|
Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for B4GALT4 |
Gene summary |
Gene information | Gene symbol | B4GALT4 | Gene ID | 8702 |
Gene name | beta-1,4-galactosyltransferase 4 | |
Synonyms | B4Gal-T4|beta4Gal-T4 | |
Cytomap | 3q13.32 | |
Type of gene | protein-coding | |
Description | beta-1,4-galactosyltransferase 4N-acetyllactosamine synthaseUDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 4UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase 4UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4UDP-galactose:beta-N- | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for B4GALT4 |
Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
CB | DOWN | ENST00000471675.1 | B4GALT4-209:protein_coding:B4GALT4 | 3.473524e+01 | -9.541333e-01 | 1.908295e-10 | 1.090028e-08 |
CB | UP | ENST00000479308.1 | B4GALT4-214:lncRNA:B4GALT4 | 7.088231e-01 | 8.729037e-01 | 5.823867e-03 | 2.232328e-02 |
CB | UP | ENST00000460321.5 | B4GALT4-205:lncRNA:B4GALT4 | 1.025874e+00 | 1.377926e+00 | 1.103916e-02 | 3.769484e-02 |
TC | UP | ENST00000470111.5 | B4GALT4-208:protein_coding:B4GALT4 | 4.685817e+00 | 1.375675e+00 | 2.292633e-10 | 3.956906e-08 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for B4GALT4 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_109632 | chr3 | 119235145:119235227:119236153:119236251:119236853:119237070 | 119236153:119236251 |
exon_skip_122982 | chr3 | 119236853:119237070:119240316:119240530:119240850:119240907 | 119240316:119240530 |
exon_skip_154955 | chr3 | 119226809:119227041:119229847:119230244:119236853:119237070 | 119229847:119230244 |
exon_skip_168221 | chr3 | 119216240:119216344:119218650:119218772:119224058:119224245 | 119218650:119218772 |
exon_skip_178987 | chr3 | 119226989:119227041:119229847:119230244:119236853:119237070 | 119229847:119230244 |
exon_skip_188809 | chr3 | 119226989:119227041:119236853:119237070:119240850:119240878 | 119236853:119237070 |
exon_skip_189218 | chr3 | 119226989:119227041:119229847:119230244:119235145:119235227 | 119229847:119230244 |
exon_skip_196504 | chr3 | 119226809:119227041:119235145:119235227:119236853:119237070 | 119235145:119235227 |
exon_skip_204241 | chr3 | 119229847:119230244:119236853:119237070:119240765:119240878 | 119236853:119237070 |
exon_skip_24574 | chr3 | 119236853:119237070:119240361:119240530:119240850:119240878 | 119240361:119240530 |
exon_skip_259770 | chr3 | 119226989:119227041:119235145:119235227:119236853:119237070 | 119235145:119235227 |
exon_skip_40896 | chr3 | 119226809:119227041:119229847:119230244:119235145:119235227 | 119229847:119230244 |
exon_skip_69480 | chr3 | 119236853:119237070:119240361:119240530:119240850:119240907 | 119240361:119240530 |
exon_skip_8320 | chr3 | 119216240:119216344:119218712:119218772:119224058:119224245 | 119218712:119218772 |
exon_skip_83884 | chr3 | 119230176:119230244:119235145:119235227:119236853:119237070 | 119235145:119235227 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
Top |
Open reading frame (ORF) annotation in the exon skipping event for B4GALT4 |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000359213 | 119229847 | 119230244 | 3UTR-3CDS |
ENST00000393765 | 119229847 | 119230244 | 3UTR-3CDS |
ENST00000483209 | 119229847 | 119230244 | 3UTR-3CDS |
ENST00000359213 | 119235145 | 119235227 | 3UTR-3UTR |
ENST00000359213 | 119218650 | 119218772 | In-frame |
ENST00000393765 | 119218650 | 119218772 | In-frame |
ENST00000483209 | 119218650 | 119218772 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000359213 | 119235145 | 119235227 | 3UTR-3UTR |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000393765 | 119229847 | 119230244 | 3UTR-3CDS |
ENST00000483209 | 119229847 | 119230244 | 3UTR-3CDS |
ENST00000359213 | 119235145 | 119235227 | 3UTR-3UTR |
ENST00000359213 | 119218650 | 119218772 | In-frame |
ENST00000393765 | 119218650 | 119218772 | In-frame |
ENST00000483209 | 119218650 | 119218772 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for B4GALT4 |
p-ENSG00000121578_img4.png |
Loci of skipped exons in ROSMAP 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 |
ENST00000359213 | 2402 | 344 | 119218650 | 119218772 | 1218 | 1339 | 225 | 265 |
ENST00000393765 | 2476 | 344 | 119218650 | 119218772 | 1292 | 1413 | 225 | 265 |
ENST00000483209 | 2511 | 344 | 119218650 | 119218772 | 1317 | 1438 | 225 | 265 |
Loci of skipped exons in MSBB 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 Mayo 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 |
ENST00000359213 | 2402 | 344 | 119218650 | 119218772 | 1218 | 1339 | 225 | 265 |
ENST00000393765 | 2476 | 344 | 119218650 | 119218772 | 1292 | 1413 | 225 | 265 |
ENST00000483209 | 2511 | 344 | 119218650 | 119218772 | 1317 | 1438 | 225 | 265 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
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 |
O60513 | 225 | 265 | 256 | 256 | Binding site | Note=UDP-alpha-D-galactose;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 256 | 256 | Binding site | Note=UDP-alpha-D-galactose;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 256 | 256 | Binding site | Note=UDP-alpha-D-galactose;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 1 | 344 | Chain | ID=PRO_0000080542;Note=Beta-1%2C4-galactosyltransferase 4 |
O60513 | 225 | 265 | 1 | 344 | Chain | ID=PRO_0000080542;Note=Beta-1%2C4-galactosyltransferase 4 |
O60513 | 225 | 265 | 1 | 344 | Chain | ID=PRO_0000080542;Note=Beta-1%2C4-galactosyltransferase 4 |
O60513 | 225 | 265 | 258 | 261 | Region | Note=N-acetyl-D-glucosamine binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 258 | 261 | Region | Note=N-acetyl-D-glucosamine binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 258 | 261 | Region | Note=N-acetyl-D-glucosamine binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 39 | 344 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O60513 | 225 | 265 | 39 | 344 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O60513 | 225 | 265 | 39 | 344 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Lost protein functional features of individual exon skipping events in MSBB. |
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 Mayo. |
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 |
O60513 | 225 | 265 | 256 | 256 | Binding site | Note=UDP-alpha-D-galactose;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 256 | 256 | Binding site | Note=UDP-alpha-D-galactose;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 256 | 256 | Binding site | Note=UDP-alpha-D-galactose;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 1 | 344 | Chain | ID=PRO_0000080542;Note=Beta-1%2C4-galactosyltransferase 4 |
O60513 | 225 | 265 | 1 | 344 | Chain | ID=PRO_0000080542;Note=Beta-1%2C4-galactosyltransferase 4 |
O60513 | 225 | 265 | 1 | 344 | Chain | ID=PRO_0000080542;Note=Beta-1%2C4-galactosyltransferase 4 |
O60513 | 225 | 265 | 258 | 261 | Region | Note=N-acetyl-D-glucosamine binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 258 | 261 | Region | Note=N-acetyl-D-glucosamine binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 258 | 261 | Region | Note=N-acetyl-D-glucosamine binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
O60513 | 225 | 265 | 39 | 344 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O60513 | 225 | 265 | 39 | 344 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O60513 | 225 | 265 | 39 | 344 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in B4GALT4 |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-1915-5p | chr3:119235213-119235220 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-141-5p | chr3:119235218-119235225 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548x-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548ae-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548j-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548aq-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548ah-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-3688-3p | chr3:119235189-119235196 | 8mer-1a | chr3:119235175-119235196 | 156.00 | -13.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548aj-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548am-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
Mayo | ENST00000359213 | 119235145 | 119235227 | hsa-miR-502-5p | chr3:119235214-119235221 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-1915-5p | chr3:119235213-119235220 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-141-5p | chr3:119235218-119235225 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548x-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548ae-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548j-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548aq-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548ah-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-3688-3p | chr3:119235189-119235196 | 8mer-1a | chr3:119235175-119235196 | 156.00 | -13.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548aj-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548am-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
MSBB | ENST00000359213 | 119235145 | 119235227 | hsa-miR-502-5p | chr3:119235214-119235221 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-1915-5p | chr3:119235213-119235220 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-141-5p | chr3:119235218-119235225 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548x-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548ae-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548j-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548aq-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548ah-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-3688-3p | chr3:119235189-119235196 | 8mer-1a | chr3:119235175-119235196 | 156.00 | -13.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548aj-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-548am-3p | chr3:119235199-119235206 | 8mer-1a | chr3:119235199-119235220 | 140.00 | -12.87 |
ROSMAP | ENST00000359213 | 119235145 | 119235227 | hsa-miR-502-5p | chr3:119235214-119235221 | 8mer-1a | chr3:119235204-119235225 | 147.00 | -13.50 |
Top |
SNVs in the skipped exons for B4GALT4 |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- 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 |
Top |
AD stage-associated exon skippint events for B4GALT4 |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for B4GALT4 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
HCC | exon_skip_83884 | rs12630690 | chr3:119211617 | 8.411272e-05 | 7.897923e-03 |
HCC | exon_skip_83884 | rs4528932 | chr3:119222594 | 8.530593e-05 | 7.969867e-03 |
HCC | exon_skip_83884 | rs4547690 | chr3:119222895 | 8.530593e-05 | 7.969867e-03 |
HCC | exon_skip_83884 | rs4234657 | chr3:119229441 | 8.530593e-05 | 7.969867e-03 |
HCC | exon_skip_83884 | rs7622158 | chr3:119199597 | 2.138211e-04 | 1.709828e-02 |
HCC | exon_skip_83884 | rs6438510 | chr3:119239356 | 2.760372e-04 | 2.110226e-02 |
HCC | exon_skip_83884 | rs3806697 | chr3:119185756 | 5.759403e-04 | 3.783694e-02 |
Top |
Correlation with RNA binding proteins (RBPs) for B4GALT4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | FUBP3 | exon_skip_83884 | 4.247280e-01 | 1.876852e-07 |
CB | NUP42 | exon_skip_83884 | 4.639415e-01 | 8.810439e-09 |
TC | KHDRBS2 | exon_skip_83884 | 4.507846e-01 | 1.430479e-08 |
TC | NOVA1 | exon_skip_83884 | 4.106769e-01 | 3.178333e-07 |
Top |
RelatedDrugs for B4GALT4 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for B4GALT4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |