOMACH | 79965916 | 79966128 | 79966025 | 79966025 | Missense_Mutation | C | T | p.T230M |
| NCIH28_PLEURA | 79965916 | 79966128 | 79966043 | 79966043 | Missense_Mutation | A | C | p.Y236S |
| DERL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 79965916 | 79966128 | 79966047 | 79966047 | Missense_Mutation | A | G | p.I237M |
| HEC6_ENDOMETRIUM | 79968063 | 79968179 | 79968125 | 79968125 | Missense_Mutation | A | G | p.I285M |
| PEO1_OVARY | 79968063 | 79968179 | 79968142 | 79968142 | Missense_Mutation | T | G | p.F291C |
| IGROV1_OVARY | 80037283 | 80037367 | 80037330 | 80037330 | Missense_Mutation | G | T | p.G539V |
| THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80057365 | 80057497 | 80057399 | 80057399 | Missense_Mutation | G | A | p.V600I |
| SW1088_CENTRAL_NERVOUS_SYSTEM | 80064654 | 80064822 | 80064742 | 80064742 | Missense_Mutation | G | A | p.E725K |
| EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 80064654 | 80064822 | 80064745 | 80064745 | Missense_Mutation | A | C | p.I726L |
| SNU1040_LARGE_INTESTINE | 80064654 | 80064822 | 80064786 | 80064786 | Missense_Mutation | T | A | p.N739K |
| HMY1_SKIN | 80071513 | 80071577 | 80071569 | 80071569 | Missense_Mutation | G | T | p.K770N |
| IGROV1_OVARY | 80074539 | 80074655 | 80074558 | 80074558 | Missense_Mutation | T | C | p.F780L |
| NCIH358_LUNG | 80074539 | 80074655 | 80074579 | 80074579 | Missense_Mutation | G | C | p.E787Q |
| ABC1_LUNG | 80074539 | 80074655 | 80074600 | 80074600 | Missense_Mutation | C | G | p.Q794E |
| LOVO_LARGE_INTESTINE | 80074539 | 80074655 | 80074604 | 80074604 | Missense_Mutation | T | A | p.L795H |
| A375_SKIN | 80074539 | 80074655 | 80074625 | 80074625 | Missense_Mutation | A | T | p.D802V |
| UMUC3_URINARY_TRACT | 79965916 | 79966128 | 79966044 | 79966044 | Nonsense_Mutation | C | G | p.Y236* |
| NCIH23_LUNG | 79965916 | 79966128 | 79966087 | 79966087 | Nonsense_Mutation | G | T | p.E251* |
| CAL27_UPPER_AERODIGESTIVE_TRACT | 80040325 | 80040434 | 80040326 | 80040326 | Splice_Site | C | T | p.T552I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MSH3 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MSH3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MSH3 |
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RelatedDrugs for MSH3 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for MSH3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| MSH3 | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| MSH3 | C0152013 | Adenocarcinoma of lung (disorder) | 1 | CTD_human |
| MSH3 | C0920269 | Microsatellite Instability | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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