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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 EBF1 |
Gene summary |
Gene information | Gene symbol | EBF1 | Gene ID | 1879 |
Gene name | EBF transcription factor 1 | |
Synonyms | COE1|EBF|O/E-1|OLF1 | |
Cytomap | 5q33.3 | |
Type of gene | protein-coding | |
Description | transcription factor COE1Collier, Olf and EBF transcription factor 1early B cell factor 1olfactory neuronal transcription factor 1 | |
Modification date | 20200320 | |
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 |
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Gene structures and expression levels for EBF1 |
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 |
STG | UP | ENST00000423161.3 | SREBF1-206:protein_coding:SREBF1 | 1.817359e+01 | 1.380411e+00 | 9.857649e-04 | 3.812144e-02 |
PG | UP | ENST00000423161.3 | SREBF1-206:protein_coding:SREBF1 | 2.449302e+01 | 8.349808e-01 | 3.327769e-03 | 3.429624e-02 |
CB | DOWN | ENST00000395756.5 | SREBF1-204:nonsense_mediated_decay:SREBF1 | 3.836843e+02 | -1.322199e+00 | 1.778133e-09 | 7.023767e-08 |
CB | UP | ENST00000517373.1 | EBF1-203:protein_coding:EBF1 | 4.060067e+01 | 1.176921e+00 | 2.316388e-09 | 8.758858e-08 |
CB | DOWN | ENST00000485080.6 | SREBF1-213:nonsense_mediated_decay:SREBF1 | 6.566212e+00 | -1.886716e+00 | 2.509937e-09 | 9.420377e-08 |
TC | DOWN | ENST00000485080.6 | SREBF1-213:nonsense_mediated_decay:SREBF1 | 1.064832e+01 | -2.367079e+00 | 2.260840e-13 | 1.023000e-10 |
TC | DOWN | ENST00000395756.5 | SREBF1-204:nonsense_mediated_decay:SREBF1 | 6.950893e+02 | -1.174354e+00 | 5.487068e-08 | 3.749523e-06 |
TC | DOWN | ENST00000578469.1 | SREBF1-218:nonsense_mediated_decay:SREBF1 | 2.562480e+00 | -1.130735e+00 | 3.364833e-04 | 4.204314e-03 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for EBF1 |
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_135636 | chr5 | 158707979:158708173:158712154:158712333:158712970:158713147 | 158712154:158712333 |
exon_skip_161194 | chr5 | 159095620:159095675:159096343:159096406:159096974:159097130 | 159096343:159096406 |
exon_skip_165319 | chr5 | 158698885:158699142:158707568:158707636:158707979:158708009 | 158707568:158707636 |
exon_skip_172683 | chr5 | 158840029:158840110:159073396:159073464:159084666:159084739 | 159073396:159073464 |
exon_skip_30508 | chr5 | 158731069:158731157:158777413:158777539:158796345:158796475 | 158777413:158777539 |
exon_skip_65275 | chr5 | 158707979:158708173:158712970:158713147:158714117:158714182 | 158712970:158713147 |
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 |
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Open reading frame (ORF) annotation in the exon skipping event for EBF1 |
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 |
ENST00000313708 | 158712154 | 158712333 | In-frame |
ENST00000313708 | 159073396 | 159073464 | 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 |
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 |
ENST00000313708 | 158777413 | 158777539 | Frame-shift |
ENST00000313708 | 159096343 | 159096406 | Frame-shift |
ENST00000313708 | 158712154 | 158712333 | In-frame |
ENST00000313708 | 159073396 | 159073464 | In-frame |
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Infer the effects of exon skipping event on protein functional features for EBF1 |
p-ENSG00000164330_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 |
ENST00000313708 | 5267 | 591 | 159073396 | 159073464 | 769 | 836 | 162 | 184 |
ENST00000313708 | 5267 | 591 | 158712154 | 158712333 | 1653 | 1831 | 456 | 516 |
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 |
ENST00000313708 | 5267 | 591 | 159073396 | 159073464 | 769 | 836 | 162 | 184 |
ENST00000313708 | 5267 | 591 | 158712154 | 158712333 | 1653 | 1831 | 456 | 516 |
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 |
Q9UH73 | 162 | 184 | 162 | 184 | Alternative sequence | ID=VSP_012304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q9UH73 | 162 | 184 | 181 | 183 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 1 | 591 | Chain | ID=PRO_0000107825;Note=Transcription factor COE1 |
Q9UH73 | 162 | 184 | 162 | 165 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 163 | 163 | Site | Note=Interaction with DNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9UH73 | 162 | 184 | 172 | 172 | Site | Note=Interaction with DNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9UH73 | 162 | 184 | 171 | 175 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 184 | 186 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 151 | 170 | Zinc finger | Note=C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9UH73 | 456 | 516 | 1 | 591 | Chain | ID=PRO_0000107825;Note=Transcription factor COE1 |
Q9UH73 | 456 | 516 | 462 | 550 | Compositional bias | Note=Pro/Ser/Thr-rich |
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 |
Q9UH73 | 162 | 184 | 162 | 184 | Alternative sequence | ID=VSP_012304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q9UH73 | 162 | 184 | 181 | 183 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 1 | 591 | Chain | ID=PRO_0000107825;Note=Transcription factor COE1 |
Q9UH73 | 162 | 184 | 162 | 165 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 163 | 163 | Site | Note=Interaction with DNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9UH73 | 162 | 184 | 172 | 172 | Site | Note=Interaction with DNA;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9UH73 | 162 | 184 | 171 | 175 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 184 | 186 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3LYR |
Q9UH73 | 162 | 184 | 151 | 170 | Zinc finger | Note=C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q9UH73 | 456 | 516 | 1 | 591 | Chain | ID=PRO_0000107825;Note=Transcription factor COE1 |
Q9UH73 | 456 | 516 | 462 | 550 | Compositional bias | Note=Pro/Ser/Thr-rich |
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3'-UTR located exon skipping events that lost miRNA binding sites in EBF1 |
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 |
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SNVs in the skipped exons for EBF1 |
- 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 |
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AD stage-associated exon skippint events for EBF1 |
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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for EBF1 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for EBF1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | PCBP4 | exon_skip_165319 | 4.776223e-01 | 3.297686e-10 |
CB | TRA2A | exon_skip_165319 | -4.143550e-01 | 8.330195e-08 |
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RelatedDrugs for EBF1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for EBF1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |