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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 TRERF1 |
Gene summary |
Gene information | Gene symbol | TRERF1 | Gene ID | 55809 |
Gene name | transcriptional regulating factor 1 | |
Synonyms | BCAR2|HSA277276|RAPA|TREP132|TReP-132|dJ139D8.5 | |
Cytomap | 6p21.1 | |
Type of gene | protein-coding | |
Description | transcriptional-regulating factor 1breast cancer anti-estrogen resistance 2rapa-1rapa-2transcriptional regulating protein 132zinc finger protein rapazinc finger transcription factor TReP-132 | |
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 |
TRERF1 | GO:0045893 | positive regulation of transcription, DNA-templated | 11349124 |
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Gene structures and expression levels for TRERF1 |
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 |
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 TRERF1 |
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_105342 | chr6 | 42259466:42259723:42263320:42263568:42264704:42264854 | 42263320:42263568 |
exon_skip_109669 | chr6 | 42258135:42258201:42259339:42259723:42264704:42264854 | 42259339:42259723 |
exon_skip_136166 | chr6 | 42232681:42232928:42236205:42236411:42243248:42243361 | 42236205:42236411 |
exon_skip_155378 | chr6 | 42300638:42300749:42362997:42363079:42451177:42451261 | 42362997:42363079 |
exon_skip_177826 | chr6 | 42265751:42265797:42268154:42269848:42300638:42300749 | 42268154:42269848 |
exon_skip_22047 | chr6 | 42258135:42258201:42259339:42259723:42263260:42263568 | 42259339:42259723 |
exon_skip_244522 | chr6 | 42259466:42259723:42263260:42263568:42264704:42264854 | 42263260:42263568 |
exon_skip_26408 | chr6 | 42259339:42259723:42263260:42263568:42264704:42264854 | 42263260:42263568 |
exon_skip_35571 | chr6 | 42265751:42265797:42268154:42269848:42300638:42300748 | 42268154:42269848 |
exon_skip_40821 | chr6 | 42232681:42232892:42236205:42236411:42243248:42243361 | 42236205:42236411 |
exon_skip_68504 | chr6 | 42259339:42259723:42263320:42263568:42264704:42264854 | 42263320:42263568 |
exon_skip_74899 | chr6 | 42300638:42300749:42362947:42363079:42451177:42451261 | 42362947:42363079 |
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 TRERF1 |
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 |
ENST00000372922 | 42268154 | 42269848 | 3UTR-3CDS |
ENST00000372922 | 42362997 | 42363079 | 3UTR-3UTR |
ENST00000372922 | 42236205 | 42236411 | In-frame |
ENST00000372922 | 42263320 | 42263568 | 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 |
ENST00000372922 | 42236205 | 42236411 | In-frame |
ENST00000372922 | 42263320 | 42263568 | In-frame |
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 |
ENST00000372922 | 42268154 | 42269848 | 3UTR-3CDS |
ENST00000372922 | 42362997 | 42363079 | 3UTR-3UTR |
ENST00000372922 | 42236205 | 42236411 | In-frame |
ENST00000372922 | 42263320 | 42263568 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TRERF1 |
p-ENSG00000124496_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 |
ENST00000372922 | 7303 | 1200 | 42263320 | 42263568 | 2199 | 2446 | 545 | 627 |
ENST00000372922 | 7303 | 1200 | 42236205 | 42236411 | 3423 | 3628 | 953 | 1021 |
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 |
ENST00000372922 | 7303 | 1200 | 42263320 | 42263568 | 2199 | 2446 | 545 | 627 |
ENST00000372922 | 7303 | 1200 | 42236205 | 42236411 | 3423 | 3628 | 953 | 1021 |
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 |
ENST00000372922 | 7303 | 1200 | 42263320 | 42263568 | 2199 | 2446 | 545 | 627 |
ENST00000372922 | 7303 | 1200 | 42236205 | 42236411 | 3423 | 3628 | 953 | 1021 |
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 |
Q96PN7 | 545 | 627 | 546 | 628 | Alternative sequence | ID=VSP_015645;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
Q96PN7 | 545 | 627 | 1 | 1200 | Chain | ID=PRO_0000197134;Note=Transcriptional-regulating factor 1 |
Q96PN7 | 545 | 627 | 553 | 749 | Compositional bias | Note=Pro-rich |
Q96PN7 | 545 | 627 | 439 | 1200 | Region | Note=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124 |
Q96PN7 | 953 | 1021 | 1 | 1200 | Chain | ID=PRO_0000197134;Note=Transcriptional-regulating factor 1 |
Q96PN7 | 953 | 1021 | 956 | 982 | Compositional bias | Note=Glu-rich |
Q96PN7 | 953 | 1021 | 954 | 954 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692 |
Q96PN7 | 953 | 1021 | 955 | 955 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692 |
Q96PN7 | 953 | 1021 | 1019 | 1019 | Natural variant | ID=VAR_050199;Note=N->T;Dbxref=dbSNP:rs35978318 |
Q96PN7 | 953 | 1021 | 439 | 1200 | Region | Note=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124 |
Q96PN7 | 953 | 1021 | 1013 | 1037 | Zinc finger | Note=C2H2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00042 |
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 |
Q96PN7 | 545 | 627 | 546 | 628 | Alternative sequence | ID=VSP_015645;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
Q96PN7 | 545 | 627 | 1 | 1200 | Chain | ID=PRO_0000197134;Note=Transcriptional-regulating factor 1 |
Q96PN7 | 545 | 627 | 553 | 749 | Compositional bias | Note=Pro-rich |
Q96PN7 | 545 | 627 | 439 | 1200 | Region | Note=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124 |
Q96PN7 | 953 | 1021 | 1 | 1200 | Chain | ID=PRO_0000197134;Note=Transcriptional-regulating factor 1 |
Q96PN7 | 953 | 1021 | 956 | 982 | Compositional bias | Note=Glu-rich |
Q96PN7 | 953 | 1021 | 954 | 954 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692 |
Q96PN7 | 953 | 1021 | 955 | 955 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692 |
Q96PN7 | 953 | 1021 | 1019 | 1019 | Natural variant | ID=VAR_050199;Note=N->T;Dbxref=dbSNP:rs35978318 |
Q96PN7 | 953 | 1021 | 439 | 1200 | Region | Note=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124 |
Q96PN7 | 953 | 1021 | 1013 | 1037 | Zinc finger | Note=C2H2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00042 |
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 |
Q96PN7 | 545 | 627 | 546 | 628 | Alternative sequence | ID=VSP_015645;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2 |
Q96PN7 | 545 | 627 | 1 | 1200 | Chain | ID=PRO_0000197134;Note=Transcriptional-regulating factor 1 |
Q96PN7 | 545 | 627 | 553 | 749 | Compositional bias | Note=Pro-rich |
Q96PN7 | 545 | 627 | 439 | 1200 | Region | Note=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124 |
Q96PN7 | 953 | 1021 | 1 | 1200 | Chain | ID=PRO_0000197134;Note=Transcriptional-regulating factor 1 |
Q96PN7 | 953 | 1021 | 956 | 982 | Compositional bias | Note=Glu-rich |
Q96PN7 | 953 | 1021 | 954 | 954 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692 |
Q96PN7 | 953 | 1021 | 955 | 955 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692 |
Q96PN7 | 953 | 1021 | 1019 | 1019 | Natural variant | ID=VAR_050199;Note=N->T;Dbxref=dbSNP:rs35978318 |
Q96PN7 | 953 | 1021 | 439 | 1200 | Region | Note=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124 |
Q96PN7 | 953 | 1021 | 1013 | 1037 | Zinc finger | Note=C2H2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00042 |
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3'-UTR located exon skipping events that lost miRNA binding sites in TRERF1 |
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 | ENST00000372922 | 42362997 | 42363079 | hsa-miR-1252-5p | chr6:42363052-42363059 | 8mer-1a | chr6:42363050-42363071 | 146.00 | -25.34 |
Mayo | ENST00000372922 | 42362997 | 42363079 | hsa-miR-7974 | chr6:42363068-42363075 | 8mer-1a | chr6:42363058-42363077 | 165.00 | -26.00 |
ROSMAP | ENST00000372922 | 42362997 | 42363079 | hsa-miR-1252-5p | chr6:42363052-42363059 | 8mer-1a | chr6:42363050-42363071 | 146.00 | -25.34 |
ROSMAP | ENST00000372922 | 42362997 | 42363079 | hsa-miR-7974 | chr6:42363068-42363075 | 8mer-1a | chr6:42363058-42363077 | 165.00 | -26.00 |
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SNVs in the skipped exons for TRERF1 |
- 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 TRERF1 |
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 TRERF1 |
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 TRERF1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
HCC | RBM3 | exon_skip_68504 | 4.469791e-01 | 3.445029e-13 |
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RelatedDrugs for TRERF1 |
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 TRERF1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |