|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for SH3RF3 |
 Gene summary |
| Gene information | Gene symbol | SH3RF3 | Gene ID | 344558 |
| Gene name | SH3 domain containing ring finger 3 | |
| Synonyms | POSH2|SH3MD4 | |
| Cytomap | 2q13 | |
| Type of gene | protein-coding | |
| Description | SH3 domain-containing RING finger protein 3SH3 multiple domains 4plenty of SH3s-2 | |
| Modification date | 20180519 | |
| UniProtAcc | Q8TEJ3 | |
| Context | PubMed: SH3RF3 [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 |
Top |
Exon skipping events across known transcript of Ensembl for SH3RF3 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. |
 |
Top |
Gene isoform structures and expression levels for SH3RF3 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for SH3RF3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_328571 | 2 | 109745996:109746569:109964129:109964405:109988041:109988137 | 109964129:109964405 | ENSG00000172985.8 | ENST00000309415.6 |
| exon_skip_328573 | 2 | 109964129:109964405:109988041:109988137:110015045:110015399 | 109988041:109988137 | ENSG00000172985.8 | ENST00000309415.6,ENST00000418513.1 |
| exon_skip_328574 | 2 | 109988041:109988137:110015045:110015399:110035994:110036098 | 110015045:110015399 | ENSG00000172985.8 | ENST00000309415.6,ENST00000418513.1 |
| exon_skip_328576 | 2 | 110015045:110015399:110035994:110036098:110048956:110049127 | 110035994:110036098 | ENSG00000172985.8 | ENST00000309415.6,ENST00000418513.1 |
| exon_skip_328579 | 2 | 110065625:110065945:110107060:110107392:110259079:110259248 | 110107060:110107392 | ENSG00000172985.8 | ENST00000309415.6 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for SH3RF3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_328571 | 2 | 109745996:109746569:109964129:109964405:109988041:109988137 | 109964129:109964405 | ENSG00000172985.8 | ENST00000309415.6 |
| exon_skip_328573 | 2 | 109964129:109964405:109988041:109988137:110015045:110015399 | 109988041:109988137 | ENSG00000172985.8 | ENST00000418513.1,ENST00000309415.6 |
| exon_skip_328574 | 2 | 109988041:109988137:110015045:110015399:110035994:110036098 | 110015045:110015399 | ENSG00000172985.8 | ENST00000418513.1,ENST00000309415.6 |
| exon_skip_328576 | 2 | 110015045:110015399:110035994:110036098:110048956:110049127 | 110035994:110036098 | ENSG00000172985.8 | ENST00000418513.1,ENST00000309415.6 |
| exon_skip_328579 | 2 | 110065625:110065945:110107060:110107392:110259079:110259248 | 110107060:110107392 | ENSG00000172985.8 | ENST00000309415.6 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SH3RF3 |
| 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 |
| ENST00000309415 | 110035994 | 110036098 | Frame-shift |
| ENST00000309415 | 110107060 | 110107392 | Frame-shift |
| ENST00000309415 | 109964129 | 109964405 | In-frame |
| ENST00000309415 | 109988041 | 109988137 | In-frame |
| ENST00000309415 | 110015045 | 110015399 | 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 |
| ENST00000309415 | 110035994 | 110036098 | Frame-shift |
| ENST00000309415 | 110107060 | 110107392 | Frame-shift |
| ENST00000309415 | 109964129 | 109964405 | In-frame |
| ENST00000309415 | 109988041 | 109988137 | In-frame |
| ENST00000309415 | 110015045 | 110015399 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SH3RF3 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| ENST00000309415 | 2666 | 882 | 109964129 | 109964405 | 574 | 849 | 191 | 283 |
| ENST00000309415 | 2666 | 882 | 109988041 | 109988137 | 850 | 945 | 283 | 315 |
| ENST00000309415 | 2666 | 882 | 110015045 | 110015399 | 946 | 1299 | 315 | 433 |
| 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 |
| ENST00000309415 | 2666 | 882 | 109964129 | 109964405 | 574 | 849 | 191 | 283 |
| ENST00000309415 | 2666 | 882 | 109988041 | 109988137 | 850 | 945 | 283 | 315 |
| ENST00000309415 | 2666 | 882 | 110015045 | 110015399 | 946 | 1299 | 315 | 433 |
| 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 |
| Q8TEJ3 | 191 | 283 | 1 | 882 | Chain | ID=PRO_0000284883;Note=E3 ubiquitin-protein ligase SH3RF3 |
| Q8TEJ3 | 191 | 283 | 194 | 253 | Domain | Note=SH3 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 191 | 283 | 256 | 319 | Domain | Note=SH3 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 283 | 315 | 1 | 882 | Chain | ID=PRO_0000284883;Note=E3 ubiquitin-protein ligase SH3RF3 |
| Q8TEJ3 | 283 | 315 | 256 | 319 | Domain | Note=SH3 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 315 | 433 | 1 | 882 | Chain | ID=PRO_0000284883;Note=E3 ubiquitin-protein ligase SH3RF3 |
| Q8TEJ3 | 315 | 433 | 256 | 319 | Domain | Note=SH3 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 315 | 433 | 400 | 400 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18220336;Dbxref=PMID:18220336 |
| Q8TEJ3 | 315 | 433 | 403 | 403 | Mutagenesis | Note=Significant loss of interaction with RAC1%3B alone or when associated with P-404 and A-406. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| Q8TEJ3 | 315 | 433 | 404 | 404 | Mutagenesis | Note=Reduced JNK activation. Significant loss of interaction with RAC1%3B alone or when associated with N-403 and A-406. S->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| Q8TEJ3 | 315 | 433 | 406 | 406 | Mutagenesis | Note=Significant loss of interaction with RAC1%3B when associated with N-403 and P-404. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| Q8TEJ3 | 315 | 433 | 369 | 439 | Region | Note=Interaction with RAC1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| 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 |
| Q8TEJ3 | 191 | 283 | 1 | 882 | Chain | ID=PRO_0000284883;Note=E3 ubiquitin-protein ligase SH3RF3 |
| Q8TEJ3 | 191 | 283 | 194 | 253 | Domain | Note=SH3 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 191 | 283 | 256 | 319 | Domain | Note=SH3 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 283 | 315 | 1 | 882 | Chain | ID=PRO_0000284883;Note=E3 ubiquitin-protein ligase SH3RF3 |
| Q8TEJ3 | 283 | 315 | 256 | 319 | Domain | Note=SH3 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 315 | 433 | 1 | 882 | Chain | ID=PRO_0000284883;Note=E3 ubiquitin-protein ligase SH3RF3 |
| Q8TEJ3 | 315 | 433 | 256 | 319 | Domain | Note=SH3 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| Q8TEJ3 | 315 | 433 | 400 | 400 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18220336;Dbxref=PMID:18220336 |
| Q8TEJ3 | 315 | 433 | 403 | 403 | Mutagenesis | Note=Significant loss of interaction with RAC1%3B alone or when associated with P-404 and A-406. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| Q8TEJ3 | 315 | 433 | 404 | 404 | Mutagenesis | Note=Reduced JNK activation. Significant loss of interaction with RAC1%3B alone or when associated with N-403 and A-406. S->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| Q8TEJ3 | 315 | 433 | 406 | 406 | Mutagenesis | Note=Significant loss of interaction with RAC1%3B when associated with N-403 and P-404. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
| Q8TEJ3 | 315 | 433 | 369 | 439 | Region | Note=Interaction with RAC1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20696164;Dbxref=PMID:20696164 |
Top |
SNVs in the skipped exons for SH3RF3 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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 |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_328571 | 109964130 | 109964405 | 109964207 | 109964207 | Frame_Shift_Del | G | - | p.K217fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_328571 | 109964130 | 109964405 | 109964285 | 109964285 | Frame_Shift_Del | C | - | p.L243fs |
| LUAD | TCGA-91-6848-01 | exon_skip_328573 | 109988042 | 109988137 | 109988056 | 109988056 | Frame_Shift_Del | G | - | p.T288fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_328573 | 109988042 | 109988137 | 109988118 | 109988119 | Frame_Shift_Ins | - | C | p.S309fs |
| HNSC | TCGA-CN-5356-01 | exon_skip_328576 | 110035995 | 110036098 | 110036087 | 110036088 | Frame_Shift_Ins | - | T | p.L464fs |
| HNSC | TCGA-CN-5356-01 | exon_skip_328576 | 110035995 | 110036098 | 110036087 | 110036088 | Frame_Shift_Ins | - | T | p.LP464fs |
| SKCM | TCGA-QB-AA9O-06 | exon_skip_328571 | 109964130 | 109964405 | 109964301 | 109964301 | Nonsense_Mutation | C | T | p.Q249* |
| SKCM | TCGA-D9-A4Z6-06 | exon_skip_328571 | 109964130 | 109964405 | 109964334 | 109964334 | Nonsense_Mutation | C | T | p.Q260* |
| - 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 |
| NCIH1573_LUNG | 109964130 | 109964405 | 109964181 | 109964181 | Missense_Mutation | G | A | p.E209K |
| TE11_OESOPHAGUS | 109964130 | 109964405 | 109964300 | 109964300 | Missense_Mutation | C | G | p.I248M |
| 253J_URINARY_TRACT | 110015046 | 110015399 | 110015071 | 110015071 | Missense_Mutation | T | A | p.I324N |
| OCILY12_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 110015046 | 110015399 | 110015081 | 110015081 | Missense_Mutation | C | A | p.D327E |
| HEC108_ENDOMETRIUM | 110015046 | 110015399 | 110015149 | 110015149 | Missense_Mutation | G | A | p.S350N |
| TYKNU_OVARY | 110015046 | 110015399 | 110015157 | 110015157 | Missense_Mutation | C | T | p.P353S |
| MLMA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 110015046 | 110015399 | 110015157 | 110015157 | Missense_Mutation | C | T | p.P353S |
| NEC8_TESTIS | 110015046 | 110015399 | 110015157 | 110015157 | Missense_Mutation | C | T | p.P353S |
| SLVL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 110015046 | 110015399 | 110015157 | 110015157 | Missense_Mutation | C | T | p.P353S |
| TC32_BONE | 110015046 | 110015399 | 110015211 | 110015211 | Missense_Mutation | G | T | p.D371Y |
| NCIH2023_LUNG | 110015046 | 110015399 | 110015235 | 110015235 | Missense_Mutation | C | G | p.R379G |
| WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 110015046 | 110015399 | 110015349 | 110015349 | Missense_Mutation | G | A | p.A417T |
| TE159T_FIBROBLAST | 110035995 | 110036098 | 110036037 | 110036037 | Missense_Mutation | C | T | p.R448W |
| D245MG_CENTRAL_NERVOUS_SYSTEM | 110035995 | 110036098 | 110036037 | 110036037 | Missense_Mutation | C | T | p.R448W |
| HEC1A_ENDOMETRIUM | 110107061 | 110107392 | 110107127 | 110107127 | Missense_Mutation | C | T | p.P739S |
| HEC1B_ENDOMETRIUM | 110107061 | 110107392 | 110107127 | 110107127 | Missense_Mutation | C | T | p.P739S |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SH3RF3 |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SH3RF3 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SH3RF3 |
Top |
RelatedDrugs for SH3RF3 |
| 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 |
Top |
RelatedDiseases for SH3RF3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SH3RF3 | C0236733 | Amphetamine-Related Disorders | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|