|
||||||
|
 | |
| |
| |
| |
| 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 MGAT4A |
 Gene summary |
| Gene information | Gene symbol | MGAT4A | Gene ID | 11320 |
| Gene name | mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A | |
| Synonyms | GNT-IV|GNT-IVA|GnT-4a | |
| Cytomap | 2q11.2 | |
| Type of gene | protein-coding | |
| Description | alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase AN-acetylglucosaminyltransferase IVaN-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase IVaUDP-GlcNAc:a-1,3-D-mannoside b-1,4-acetylglucosaminyltransferase IVUD | |
| Modification date | 20180522 | |
| UniProtAcc | Q9UM21 | |
| Context | PubMed: MGAT4A [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 MGAT4A 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 MGAT4A |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for MGAT4A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_342046 | 2 | 99260385:99260516:99261890:99262005:99271907:99271983 | 99261890:99262005 | ENSG00000071073.8 | ENST00000393487.1,ENST00000409391.1,ENST00000414521.2,ENST00000264968.3 |
| exon_skip_342049 | 2 | 99274680:99274727:99279508:99279642:99291497:99291638 | 99279508:99279642 | ENSG00000071073.8 | ENST00000393487.1,ENST00000409391.1,ENST00000264968.3 |
| exon_skip_342050 | 2 | 99291497:99291638:99294766:99294934:99342701:99343030 | 99294766:99294934 | ENSG00000071073.8 | ENST00000393487.1,ENST00000409391.1,ENST00000484936.1 |
| exon_skip_342052 | 2 | 99294883:99294934:99342701:99343030:99347510:99347556 | 99342701:99343030 | ENSG00000071073.8 | ENST00000393487.1,ENST00000460768.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for MGAT4A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_342046 | 2 | 99260385:99260516:99261890:99262005:99271907:99271983 | 99261890:99262005 | ENSG00000071073.8 | ENST00000264968.3,ENST00000393487.1,ENST00000414521.2,ENST00000409391.1 |
| exon_skip_342049 | 2 | 99274680:99274727:99279508:99279642:99291497:99291638 | 99279508:99279642 | ENSG00000071073.8 | ENST00000264968.3,ENST00000393487.1,ENST00000409391.1 |
| exon_skip_342052 | 2 | 99294883:99294934:99342701:99343030:99347510:99347556 | 99342701:99343030 | ENSG00000071073.8 | ENST00000393487.1,ENST00000460768.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for MGAT4A |
| 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 |
| ENST00000393487 | 99342701 | 99343030 | 3UTR-3CDS |
| ENST00000264968 | 99261890 | 99262005 | Frame-shift |
| ENST00000393487 | 99261890 | 99262005 | Frame-shift |
| ENST00000409391 | 99261890 | 99262005 | Frame-shift |
| ENST00000264968 | 99279508 | 99279642 | Frame-shift |
| ENST00000393487 | 99279508 | 99279642 | Frame-shift |
| ENST00000409391 | 99279508 | 99279642 | Frame-shift |
| ENST00000393487 | 99294766 | 99294934 | In-frame |
| ENST00000409391 | 99294766 | 99294934 | 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 |
| ENST00000393487 | 99342701 | 99343030 | 3UTR-3CDS |
| ENST00000264968 | 99261890 | 99262005 | Frame-shift |
| ENST00000393487 | 99261890 | 99262005 | Frame-shift |
| ENST00000409391 | 99261890 | 99262005 | Frame-shift |
| ENST00000264968 | 99279508 | 99279642 | Frame-shift |
| ENST00000393487 | 99279508 | 99279642 | Frame-shift |
| ENST00000409391 | 99279508 | 99279642 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for MGAT4A |
| 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 |
| ENST00000393487 | 8399 | 535 | 99294766 | 99294934 | 409 | 576 | 31 | 87 |
| ENST00000409391 | 2035 | 535 | 99294766 | 99294934 | 444 | 611 | 31 | 87 |
| 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 |
| Q9UM21 | 31 | 87 | 7 | 134 | Alternative sequence | ID=VSP_046076;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UM21 | 31 | 87 | 7 | 134 | Alternative sequence | ID=VSP_046076;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UM21 | 31 | 87 | 1 | 535 | Chain | ID=PRO_0000288581;Note=Alpha-1%2C3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A |
| Q9UM21 | 31 | 87 | 1 | 535 | Chain | ID=PRO_0000288581;Note=Alpha-1%2C3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A |
| Q9UM21 | 31 | 87 | 28 | 63 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM21 | 31 | 87 | 28 | 63 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM21 | 31 | 87 | 77 | 77 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM21 | 31 | 87 | 77 | 77 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM21 | 31 | 87 | 28 | 535 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UM21 | 31 | 87 | 28 | 535 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 MGAT4A |
| - 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. |
| - 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_342046 | 99261891 | 99262005 | 99261956 | 99261956 | Frame_Shift_Del | T | - | p.N275fs |
| STAD | TCGA-CG-5733-01 | exon_skip_342046 | 99261891 | 99262005 | 99261956 | 99261956 | Frame_Shift_Del | T | - | p.N275fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_342046 | 99261891 | 99262005 | 99261977 | 99261977 | Frame_Shift_Del | T | - | p.N268fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_342052 | 99342702 | 99343030 | 99342734 | 99342734 | Frame_Shift_Del | A | - | p.L21fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_342052 | 99342702 | 99343030 | 99342769 | 99342769 | Frame_Shift_Del | G | - | p.A9fs |
| UCS | TCGA-ND-A4WC-01 | exon_skip_342050 | 99294767 | 99294934 | 99294911 | 99294911 | Nonsense_Mutation | C | A | p.E40* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_342050 | 99294767 | 99294934 | 99294911 | 99294911 | Nonsense_Mutation | C | A | p.E40X |
| STAD | TCGA-D7-A4YY-01 | exon_skip_342050 | 99294767 | 99294934 | 99294914 | 99294914 | Nonsense_Mutation | G | A | p.R39* |
| STAD | TCGA-D7-A4YY-01 | exon_skip_342050 | 99294767 | 99294934 | 99294914 | 99294914 | Nonsense_Mutation | G | A | p.R39X |
| COAD | TCGA-A6-5665-01 | exon_skip_342050 | 99294767 | 99294934 | 99294930 | 99294930 | Nonsense_Mutation | T | - | p.L34X |
| - 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 |
| HEC108_ENDOMETRIUM | 99261891 | 99262005 | 99261956 | 99261956 | Frame_Shift_Del | T | - | p.N275fs |
| JHUEM7_ENDOMETRIUM | 99261891 | 99262005 | 99261957 | 99261957 | Missense_Mutation | T | G | p.N275H |
| HEC6_ENDOMETRIUM | 99261891 | 99262005 | 99261998 | 99261998 | Missense_Mutation | T | C | p.D261G |
| MEWO_SKIN | 99279509 | 99279642 | 99279553 | 99279553 | Missense_Mutation | G | A | p.P165S |
| SNU407_LARGE_INTESTINE | 99294767 | 99294934 | 99294856 | 99294856 | Missense_Mutation | C | T | p.R58H |
| RF48_STOMACH | 99294767 | 99294934 | 99294857 | 99294857 | Missense_Mutation | G | A | p.R58C |
| COLO829_SKIN | 99294767 | 99294934 | 99294884 | 99294884 | Nonsense_Mutation | G | A | p.R49* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MGAT4A |
| 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 MGAT4A |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MGAT4A |
Top |
RelatedDrugs for MGAT4A |
| 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 MGAT4A |
| 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)
|