|
||||||
|
 | |
| |
| |
| 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 PMS1 |
 Gene summary |
| Gene information | Gene symbol | PMS1 | Gene ID | 5378 |
| Gene name | PMS1 homolog 1, mismatch repair system component | |
| Synonyms | HNPCC3|MLH2|PMSL1|hPMS1 | |
| Cytomap | 2q32.2 | |
| Type of gene | protein-coding | |
| Description | PMS1 protein homolog 1DNA mismatch repair protein PMS1PMS1 postmeiotic segregation increased 1human homolog of yeast mutLmismatch repair gene PMSL1rhabdomyosarcoma antigen MU-RMS-40.10Brhabdomyosarcoma antigen MU-RMS-40.10E | |
| Modification date | 20200327 | |
| UniProtAcc | B7ZAA0, C9J4L1, C9JF76, C9JKP0, E9PC40, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for PMS1 |
| 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. |
 |
ENSG00000064933
| 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 |
| CB | DOWN | ENST00000452382.1 | PMS1-218:protein_coding:PMS1 | 3.967642e+01 | -1.113331e+00 | 3.100792e-04 | 1.925396e-03 |
| CB | DOWN | ENST00000450931.5 | PMS1-217:nonsense_mediated_decay:PMS1 | 3.191585e+01 | -9.101440e-01 | 4.123449e-04 | 2.447703e-03 |
| CB | DOWN | ENST00000342075.8 | PMS1-201:nonsense_mediated_decay:PMS1 | 1.904211e+02 | -8.296821e-01 | 2.229899e-03 | 1.008177e-02 |
| CB | UP | ENST00000424766.5 | PMS1-211:protein_coding:PMS1 | 3.223975e+00 | 8.874357e-01 | 3.647781e-03 | 1.515884e-02 |
| CB | UP | ENST00000624204.3 | PMS1-221:protein_coding:PMS1 | 5.634465e+01 | 1.765826e+00 | 1.412109e-02 | 4.594125e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PMS1 |
| 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_103066 | chr2 | 189843968:189844080:189852655:189852777:189853939:189854082 | 189852655:189852777 |
| exon_skip_131808 | chr2 | 189791790:189791941:189805652:189805754:189818017:189818180 | 189805652:189805754 |
| exon_skip_159028 | chr2 | 189863743:189863974:189867799:189867929:189873496:189873528 | 189867799:189867929 |
| exon_skip_165787 | chr2 | 189805652:189805754:189818017:189818180:189843964:189844080 | 189818017:189818180 |
| exon_skip_174444 | chr2 | 189791790:189791941:189795769:189795951:189805652:189805754 | 189795769:189795951 |
| exon_skip_224155 | chr2 | 189791810:189791941:189795769:189795951:189818017:189818180 | 189795769:189795951 |
| exon_skip_235151 | chr2 | 189791790:189791941:189795769:189795951:189818017:189818180 | 189795769:189795951 |
| exon_skip_250295 | chr2 | 189795769:189795951:189805652:189805754:189818017:189818180 | 189805652:189805754 |
| exon_skip_256972 | chr2 | 189818127:189818180:189843964:189844080:189852655:189852762 | 189843964:189844080 |
| exon_skip_292206 | chr2 | 189854239:189855128:189867799:189867929:189873496:189873528 | 189867799:189867929 |
| exon_skip_293181 | chr2 | 189854239:189855128:189863743:189863974:189873496:189873528 | 189863743:189863974 |
| exon_skip_294893 | chr2 | 189843964:189844080:189852655:189852777:189853939:189854082 | 189852655:189852777 |
| exon_skip_30063 | chr2 | 189784513:189784564:189785346:189785471:189791790:189791941 | 189785346:189785471 |
| exon_skip_32142 | chr2 | 189791810:189791941:189795769:189795951:189805652:189805754 | 189795769:189795951 |
| exon_skip_43592 | chr2 | 189854239:189855128:189863743:189863974:189867799:189867929 | 189863743:189863974 |
| exon_skip_49423 | chr2 | 189864079:189864228:189867799:189867929:189873496:189873528 | 189867799:189867929 |
| exon_skip_5800 | chr2 | 189818127:189818180:189852655:189852777:189853939:189854082 | 189852655:189852777 |
| exon_skip_64803 | chr2 | 189791810:189791941:189805652:189805754:189818017:189818180 | 189805652:189805754 |
| exon_skip_71166 | chr2 | 189854239:189855128:189863743:189864228:189867799:189867929 | 189863743:189864228 |
| exon_skip_7776 | chr2 | 189854239:189855128:189855829:189855916:189863743:189863974 | 189855829:189855916 |
| exon_skip_85362 | chr2 | 189863743:189864228:189867799:189867929:189873496:189873528 | 189867799:189867929 |
| exon_skip_91363 | chr2 | 189795769:189795951:189818017:189818180:189843964:189844080 | 189818017:189818180 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PMS1 |
| 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 |
| ENST00000441310 | 189805652 | 189805754 | Frame-shift |
| ENST00000441310 | 189818017 | 189818180 | Frame-shift |
| ENST00000441310 | 189867799 | 189867929 | Frame-shift |
| ENST00000441310 | 189795769 | 189795951 | In-frame |
| ENST00000441310 | 189843964 | 189844080 | In-frame |
| ENST00000441310 | 189852655 | 189852777 | In-frame |
| ENST00000441310 | 189863743 | 189864228 | 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 |
| ENST00000441310 | 189805652 | 189805754 | Frame-shift |
| ENST00000441310 | 189795769 | 189795951 | In-frame |
| ENST00000441310 | 189843964 | 189844080 | In-frame |
| ENST00000441310 | 189852655 | 189852777 | In-frame |
| ENST00000441310 | 189863743 | 189864228 | 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 |
| ENST00000441310 | 189805652 | 189805754 | Frame-shift |
| ENST00000441310 | 189867799 | 189867929 | Frame-shift |
| ENST00000441310 | 189795769 | 189795951 | In-frame |
| ENST00000441310 | 189843964 | 189844080 | In-frame |
| ENST00000441310 | 189852655 | 189852777 | In-frame |
| ENST00000441310 | 189863743 | 189864228 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PMS1 |
p-ENSG00000064933_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 |
| ENST00000441310 | 3242 | 932 | 189795769 | 189795951 | 367 | 548 | 44 | 105 |
| ENST00000441310 | 3242 | 932 | 189843964 | 189844080 | 817 | 932 | 194 | 233 |
| ENST00000441310 | 3242 | 932 | 189852655 | 189852777 | 934 | 1055 | 233 | 274 |
| ENST00000441310 | 3242 | 932 | 189863743 | 189864228 | 2091 | 2575 | 619 | 780 |
| 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 |
| ENST00000441310 | 3242 | 932 | 189795769 | 189795951 | 367 | 548 | 44 | 105 |
| ENST00000441310 | 3242 | 932 | 189843964 | 189844080 | 817 | 932 | 194 | 233 |
| ENST00000441310 | 3242 | 932 | 189852655 | 189852777 | 934 | 1055 | 233 | 274 |
| ENST00000441310 | 3242 | 932 | 189863743 | 189864228 | 2091 | 2575 | 619 | 780 |
| 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 |
| ENST00000441310 | 3242 | 932 | 189795769 | 189795951 | 367 | 548 | 44 | 105 |
| ENST00000441310 | 3242 | 932 | 189843964 | 189844080 | 817 | 932 | 194 | 233 |
| ENST00000441310 | 3242 | 932 | 189852655 | 189852777 | 934 | 1055 | 233 | 274 |
| ENST00000441310 | 3242 | 932 | 189863743 | 189864228 | 2091 | 2575 | 619 | 780 |
| 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 |
| P54277 | 44 | 105 | 1 | 176 | Alternative sequence | ID=VSP_047692;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 44 | 105 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 194 | 233 | 195 | 233 | Alternative sequence | ID=VSP_043371;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 194 | 233 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 194 | 233 | 202 | 202 | Natural variant | ID=VAR_014877;Note=R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066459 |
| P54277 | 233 | 274 | 195 | 233 | Alternative sequence | ID=VSP_043371;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 233 | 274 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 619 | 780 | 619 | 619 | Alternative sequence | ID=VSP_042676;Note=In isoform 2 and isoform 4. K->N;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 619 | 780 | 620 | 781 | Alternative sequence | ID=VSP_042677;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 619 | 780 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 619 | 780 | 571 | 639 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
| P54277 | 619 | 780 | 614 | 625 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| P54277 | 619 | 780 | 629 | 638 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| P54277 | 619 | 780 | 632 | 632 | Natural variant | ID=VAR_014878;Note=N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066456 |
| P54277 | 619 | 780 | 720 | 720 | Natural variant | ID=VAR_014879;Note=E->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066455 |
| P54277 | 619 | 780 | 626 | 628 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| 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 |
| P54277 | 44 | 105 | 1 | 176 | Alternative sequence | ID=VSP_047692;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 44 | 105 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 194 | 233 | 195 | 233 | Alternative sequence | ID=VSP_043371;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 194 | 233 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 194 | 233 | 202 | 202 | Natural variant | ID=VAR_014877;Note=R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066459 |
| P54277 | 233 | 274 | 195 | 233 | Alternative sequence | ID=VSP_043371;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 233 | 274 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 619 | 780 | 619 | 619 | Alternative sequence | ID=VSP_042676;Note=In isoform 2 and isoform 4. K->N;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 619 | 780 | 620 | 781 | Alternative sequence | ID=VSP_042677;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 619 | 780 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 619 | 780 | 571 | 639 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
| P54277 | 619 | 780 | 614 | 625 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| P54277 | 619 | 780 | 629 | 638 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| P54277 | 619 | 780 | 632 | 632 | Natural variant | ID=VAR_014878;Note=N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066456 |
| P54277 | 619 | 780 | 720 | 720 | Natural variant | ID=VAR_014879;Note=E->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066455 |
| P54277 | 619 | 780 | 626 | 628 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| 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 |
| P54277 | 44 | 105 | 1 | 176 | Alternative sequence | ID=VSP_047692;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 44 | 105 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 194 | 233 | 195 | 233 | Alternative sequence | ID=VSP_043371;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 194 | 233 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 194 | 233 | 202 | 202 | Natural variant | ID=VAR_014877;Note=R->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066459 |
| P54277 | 233 | 274 | 195 | 233 | Alternative sequence | ID=VSP_043371;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 233 | 274 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 619 | 780 | 619 | 619 | Alternative sequence | ID=VSP_042676;Note=In isoform 2 and isoform 4. K->N;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 619 | 780 | 620 | 781 | Alternative sequence | ID=VSP_042677;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
| P54277 | 619 | 780 | 1 | 932 | Chain | ID=PRO_0000178004;Note=PMS1 protein homolog 1 |
| P54277 | 619 | 780 | 571 | 639 | DNA binding | Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00267 |
| P54277 | 619 | 780 | 614 | 625 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| P54277 | 619 | 780 | 629 | 638 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
| P54277 | 619 | 780 | 632 | 632 | Natural variant | ID=VAR_014878;Note=N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066456 |
| P54277 | 619 | 780 | 720 | 720 | Natural variant | ID=VAR_014879;Note=E->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs2066455 |
| P54277 | 619 | 780 | 626 | 628 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2CS1 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in PMS1 |
| 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 |
Top |
SNVs in the skipped exons for PMS1 |
| - 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 |
Top |
AD stage-associated exon skippint events for PMS1 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PMS1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_71166 | rs5743047 | chr2:189819942 | 1.686867e-05 | 1.992513e-03 |
Top |
Correlation with RNA binding proteins (RBPs) for PMS1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | HNRNPDL | exon_skip_183444 | 5.533300e-01 | 4.105058e-12 |
| CB | TARDBP | exon_skip_250295 | -4.860144e-01 | 4.581010e-09 |
| CB | FUBP1 | exon_skip_250295 | -4.529172e-01 | 6.283047e-08 |
| CB | RBM3 | exon_skip_71166 | 4.580254e-01 | 1.438866e-09 |
| CB | TRA2A | exon_skip_71166 | -4.368342e-01 | 9.566269e-09 |
| CB | HNRNPDL | exon_skip_71166 | 4.508850e-01 | 2.764052e-09 |
| HCC | FUBP1 | exon_skip_71166 | -4.005738e-01 | 9.909527e-10 |
| IFG | A1CF | exon_skip_256972 | 4.494387e-01 | 2.419942e-02 |
| PCC | PTBP1 | exon_skip_183444 | -4.235925e-01 | 1.700216e-09 |
Top |
RelatedDrugs for PMS1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for PMS1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|