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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 SCAF4 |
 Gene summary |
| Gene information | Gene symbol | SCAF4 | Gene ID | 57466 |
| Gene name | SR-related CTD associated factor 4 | |
| Synonyms | SFRS15|SRA4 | |
| Cytomap | 21q22.11 | |
| Type of gene | protein-coding | |
| Description | splicing factor, arginine/serine-rich 15CTD-binding SR-like protein rA4SR-like CTD-associated factor 4pre-mRNA splicing SR protein rA4splicing factor serine alanine 15 | |
| Modification date | 20180519 | |
| UniProtAcc | O95104 | |
| Context | PubMed: SCAF4 [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 SCAF4 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 SCAF4 |
| 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 SCAF4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_361541 | 21 | 33068881:33069063:33073307:33073484:33074088:33074136 | 33073307:33073484 | ENSG00000156304.10 | ENST00000434667.3,ENST00000399804.1,ENST00000286835.7 |
| exon_skip_361542 | 21 | 33076077:33076239:33077735:33077780:33078586:33078670 | 33077735:33077780 | ENSG00000156304.10 | ENST00000399804.1,ENST00000286835.7,ENST00000485790.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SCAF4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_361541 | 21 | 33068881:33069063:33073307:33073484:33074088:33074136 | 33073307:33073484 | ENSG00000156304.10 | ENST00000286835.7,ENST00000399804.1,ENST00000434667.3 |
| exon_skip_361542 | 21 | 33076077:33076239:33077735:33077780:33078586:33078670 | 33077735:33077780 | ENSG00000156304.10 | ENST00000286835.7,ENST00000399804.1,ENST00000485790.1 |
| 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 SCAF4 |
| 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 |
| ENST00000286835 | 33073307 | 33073484 | In-frame |
| ENST00000286835 | 33077735 | 33077780 | 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 |
| ENST00000286835 | 33073307 | 33073484 | In-frame |
| ENST00000286835 | 33077735 | 33077780 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SCAF4 |
| 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 |
| ENST00000286835 | 4210 | 1147 | 33077735 | 33077780 | 498 | 542 | 38 | 53 |
| ENST00000286835 | 4210 | 1147 | 33073307 | 33073484 | 984 | 1160 | 200 | 259 |
| 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 |
| ENST00000286835 | 4210 | 1147 | 33077735 | 33077780 | 498 | 542 | 38 | 53 |
| ENST00000286835 | 4210 | 1147 | 33073307 | 33073484 | 984 | 1160 | 200 | 259 |
| 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 |
| O95104 | 38 | 53 | 38 | 52 | Alternative sequence | ID=VSP_047351;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O95104 | 38 | 53 | 1 | 1147 | Chain | ID=PRO_0000081943;Note=Splicing factor%2C arginine/serine-rich 15 |
| O95104 | 38 | 53 | 1 | 139 | Domain | Note=CID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00724 |
| O95104 | 38 | 53 | 49 | 49 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| O95104 | 200 | 259 | 1 | 1147 | Chain | ID=PRO_0000081943;Note=Splicing factor%2C arginine/serine-rich 15 |
| 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 |
| O95104 | 38 | 53 | 38 | 52 | Alternative sequence | ID=VSP_047351;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O95104 | 38 | 53 | 1 | 1147 | Chain | ID=PRO_0000081943;Note=Splicing factor%2C arginine/serine-rich 15 |
| O95104 | 38 | 53 | 1 | 139 | Domain | Note=CID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00724 |
| O95104 | 38 | 53 | 49 | 49 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| O95104 | 200 | 259 | 1 | 1147 | Chain | ID=PRO_0000081943;Note=Splicing factor%2C arginine/serine-rich 15 |
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SNVs in the skipped exons for SCAF4 |
| - 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-AD-6964-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P235fs |
| COAD | TCGA-AZ-6598-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P235fs |
| COAD | TCGA-D5-6927-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P235fs |
| STAD | TCGA-B7-5816-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P250fs |
| STAD | TCGA-BR-4361-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P250fs |
| STAD | TCGA-HU-A4GQ-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P250fs |
| UCEC | TCGA-D1-A163-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P250fs |
| UCEC | TCGA-D1-A17U-01 | exon_skip_361541 | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P250fs |
| UCEC | TCGA-BG-A0M3-01 | exon_skip_361541 | 33073308 | 33073484 | 33073335 | 33073336 | Frame_Shift_Ins | - | G | p.P250fs |
| LUAD | TCGA-17-Z001-01 | exon_skip_361541 | 33073308 | 33073484 | 33073388 | 33073388 | Nonsense_Mutation | G | A | p.Q233* |
| BLCA | TCGA-GU-A764-01 | exon_skip_361541 | 33073308 | 33073484 | 33073481 | 33073481 | Nonsense_Mutation | G | A | p.Q202* |
| UCEC | TCGA-D1-A16J-01 | exon_skip_361541 | 33073308 | 33073484 | 33073481 | 33073481 | Nonsense_Mutation | G | A | p.Q202* |
| - 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 |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| SNGM_ENDOMETRIUM | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| HCT116_LARGE_INTESTINE | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| SNU1_STOMACH | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| JHUEM1_ENDOMETRIUM | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| SW48_LARGE_INTESTINE | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| SKMEL2_SKIN | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| SNUC5_LARGE_INTESTINE | 33073308 | 33073484 | 33073336 | 33073336 | Frame_Shift_Del | G | - | p.P251fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 33073308 | 33073484 | 33073423 | 33073423 | Missense_Mutation | T | C | p.N221S |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 33073308 | 33073484 | 33073423 | 33073423 | Missense_Mutation | T | C | p.N221S |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 33073308 | 33073484 | 33073448 | 33073448 | Missense_Mutation | T | G | p.K213Q |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 33073308 | 33073484 | 33073448 | 33073448 | Missense_Mutation | T | G | p.K213Q |
| JHUEM7_ENDOMETRIUM | 33077736 | 33077780 | 33077779 | 33077779 | Splice_Site | A | C | p.L39R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCAF4 |
| 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 SCAF4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SCAF4 |
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RelatedDrugs for SCAF4 |
| 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 SCAF4 |
| 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)
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