|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for CMAS |
 Gene summary |
| Gene information | Gene symbol | CMAS | Gene ID | 55907 |
| Gene name | cytidine monophosphate N-acetylneuraminic acid synthetase | |
| Synonyms | CSS | |
| Cytomap | 12p12.1 | |
| Type of gene | protein-coding | |
| Description | N-acylneuraminate cytidylyltransferaseCMP-N-acetylneuraminic acid synthaseCMP-N-acetylneuraminic acid synthetaseCMP-Neu5Ac synthetaseCMP-NeuNAc synthaseCMP-NeuNAc synthetaseCMP-sialic acid synthetasecytidine 5'-monophosphate N-acetylneuraminic acid | |
| Modification date | 20180523 | |
| UniProtAcc | Q8NFW8 | |
| Context | PubMed: CMAS [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 |
Top |
Exon skipping events across known transcript of Ensembl for CMAS 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. |
 |
Top |
Gene isoform structures and expression levels for CMAS |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CMAS |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_80658 | 12 | 22199220:22199497:22208082:22208225:22208388:22208544 | 22208082:22208225 | ENSG00000111726.8 | ENST00000534981.1 |
| exon_skip_80661 | 12 | 22208390:22208544:22211500:22211634:22213765:22213860 | 22211500:22211634 | ENSG00000111726.8 | ENST00000538498.1,ENST00000229329.2,ENST00000534981.1 |
| exon_skip_80665 | 12 | 22213765:22213860:22214214:22214386:22215214:22215347 | 22214214:22214386 | ENSG00000111726.8 | ENST00000229329.2,ENST00000535610.1,ENST00000537658.1 |
| exon_skip_80668 | 12 | 22213765:22213860:22215214:22215368:22218054:22218597 | 22215214:22215368 | ENSG00000111726.8 | ENST00000534981.1 |
| exon_skip_80669 | 12 | 22214214:22214386:22215214:22215368:22218054:22218597 | 22215214:22215368 | ENSG00000111726.8 | ENST00000229329.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CMAS |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_80658 | 12 | 22199220:22199497:22208082:22208225:22208388:22208544 | 22208082:22208225 | ENSG00000111726.8 | ENST00000534981.1 |
| exon_skip_80661 | 12 | 22208390:22208544:22211500:22211634:22213765:22213860 | 22211500:22211634 | ENSG00000111726.8 | ENST00000229329.2,ENST00000534981.1,ENST00000538498.1 |
| exon_skip_80665 | 12 | 22213765:22213860:22214214:22214386:22215214:22215347 | 22214214:22214386 | ENSG00000111726.8 | ENST00000229329.2,ENST00000535610.1,ENST00000537658.1 |
| exon_skip_80668 | 12 | 22213765:22213860:22215214:22215368:22218054:22218597 | 22215214:22215368 | ENSG00000111726.8 | ENST00000534981.1 |
| exon_skip_80669 | 12 | 22214214:22214386:22215214:22215368:22218054:22218597 | 22215214:22215368 | ENSG00000111726.8 | ENST00000229329.2 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CMAS |
| 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 |
| ENST00000229329 | 22211500 | 22211634 | Frame-shift |
| ENST00000229329 | 22214214 | 22214386 | Frame-shift |
| ENST00000229329 | 22215214 | 22215368 | Frame-shift |
| 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 |
| ENST00000229329 | 22211500 | 22211634 | Frame-shift |
| ENST00000229329 | 22214214 | 22214386 | Frame-shift |
| ENST00000229329 | 22215214 | 22215368 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for CMAS |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
Top |
SNVs in the skipped exons for CMAS |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
CMAS_BRCA_exon_skip_80665_psi_boxplot.png |
CMAS_OV_exon_skip_80665_psi_boxplot.png |
CMAS_STAD_exon_skip_80665_psi_boxplot.png |
| - 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_80658 | 22208083 | 22208225 | 22208126 | 22208126 | Frame_Shift_Del | A | - | p.K102fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_80661 | 22211501 | 22211634 | 22211595 | 22211595 | Frame_Shift_Del | T | - | p.Y218fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_80668 exon_skip_80669 | 22215215 | 22215368 | 22215262 | 22215262 | Frame_Shift_Del | T | - | p.S336fs |
| STAD | TCGA-BR-4256-01 | exon_skip_80665 | 22214215 | 22214386 | 22214223 | 22214224 | Frame_Shift_Ins | - | A | p.Y266fs |
| LGG | TCGA-DU-6407-02 | exon_skip_80661 | 22211501 | 22211634 | 22211561 | 22211561 | Nonsense_Mutation | G | A | p.W207* |
| LUAD | TCGA-J2-A4AD-01 | exon_skip_80661 | 22211501 | 22211634 | 22211632 | 22211632 | Nonsense_Mutation | C | T | p.Q231* |
| BRCA | TCGA-AR-A256-01 | exon_skip_80665 | 22214215 | 22214386 | 22214246 | 22214246 | Nonsense_Mutation | G | T | p.E274* |
| UCEC | TCGA-D1-A16X-01 | exon_skip_80665 | 22214215 | 22214386 | 22214321 | 22214321 | Nonsense_Mutation | G | T | p.E299* |
| SKCM | TCGA-ER-A198-06 | exon_skip_80668 exon_skip_80669 | 22215215 | 22215368 | 22215349 | 22215349 | Nonsense_Mutation | G | A | p.W365* |
| OV | TCGA-13-1509-01 | exon_skip_80665 | 22214215 | 22214386 | 22214388 | 22214388 | Splice_Site | T | G | e6+2 |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-AR-A256-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_80665 | |
| Skipped exon start: 22214215 | |
| Skipped exon end: 22214386 | |
| Mutation start: 22214246 | |
| Mutation end: 22214246 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: p.E274* | |
exon_skip_286384_BRCA_TCGA-AR-A256-01.png | |
exon_skip_80665_BRCA_TCGA-AR-A256-01.png | |
 | Sample: TCGA-D1-A16X-01 |
| Cancer type: UCEC | |
| ESID: exon_skip_80665 | |
| Skipped exon start: 22214215 | |
| Skipped exon end: 22214386 | |
| Mutation start: 22214321 | |
| Mutation end: 22214321 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: p.E299* | |
exon_skip_34951_UCEC_TCGA-D1-A16X-01.png | |
exon_skip_479551_UCEC_TCGA-D1-A16X-01.png | |
exon_skip_80665_UCEC_TCGA-D1-A16X-01.png | |
exon_skip_97620_UCEC_TCGA-D1-A16X-01.png | |
| - 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 |
| HCT15_LARGE_INTESTINE | 22214215 | 22214386 | 22214219 | 22214219 | Frame_Shift_Del | G | - | p.G265fs |
| M059K_CENTRAL_NERVOUS_SYSTEM | 22208083 | 22208225 | 22208094 | 22208094 | Missense_Mutation | C | T | p.S91L |
| HCC2998_LARGE_INTESTINE | 22208083 | 22208225 | 22208151 | 22208151 | Missense_Mutation | G | A | p.R110Q |
| HEC108_ENDOMETRIUM | 22208083 | 22208225 | 22208201 | 22208201 | Missense_Mutation | A | G | p.I127V |
| COLO680N_OESOPHAGUS | 22208083 | 22208225 | 22208219 | 22208219 | Missense_Mutation | C | T | p.H133Y |
| SNU1040_LARGE_INTESTINE | 22211501 | 22211634 | 22211549 | 22211549 | Missense_Mutation | G | A | p.R203H |
| HCC515_LUNG | 22211501 | 22211634 | 22211622 | 22211622 | Missense_Mutation | G | A | p.M227I |
| ASPC1_PANCREAS | 22214215 | 22214386 | 22214268 | 22214268 | Missense_Mutation | A | G | p.N281S |
| NH6_AUTONOMIC_GANGLIA | 22215215 | 22215368 | 22215309 | 22215309 | Missense_Mutation | C | A | p.A352E |
| IGROV1_OVARY | 22215215 | 22215368 | 22215360 | 22215360 | Missense_Mutation | C | T | p.A369V |
| SNU81_LARGE_INTESTINE | 22208083 | 22208225 | 22208204 | 22208204 | Nonsense_Mutation | G | T | p.E128* |
| HEC251_ENDOMETRIUM | 22211501 | 22211634 | 22211628 | 22211628 | Nonsense_Mutation | C | A | p.Y229* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CMAS |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CMAS |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CMAS |
Top |
RelatedDrugs for CMAS |
| 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 |
Top |
RelatedDiseases for CMAS |
| 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)
|