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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 B4GALNT1 |
 Gene summary |
| Gene information | Gene symbol | B4GALNT1 | Gene ID | 2583 |
| Gene name | beta-1,4-N-acetyl-galactosaminyltransferase 1 | |
| Synonyms | GALGT|GALNACT|GalNAc-T|SPG26 | |
| Cytomap | 12q13.3 | |
| Type of gene | protein-coding | |
| Description | beta-1,4 N-acetylgalactosaminyltransferase 1GD2 synthase, GM2 synthaseGM2/GD2 synthaseUDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acety | |
| Modification date | 20180519 | |
| UniProtAcc | Q00973 | |
| Context | PubMed: B4GALNT1 [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 B4GALNT1 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 B4GALNT1 |
| 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 B4GALNT1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_94223 | 12 | 58020723:58020744:58021400:58021641:58021904:58022045 | 58021400:58021641 | ENSG00000135454.9 | ENST00000341156.4,ENST00000552798.1,ENST00000418555.2 |
| exon_skip_94224 | 12 | 58020723:58020744:58021400:58021674:58021904:58022045 | 58021400:58021674 | ENSG00000135454.9 | ENST00000547741.1 |
| exon_skip_94238 | 12 | 58022495:58022686:58022830:58022929:58023934:58024115 | 58022830:58022929 | ENSG00000135454.9 | ENST00000341156.4,ENST00000553142.1,ENST00000552798.1,ENST00000418555.2 |
| exon_skip_94239 | 12 | 58022495:58022686:58022830:58022957:58023934:58024115 | 58022830:58022957 | ENSG00000135454.9 | ENST00000549391.1 |
| exon_skip_94244 | 12 | 58023934:58024115:58024260:58024301:58024762:58024869 | 58024260:58024301 | ENSG00000135454.9 | ENST00000341156.4,ENST00000552350.1,ENST00000553142.1,ENST00000449184.3,ENST00000550764.1,ENST00000418555.2,ENST00000548888.1,ENST00000549391.1 |
| exon_skip_94245 | 12 | 58024779:58024869:58024982:58025037:58025697:58025916 | 58024982:58025037 | ENSG00000135454.9 | ENST00000552219.1 |
| exon_skip_94246 | 12 | 58024779:58024869:58024982:58025147:58025697:58025916 | 58024982:58025147 | ENSG00000135454.9 | ENST00000341156.4,ENST00000552350.1,ENST00000553142.1,ENST00000449184.3,ENST00000550764.1,ENST00000552798.1,ENST00000548888.1 |
| exon_skip_94247 | 12 | 58024982:58025037:58025121:58025147:58025697:58025916 | 58025121:58025147 | ENSG00000135454.9 | ENST00000550943.1,ENST00000548487.1 |
| exon_skip_94248 | 12 | 58025697:58025916:58026323:58026364:58026554:58026726 | 58026323:58026364 | ENSG00000135454.9 | ENST00000551220.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for B4GALNT1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_94223 | 12 | 58020723:58020744:58021400:58021641:58021904:58022045 | 58021400:58021641 | ENSG00000135454.9 | ENST00000341156.4,ENST00000418555.2,ENST00000552798.1 |
| exon_skip_94224 | 12 | 58020723:58020744:58021400:58021674:58021904:58022045 | 58021400:58021674 | ENSG00000135454.9 | ENST00000547741.1 |
| exon_skip_94238 | 12 | 58022495:58022686:58022830:58022929:58023934:58024115 | 58022830:58022929 | ENSG00000135454.9 | ENST00000553142.1,ENST00000341156.4,ENST00000418555.2,ENST00000552798.1 |
| exon_skip_94239 | 12 | 58022495:58022686:58022830:58022957:58023934:58024115 | 58022830:58022957 | ENSG00000135454.9 | ENST00000549391.1 |
| exon_skip_94244 | 12 | 58023934:58024115:58024260:58024301:58024762:58024869 | 58024260:58024301 | ENSG00000135454.9 | ENST00000553142.1,ENST00000341156.4,ENST00000418555.2,ENST00000549391.1,ENST00000449184.3,ENST00000550764.1,ENST00000552350.1,ENST00000548888.1 |
| exon_skip_94245 | 12 | 58024779:58024869:58024982:58025037:58025697:58025916 | 58024982:58025037 | ENSG00000135454.9 | ENST00000552219.1 |
| exon_skip_94246 | 12 | 58024779:58024869:58024982:58025147:58025697:58025916 | 58024982:58025147 | ENSG00000135454.9 | ENST00000553142.1,ENST00000341156.4,ENST00000552798.1,ENST00000449184.3,ENST00000550764.1,ENST00000552350.1,ENST00000548888.1 |
| exon_skip_94247 | 12 | 58024982:58025037:58025121:58025147:58025697:58025916 | 58025121:58025147 | ENSG00000135454.9 | ENST00000548487.1,ENST00000550943.1 |
| exon_skip_94248 | 12 | 58025697:58025916:58026323:58026364:58026554:58026726 | 58026323:58026364 | ENSG00000135454.9 | ENST00000551220.1 |
| 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 B4GALNT1 |
| 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 |
| ENST00000341156 | 58021400 | 58021641 | Frame-shift |
| ENST00000341156 | 58024260 | 58024301 | Frame-shift |
| ENST00000341156 | 58022830 | 58022929 | In-frame |
| ENST00000341156 | 58024982 | 58025147 | 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 |
| ENST00000341156 | 58021400 | 58021641 | Frame-shift |
| ENST00000341156 | 58024260 | 58024301 | Frame-shift |
| ENST00000341156 | 58022830 | 58022929 | In-frame |
| ENST00000341156 | 58024982 | 58025147 | In-frame |
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Infer the effects of exon skipping event on protein functional features for B4GALNT1 |
| 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 |
| ENST00000341156 | 3053 | 533 | 58024982 | 58025147 | 804 | 968 | 73 | 127 |
| ENST00000341156 | 3053 | 533 | 58022830 | 58022929 | 1298 | 1396 | 237 | 270 |
| 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 |
| ENST00000341156 | 3053 | 533 | 58024982 | 58025147 | 804 | 968 | 73 | 127 |
| ENST00000341156 | 3053 | 533 | 58022830 | 58022929 | 1298 | 1396 | 237 | 270 |
| 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 |
| Q00973 | 73 | 127 | 74 | 128 | Alternative sequence | ID=VSP_055039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q00973 | 73 | 127 | 1 | 533 | Chain | ID=PRO_0000059100;Note=Beta-1%2C4 N-acetylgalactosaminyltransferase 1 |
| Q00973 | 73 | 127 | 80 | 80 | Disulfide bond | Note=Interchain (with C-412);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11018043;Dbxref=PMID:11018043 |
| Q00973 | 73 | 127 | 82 | 82 | Disulfide bond | Note=Interchain (with C-529);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11018043;Dbxref=PMID:11018043 |
| Q00973 | 73 | 127 | 79 | 79 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q00973 | 73 | 127 | 26 | 533 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q00973 | 237 | 270 | 238 | 328 | Alternative sequence | ID=VSP_055040;Note=In isoform 3. VRFSTEGHEAAFTIRIRHPPNPRLYPPGSLPQGAQYNISALVTIATKTFLRYDRLRALITSIRRFYPTVTVVIADDSDKPERVSGPYVEHY->GARPGWRDGQAGQTEKNQKGWSGQMAEGMGGIWAMARAVQPHNGCFNWTSRARGRKGAFVHLGLEQARGKPEPWVCLPFRPTVGGPRKRLV;Ontology_term=ECO:0000303;evidence=EC |
| Q00973 | 237 | 270 | 1 | 533 | Chain | ID=PRO_0000059100;Note=Beta-1%2C4 N-acetylgalactosaminyltransferase 1 |
| Q00973 | 237 | 270 | 26 | 533 | 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 |
| Q00973 | 73 | 127 | 74 | 128 | Alternative sequence | ID=VSP_055039;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q00973 | 73 | 127 | 1 | 533 | Chain | ID=PRO_0000059100;Note=Beta-1%2C4 N-acetylgalactosaminyltransferase 1 |
| Q00973 | 73 | 127 | 80 | 80 | Disulfide bond | Note=Interchain (with C-412);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11018043;Dbxref=PMID:11018043 |
| Q00973 | 73 | 127 | 82 | 82 | Disulfide bond | Note=Interchain (with C-529);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11018043;Dbxref=PMID:11018043 |
| Q00973 | 73 | 127 | 79 | 79 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q00973 | 73 | 127 | 26 | 533 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q00973 | 237 | 270 | 238 | 328 | Alternative sequence | ID=VSP_055040;Note=In isoform 3. VRFSTEGHEAAFTIRIRHPPNPRLYPPGSLPQGAQYNISALVTIATKTFLRYDRLRALITSIRRFYPTVTVVIADDSDKPERVSGPYVEHY->GARPGWRDGQAGQTEKNQKGWSGQMAEGMGGIWAMARAVQPHNGCFNWTSRARGRKGAFVHLGLEQARGKPEPWVCLPFRPTVGGPRKRLV;Ontology_term=ECO:0000303;evidence=EC |
| Q00973 | 237 | 270 | 1 | 533 | Chain | ID=PRO_0000059100;Note=Beta-1%2C4 N-acetylgalactosaminyltransferase 1 |
| Q00973 | 237 | 270 | 26 | 533 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for B4GALNT1 |
| - 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 |
| COAD | TCGA-A6-6780-01 | exon_skip_94246 | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| COAD | TCGA-AA-3663-01 | exon_skip_94246 | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| COAD | TCGA-G4-6586-01 | exon_skip_94246 | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_94246 | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| BRCA | TCGA-E9-A1NC-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.L89fs |
| COAD | TCGA-AZ-6598-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.G88fs |
| COAD | TCGA-CM-5861-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.G88fs |
| COAD | TCGA-G4-6309-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.G88fs |
| LUAD | TCGA-64-1678-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.A88fs |
| LUAD | TCGA-69-7980-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.G88fs |
| PRAD | TCGA-EJ-7784-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.A88fs |
| PRAD | TCGA-KK-A59Z-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.A88fs |
| SKCM | TCGA-D9-A6E9-06 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.A88fs |
| UCEC | TCGA-B5-A0K2-01 | exon_skip_94246 | 58024983 | 58025147 | 58025102 | 58025103 | Frame_Shift_Ins | - | C | p.G88fs |
| STAD | TCGA-CD-A4MG-01 | exon_skip_94246 | 58024983 | 58025147 | 58025103 | 58025104 | Frame_Shift_Ins | - | C | p.G88fs |
| STAD | TCGA-F1-6177-01 | exon_skip_94246 | 58024983 | 58025147 | 58025103 | 58025104 | Frame_Shift_Ins | - | C | p.G88fs |
| - 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 |
| KMRC2_KIDNEY | 58021401 | 58021641 | 58021425 | 58021425 | Frame_Shift_Del | G | - | p.R454fs |
| KMRC2_KIDNEY | 58021401 | 58021674 | 58021425 | 58021425 | Frame_Shift_Del | G | - | p.R454fs |
| HEC108_ENDOMETRIUM | 58021401 | 58021641 | 58021634 | 58021634 | Frame_Shift_Del | C | - | p.G384fs |
| HEC108_ENDOMETRIUM | 58021401 | 58021674 | 58021634 | 58021634 | Frame_Shift_Del | C | - | p.G384fs |
| OC316_OVARY | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| KM12_LARGE_INTESTINE | 58024983 | 58025147 | 58025103 | 58025103 | Frame_Shift_Del | C | - | p.G88fs |
| OC316_OVARY | 58021401 | 58021641 | 58021535 | 58021535 | Missense_Mutation | C | T | p.R417H |
| OC316_OVARY | 58021401 | 58021674 | 58021535 | 58021535 | Missense_Mutation | C | T | p.R417H |
| OC314_OVARY | 58021401 | 58021641 | 58021535 | 58021535 | Missense_Mutation | C | T | p.R417H |
| OC314_OVARY | 58021401 | 58021674 | 58021535 | 58021535 | Missense_Mutation | C | T | p.R417H |
| TTC466_BONE | 58021401 | 58021641 | 58021595 | 58021595 | Missense_Mutation | C | G | p.R397P |
| TTC466_BONE | 58021401 | 58021674 | 58021595 | 58021595 | Missense_Mutation | C | G | p.R397P |
| DU145_PROSTATE | 58021401 | 58021641 | 58021602 | 58021602 | Missense_Mutation | T | A | p.T395S |
| DU145_PROSTATE | 58021401 | 58021674 | 58021602 | 58021602 | Missense_Mutation | T | A | p.T395S |
| EW8_BONE | 58024983 | 58025147 | 58025022 | 58025022 | Missense_Mutation | G | A | p.S115F |
| EW8_BONE | 58024983 | 58025037 | 58025022 | 58025022 | Missense_Mutation | G | A | p.S115F |
| RH1_SOFT_TISSUE | 58024983 | 58025147 | 58025022 | 58025022 | Missense_Mutation | G | A | p.S115F |
| RH1_SOFT_TISSUE | 58024983 | 58025037 | 58025022 | 58025022 | Missense_Mutation | G | A | p.S115F |
| SKN_ENDOMETRIUM | 58024261 | 58024301 | 58024301 | 58024301 | Splice_Site | C | T | p.G164E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for B4GALNT1 |
| 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 B4GALNT1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for B4GALNT1 |
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RelatedDrugs for B4GALNT1 |
| 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 B4GALNT1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| B4GALNT1 | C1836632 | SPASTIC PARAPLEGIA 26, AUTOSOMAL RECESSIVE (disorder) | 1 | ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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