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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 MCM9 |
 Gene summary |
| Gene information | Gene symbol | MCM9 | Gene ID | 254394 |
| Gene name | minichromosome maintenance 9 homologous recombination repair factor | |
| Synonyms | C6orf61|MCMDC1|ODG4|dJ329L24.1|dJ329L24.3 | |
| Cytomap | 6q22.31 | |
| Type of gene | protein-coding | |
| Description | DNA helicase MCM9DNA replication licensing factor MCM9mini-chromosome maintenance deficient domain-containing protein 1minichromosome maintenance complex component 9 | |
| Modification date | 20180519 | |
| UniProtAcc | Q9NXL9 | |
| Context | PubMed: MCM9 [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 |
| MCM9 | GO:0000724 | double-strand break repair via homologous recombination | 22771115 |
| MCM9 | GO:0006974 | cellular response to DNA damage stimulus | 22771115 |
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Exon skipping events across known transcript of Ensembl for MCM9 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 MCM9 |
| 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 MCM9 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_462026 | 6 | 119137343:119137457:119147309:119147455:119147944:119148027 | 119147309:119147455 | ENSG00000111877.13 | ENST00000316316.6,ENST00000458674.2 |
| exon_skip_462027 | 6 | 119147944:119148027:119149089:119149293:119150210:119150413 | 119149089:119149293 | ENSG00000111877.13 | ENST00000316316.6 |
| exon_skip_462028 | 6 | 119150210:119150413:119177533:119177708:119215190:119215436 | 119177533:119177708 | ENSG00000111877.13 | ENST00000505485.1 |
| exon_skip_462029 | 6 | 119150210:119150413:119177533:119177708:119232814:119232934 | 119177533:119177708 | ENSG00000111877.13 | ENST00000316316.6 |
| exon_skip_462032 | 6 | 119232814:119232934:119234459:119234585:119238725:119238926 | 119234459:119234585 | ENSG00000111877.13 | ENST00000316316.6,ENST00000316068.3 |
| exon_skip_462035 | 6 | 119245127:119245292:119252584:119252903:119256055:119256189 | 119252584:119252903 | ENSG00000111877.13 | ENST00000316068.3 |
| exon_skip_462036 | 6 | 119252654:119252903:119253771:119253905:119256055:119256189 | 119253771:119253905 | ENSG00000111877.13 | ENST00000425154.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for MCM9 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_462026 | 6 | 119137343:119137457:119147309:119147455:119147944:119148027 | 119147309:119147455 | ENSG00000111877.13 | ENST00000316316.6,ENST00000458674.2 |
| exon_skip_462027 | 6 | 119147944:119148027:119149089:119149293:119150210:119150413 | 119149089:119149293 | ENSG00000111877.13 | ENST00000316316.6 |
| exon_skip_462028 | 6 | 119150210:119150413:119177533:119177708:119215190:119215436 | 119177533:119177708 | ENSG00000111877.13 | ENST00000505485.1 |
| exon_skip_462029 | 6 | 119150210:119150413:119177533:119177708:119232814:119232934 | 119177533:119177708 | ENSG00000111877.13 | ENST00000316316.6 |
| exon_skip_462032 | 6 | 119232814:119232934:119234459:119234585:119238725:119238926 | 119234459:119234585 | ENSG00000111877.13 | ENST00000316316.6,ENST00000316068.3 |
| exon_skip_462035 | 6 | 119245127:119245292:119252584:119252903:119256055:119256189 | 119252584:119252903 | ENSG00000111877.13 | ENST00000316068.3 |
| exon_skip_462036 | 6 | 119252654:119252903:119253771:119253905:119256055:119256189 | 119253771:119253905 | ENSG00000111877.13 | ENST00000425154.2 |
| 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 MCM9 |
| 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 |
| ENST00000316316 | 119147309 | 119147455 | Frame-shift |
| ENST00000316316 | 119177533 | 119177708 | Frame-shift |
| ENST00000316316 | 119149089 | 119149293 | In-frame |
| ENST00000316316 | 119234459 | 119234585 | 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 |
| ENST00000316316 | 119147309 | 119147455 | Frame-shift |
| ENST00000316316 | 119177533 | 119177708 | Frame-shift |
| ENST00000316316 | 119149089 | 119149293 | In-frame |
| ENST00000316316 | 119234459 | 119234585 | In-frame |
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Infer the effects of exon skipping event on protein functional features for MCM9 |
| 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 |
| ENST00000316316 | 5118 | 1143 | 119234459 | 119234585 | 1192 | 1317 | 301 | 343 |
| ENST00000316316 | 5118 | 1143 | 119149089 | 119149293 | 1816 | 2019 | 509 | 577 |
| 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 |
| ENST00000316316 | 5118 | 1143 | 119234459 | 119234585 | 1192 | 1317 | 301 | 343 |
| ENST00000316316 | 5118 | 1143 | 119149089 | 119149293 | 1816 | 2019 | 509 | 577 |
| 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 |
| Q9NXL9 | 301 | 343 | 1 | 381 | Alternative sequence | ID=VSP_044180;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NXL9 | 301 | 343 | 1 | 1143 | Chain | ID=PRO_0000089513;Note=DNA helicase MCM9 |
| Q9NXL9 | 301 | 343 | 300 | 505 | Domain | Note=MCM;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NXL9 | 509 | 577 | 392 | 1143 | Alternative sequence | ID=VSP_028014;Note=In isoform S. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NXL9 | 509 | 577 | 1 | 1143 | Chain | ID=PRO_0000089513;Note=DNA helicase MCM9 |
| Q9NXL9 | 509 | 577 | 558 | 558 | Sequence conflict | Note=C->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q9NXL9 | 301 | 343 | 1 | 381 | Alternative sequence | ID=VSP_044180;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NXL9 | 301 | 343 | 1 | 1143 | Chain | ID=PRO_0000089513;Note=DNA helicase MCM9 |
| Q9NXL9 | 301 | 343 | 300 | 505 | Domain | Note=MCM;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9NXL9 | 509 | 577 | 392 | 1143 | Alternative sequence | ID=VSP_028014;Note=In isoform S. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9NXL9 | 509 | 577 | 1 | 1143 | Chain | ID=PRO_0000089513;Note=DNA helicase MCM9 |
| Q9NXL9 | 509 | 577 | 558 | 558 | Sequence conflict | Note=C->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for MCM9 |
| - 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-G3-A3CJ-01 | exon_skip_462027 | 119149090 | 119149293 | 119149111 | 119149111 | Frame_Shift_Del | T | - | p.S571fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_462032 | 119234460 | 119234585 | 119234497 | 119234497 | Frame_Shift_Del | C | - | p.G331fs |
| KIRC | TCGA-B4-5838-01 | exon_skip_462035 | 119252585 | 119252903 | 119252784 | 119252784 | Frame_Shift_Del | A | - | p.D35fs |
| LIHC | TCGA-DD-AAW1-01 | exon_skip_462026 | 119147310 | 119147455 | 119147392 | 119147392 | Nonsense_Mutation | G | A | p.Q627X |
| - 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 |
| CAS1_CENTRAL_NERVOUS_SYSTEM | 119147310 | 119147455 | 119147370 | 119147370 | Missense_Mutation | A | G | p.L634P |
| NUGC3_STOMACH | 119147310 | 119147455 | 119147371 | 119147371 | Missense_Mutation | G | T | p.L634I |
| JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119149090 | 119149293 | 119149123 | 119149123 | Missense_Mutation | G | A | p.R567W |
| 2313287_STOMACH | 119149090 | 119149293 | 119149135 | 119149135 | Missense_Mutation | G | A | p.R563W |
| TOV21G_OVARY | 119177534 | 119177708 | 119177702 | 119177702 | Missense_Mutation | G | A | p.T386M |
| OVCA433_OVARY | 119234460 | 119234585 | 119234513 | 119234513 | Missense_Mutation | A | G | p.M326T |
| CW2_LARGE_INTESTINE | 119252585 | 119252903 | 119252605 | 119252605 | Missense_Mutation | T | C | p.N95S |
| DU145_PROSTATE | 119252585 | 119252903 | 119252629 | 119252629 | Missense_Mutation | G | A | p.P87L |
| TK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119252585 | 119252903 | 119252680 | 119252680 | Missense_Mutation | T | C | p.D70G |
| SARC9371_BONE | 119252585 | 119252903 | 119252695 | 119252695 | Missense_Mutation | A | T | p.V65E |
| 647V_URINARY_TRACT | 119252585 | 119252903 | 119252696 | 119252696 | Missense_Mutation | C | T | p.V65M |
| SARC9371_BONE | 119252585 | 119252903 | 119252696 | 119252696 | Missense_Mutation | C | T | p.V65M |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119252585 | 119252903 | 119252758 | 119252758 | Missense_Mutation | G | A | p.A44V |
| MCC13_SKIN | 119252585 | 119252903 | 119252794 | 119252794 | Missense_Mutation | C | T | p.R32K |
| CAL33_UPPER_AERODIGESTIVE_TRACT | 119252585 | 119252903 | 119252819 | 119252819 | Missense_Mutation | C | T | p.D24N |
| ES2_OVARY | 119252585 | 119252903 | 119252834 | 119252834 | Missense_Mutation | C | T | p.E19K |
| HAL01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 119252585 | 119252903 | 119252855 | 119252855 | Missense_Mutation | C | T | p.V12M |
| NCIH522_LUNG | 119252585 | 119252903 | 119252861 | 119252861 | Missense_Mutation | C | G | p.G10R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MCM9 |
| 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 MCM9 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MCM9 |
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RelatedDrugs for MCM9 |
| 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 MCM9 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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