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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 SYNM |
 Gene summary |
| Gene information | Gene symbol | SYNM | Gene ID | 23336 |
| Gene name | synemin | |
| Synonyms | DMN|SYN | |
| Cytomap | 15q26.3 | |
| Type of gene | protein-coding | |
| Description | synemindesmuslinsynemin alphasynemin betasynemin, intermediate filament protein | |
| Modification date | 20180519 | |
| UniProtAcc | O15061 | |
| Context | PubMed: SYNM [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 |
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Exon skipping events across known transcript of Ensembl for SYNM 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 SYNM |
| 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 SYNM |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENSG00000182253.10 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SYNM |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENSG00000182253.10 | ENST00000560674.1,ENST00000558420.1,ENST00000328642.7 |
| 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 SYNM |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for SYNM |
| 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 |
| 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 |
| 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 |
| 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 |
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SNVs in the skipped exons for SYNM |
| - 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 |
| UCEC | TCGA-B5-A11U-01 | exon_skip_125224 | 99669572 | 99672018 | 99670283 | 99670284 | Frame_Shift_Del | GA | - | p.E575fs |
| LIHC | TCGA-DD-A3A1-01 | exon_skip_125224 | 99669572 | 99672018 | 99670316 | 99670316 | Frame_Shift_Del | C | - | p.S583fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_125224 | 99669572 | 99672018 | 99670335 | 99670335 | Frame_Shift_Del | G | - | p.E589fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_125224 | 99669572 | 99672018 | 99670350 | 99670350 | Frame_Shift_Del | T | - | p.G594fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_125224 | 99669572 | 99672018 | 99670619 | 99670619 | Frame_Shift_Del | A | - | p.E684fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_125224 | 99669572 | 99672018 | 99670989 | 99670989 | Frame_Shift_Del | T | - | p.P807fs |
| STAD | TCGA-CG-5728-01 | exon_skip_125224 | 99669572 | 99672018 | 99671083 | 99671083 | Frame_Shift_Del | G | - | p.P838fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_125224 | 99669572 | 99672018 | 99671187 | 99671187 | Frame_Shift_Del | A | - | p.R875fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_125224 | 99669572 | 99672018 | 99671398 | 99671398 | Frame_Shift_Del | C | - | p.P944fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_125224 | 99669572 | 99672018 | 99671500 | 99671500 | Frame_Shift_Del | C | - | p.P978fs |
| UCEC | TCGA-D1-A160-01 | exon_skip_125224 | 99669572 | 99672018 | 99670282 | 99670283 | Frame_Shift_Ins | - | GA | p.E576fs |
| STAD | TCGA-D7-A4YY-01 | exon_skip_125224 | 99669572 | 99672018 | 99670283 | 99670284 | Frame_Shift_Ins | - | GA | p.R572fs |
| UCEC | TCGA-AP-A059-01 | exon_skip_125224 | 99669572 | 99672018 | 99670118 | 99670118 | Nonsense_Mutation | C | T | p.Q518* |
| UCEC | TCGA-AP-A059-01 | exon_skip_125224 | 99669572 | 99672018 | 99670984 | 99670984 | Nonsense_Mutation | C | T | p.Q806* |
| KICH | TCGA-KO-8408-01 | exon_skip_125224 | 99669572 | 99672018 | 99671287 | 99671287 | Nonsense_Mutation | A | T | p.K907* |
| UCEC | TCGA-BS-A0UV-01 | exon_skip_125224 | 99669572 | 99672018 | 99671320 | 99671320 | Nonsense_Mutation | G | T | p.E918* |
| UCEC | TCGA-BS-A0UV-01 | exon_skip_125224 | 99669572 | 99672018 | 99671341 | 99671341 | Nonsense_Mutation | G | T | p.E925* |
| BRCA | TCGA-B6-A0RG-01 | exon_skip_125224 | 99669572 | 99672018 | 99671359 | 99671359 | Nonsense_Mutation | G | T | p.E931* |
| - 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 |
| HEC151_ENDOMETRIUM | 99669572 | 99672018 | 99671083 | 99671083 | Frame_Shift_Del | G | - | p.G555fs |
| CAL51_BREAST | 99669572 | 99672018 | 99671083 | 99671083 | Frame_Shift_Del | G | - | p.G555fs |
| BICR22_UPPER_AERODIGESTIVE_TRACT | 99669572 | 99672018 | 99669708 | 99669708 | Missense_Mutation | C | A | p.H95Q |
| HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99669791 | 99669791 | Missense_Mutation | C | T | p.T123I |
| CW2_LARGE_INTESTINE | 99669572 | 99672018 | 99669860 | 99669860 | Missense_Mutation | A | G | p.Y146C |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99669889 | 99669889 | Missense_Mutation | G | A | p.V156M |
| JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99669959 | 99669959 | Missense_Mutation | C | T | p.S179F |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99669980 | 99669980 | Missense_Mutation | A | G | p.Y186C |
| HEC251_ENDOMETRIUM | 99669572 | 99672018 | 99669989 | 99669989 | Missense_Mutation | G | A | p.R189H |
| P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99670018 | 99670018 | Missense_Mutation | G | C | p.E199Q |
| SNU81_LARGE_INTESTINE | 99669572 | 99672018 | 99670115 | 99670115 | Missense_Mutation | G | A | p.R231Q |
| SNU1040_LARGE_INTESTINE | 99669572 | 99672018 | 99670175 | 99670175 | Missense_Mutation | T | C | p.L251P |
| BXPC3_PANCREAS | 99669572 | 99672018 | 99670200 | 99670200 | Missense_Mutation | A | C | p.L259F |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99670211 | 99670211 | Missense_Mutation | C | T | p.A263V |
| JL1_PLEURA | 99669572 | 99672018 | 99670246 | 99670246 | Missense_Mutation | G | A | p.A275T |
| HCC515_LUNG | 99669572 | 99672018 | 99670298 | 99670298 | Missense_Mutation | C | T | p.P292L |
| SCC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99670325 | 99670325 | Missense_Mutation | G | A | p.R301K |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 99669572 | 99672018 | 99670358 | 99670358 | Missense_Mutation | C | T | p.T312M |
| NCIH1770_LUNG | 99669572 | 99672018 | 99670562 | 99670562 | Missense_Mutation | C | T | p.T380I |
| NCIH2106_LUNG | 99669572 | 99672018 | 99670562 | 99670562 | Missense_Mutation | C | T | p.T380I |
| GP2D_LARGE_INTESTINE | 99669572 | 99672018 | 99670598 | 99670598 | Missense_Mutation | G | A | p.G392E |
| GP5D_LARGE_INTESTINE | 99669572 | 99672018 | 99670598 | 99670598 | Missense_Mutation | G | A | p.G392E |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99670791 | 99670791 | Missense_Mutation | G | T | p.K456N |
| SW156_KIDNEY | 99669572 | 99672018 | 99670805 | 99670805 | Missense_Mutation | A | C | p.E461A |
| HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99670810 | 99670810 | Missense_Mutation | G | A | p.V463M |
| MDAMB361_BREAST | 99669572 | 99672018 | 99670842 | 99670842 | Missense_Mutation | G | T | p.E473D |
| HCT15_LARGE_INTESTINE | 99669572 | 99672018 | 99670851 | 99670851 | Missense_Mutation | G | T | p.E476D |
| NCIH322_LUNG | 99669572 | 99672018 | 99670851 | 99670851 | Missense_Mutation | G | T | p.E476D |
| WM88_SKIN | 99669572 | 99672018 | 99670854 | 99670854 | Missense_Mutation | G | C | p.E477D |
| HS746T_STOMACH | 99669572 | 99672018 | 99670914 | 99670914 | Missense_Mutation | G | T | p.L497F |
| EB3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99671097 | 99671099 | Missense_Mutation | AGA | GAT | p.D559I |
| NCIH2172_LUNG | 99669572 | 99672018 | 99671177 | 99671177 | Missense_Mutation | A | G | p.Q585R |
| MEWO_SKIN | 99669572 | 99672018 | 99671207 | 99671207 | Missense_Mutation | G | A | p.G595D |
| CW2_LARGE_INTESTINE | 99669572 | 99672018 | 99671262 | 99671262 | Missense_Mutation | G | T | p.E613D |
| NCIH748_LUNG | 99669572 | 99672018 | 99671276 | 99671276 | Missense_Mutation | C | A | p.S618Y |
| OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99671525 | 99671525 | Missense_Mutation | A | G | p.K701R |
| A204_SOFT_TISSUE | 99669572 | 99672018 | 99671537 | 99671537 | Missense_Mutation | G | A | p.G705D |
| TTC642_SOFT_TISSUE | 99669572 | 99672018 | 99671537 | 99671537 | Missense_Mutation | G | A | p.G705D |
| SNUC2A_LARGE_INTESTINE | 99669572 | 99672018 | 99671578 | 99671578 | Missense_Mutation | G | A | p.V719I |
| SNUC2B_LARGE_INTESTINE | 99669572 | 99672018 | 99671578 | 99671578 | Missense_Mutation | G | A | p.V719I |
| SW1710_URINARY_TRACT | 99669572 | 99672018 | 99671578 | 99671578 | Missense_Mutation | G | A | p.V719I |
| PCI6A_UPPER_AERODIGESTIVE_TRACT | 99669572 | 99672018 | 99671596 | 99671596 | Missense_Mutation | G | A | p.A725T |
| CL11_LARGE_INTESTINE | 99669572 | 99672018 | 99671602 | 99671602 | Missense_Mutation | C | T | p.R727W |
| OVCA420_OVARY | 99669572 | 99672018 | 99671617 | 99671618 | Missense_Mutation | GA | TT | p.E732L |
| KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99671643 | 99671643 | Missense_Mutation | G | T | p.E740D |
| ECC10_STOMACH | 99669572 | 99672018 | 99671764 | 99671764 | Missense_Mutation | C | A | p.R781S |
| D425_CENTRAL_NERVOUS_SYSTEM | 99669572 | 99672018 | 99671782 | 99671782 | Missense_Mutation | C | A | p.L787M |
| OE33_OESOPHAGUS | 99669572 | 99672018 | 99671843 | 99671843 | Missense_Mutation | G | A | p.R807H |
| MDAPCA2B_PROSTATE | 99669572 | 99672018 | 99671904 | 99671904 | Missense_Mutation | G | C | p.Q827H |
| KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99671950 | 99671950 | Missense_Mutation | C | T | p.L843F |
| OVK18_OVARY | 99669572 | 99672018 | 99671957 | 99671957 | Missense_Mutation | C | T | p.P845L |
| HCC2450_LUNG | 99669572 | 99672018 | 99671992 | 99671992 | Missense_Mutation | G | A | p.E857K |
| MRKNU1_BREAST | 99669572 | 99672018 | 99670162 | 99670162 | Nonsense_Mutation | G | T | p.E247* |
| MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99669572 | 99672018 | 99670777 | 99670777 | Nonsense_Mutation | G | T | p.E452* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYNM |
| 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 |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 | GBM | rs260087 | chr15:99671760 | T/C | 3.62e-04 |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 | LGG | rs260087 | chr15:99671760 | T/C | 2.15e-03 |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 | KIRC | rs260087 | chr15:99671760 | T/C | 5.45e-05 |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 | KIRC | rs3743248 | chr15:99670989 | T/C | 1.07e-04 |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 | PRAD | rs5030699 | chr15:99671795 | C/T | 2.76e-06 |
| exon_skip_125224 | 15 | 99666926:99666997:99669571:99672018:99672954:99675788 | 99669571:99672018 | ENST00000558420.1,ENST00000560674.1,ENST00000328642.7 | PRAD | rs3743244 | chr15:99670265 | C/T | 9.04e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYNM |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYNM |
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RelatedDrugs for SYNM |
| 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 SYNM |
| 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)
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