|
||||||
|
 | |
| |
| |
| |
| 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 STMN4 |
 Gene summary |
| Gene information | Gene symbol | STMN4 | Gene ID | 81551 |
| Gene name | stathmin 4 | |
| Synonyms | RB3 | |
| Cytomap | 8p21.2 | |
| Type of gene | protein-coding | |
| Description | stathmin-4stathmin-like 4stathmin-like protein B3stathmin-like-protein RB3 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9H169 | |
| Context | PubMed: STMN4 [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 STMN4 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 STMN4 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for STMN4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_488849 | 8 | 27093991:27094422:27096742:27096796:27097487:27097679 | 27096742:27096796 | ENSG00000015592.12 | ENST00000523048.1,ENST00000519997.1 |
| exon_skip_488850 | 8 | 27093991:27094422:27097487:27097679:27098570:27098776 | 27097487:27097679 | ENSG00000015592.12 | ENST00000265770.7,ENST00000350889.4 |
| exon_skip_488852 | 8 | 27098684:27098779:27099193:27099274:27099626:27100009 | 27099193:27099274 | ENSG00000015592.12 | ENST00000522750.1 |
| exon_skip_488853 | 8 | 27098684:27098779:27099193:27099274:27099913:27100009 | 27099193:27099274 | ENSG00000015592.12 | ENST00000523048.1,ENST00000350889.4,ENST00000522908.1 |
| exon_skip_488856 | 8 | 27098684:27098779:27099913:27100009:27101227:27101318 | 27099913:27100009 | ENSG00000015592.12 | ENST00000265770.7,ENST00000519614.1 |
| exon_skip_488857 | 8 | 27098684:27098779:27099913:27100009:27115867:27115903 | 27099913:27100009 | ENSG00000015592.12 | ENST00000519997.1 |
| exon_skip_488859 | 8 | 27099913:27100009:27101227:27101318:27115867:27115903 | 27101227:27101318 | ENSG00000015592.12 | ENST00000523048.1,ENST00000265770.7,ENST00000522750.1,ENST00000519614.1,ENST00000522908.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for STMN4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_488849 | 8 | 27093991:27094422:27096742:27096796:27097487:27097679 | 27096742:27096796 | ENSG00000015592.12 | ENST00000519997.1,ENST00000523048.1 |
| exon_skip_488850 | 8 | 27093991:27094422:27097487:27097679:27098570:27098776 | 27097487:27097679 | ENSG00000015592.12 | ENST00000350889.4,ENST00000265770.7 |
| exon_skip_488852 | 8 | 27098684:27098779:27099193:27099274:27099626:27100009 | 27099193:27099274 | ENSG00000015592.12 | ENST00000522750.1 |
| exon_skip_488853 | 8 | 27098684:27098779:27099193:27099274:27099913:27100009 | 27099193:27099274 | ENSG00000015592.12 | ENST00000350889.4,ENST00000523048.1,ENST00000522908.1 |
| exon_skip_488856 | 8 | 27098684:27098779:27099913:27100009:27101227:27101318 | 27099913:27100009 | ENSG00000015592.12 | ENST00000265770.7,ENST00000519614.1 |
| exon_skip_488857 | 8 | 27098684:27098779:27099913:27100009:27115867:27115903 | 27099913:27100009 | ENSG00000015592.12 | ENST00000519997.1 |
| exon_skip_488859 | 8 | 27099913:27100009:27101227:27101318:27115867:27115903 | 27101227:27101318 | ENSG00000015592.12 | ENST00000265770.7,ENST00000523048.1,ENST00000519614.1,ENST00000522908.1,ENST00000522750.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for STMN4 |
| 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 |
| ENST00000265770 | 27101227 | 27101318 | 3UTR-3CDS |
| ENST00000265770 | 27097487 | 27097679 | In-frame |
| ENST00000265770 | 27099913 | 27100009 | 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 |
| ENST00000265770 | 27101227 | 27101318 | 3UTR-3CDS |
| ENST00000265770 | 27097487 | 27097679 | In-frame |
| ENST00000265770 | 27099913 | 27100009 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for STMN4 |
| 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 |
| ENST00000265770 | 1267 | 189 | 27099913 | 27100009 | 151 | 246 | 4 | 36 |
| ENST00000265770 | 1267 | 189 | 27097487 | 27097679 | 456 | 647 | 106 | 170 |
| 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 |
| ENST00000265770 | 1267 | 189 | 27099913 | 27100009 | 151 | 246 | 4 | 36 |
| ENST00000265770 | 1267 | 189 | 27097487 | 27097679 | 456 | 647 | 106 | 170 |
| 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 |
| Q9H169 | 4 | 36 | 1 | 9 | Alternative sequence | ID=VSP_055279;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9H169 | 4 | 36 | 36 | 36 | Alternative sequence | ID=VSP_006279;Note=In isoform 2 and isoform 4. E->EGWCGRQCRRKDESQRKDSADWRERRAQ;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q9H169 | 4 | 36 | 1 | 189 | Chain | ID=PRO_0000182406;Note=Stathmin-4 |
| Q9H169 | 4 | 36 | 20 | 20 | Lipidation | Note=S-palmitoyl cysteine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q93045 |
| Q9H169 | 4 | 36 | 22 | 22 | Lipidation | Note=S-palmitoyl cysteine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q93045 |
| Q9H169 | 4 | 36 | 11 | 11 | Sequence conflict | Note=K->M;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9H169 | 106 | 170 | 1 | 189 | Chain | ID=PRO_0000182406;Note=Stathmin-4 |
| Q9H169 | 106 | 170 | 90 | 188 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H169 | 106 | 170 | 48 | 189 | Domain | Note=SLD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00998 |
| Q9H169 | 106 | 170 | 91 | 182 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BR1 |
| 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 |
| Q9H169 | 4 | 36 | 1 | 9 | Alternative sequence | ID=VSP_055279;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9H169 | 4 | 36 | 36 | 36 | Alternative sequence | ID=VSP_006279;Note=In isoform 2 and isoform 4. E->EGWCGRQCRRKDESQRKDSADWRERRAQ;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q9H169 | 4 | 36 | 1 | 189 | Chain | ID=PRO_0000182406;Note=Stathmin-4 |
| Q9H169 | 4 | 36 | 20 | 20 | Lipidation | Note=S-palmitoyl cysteine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q93045 |
| Q9H169 | 4 | 36 | 22 | 22 | Lipidation | Note=S-palmitoyl cysteine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q93045 |
| Q9H169 | 4 | 36 | 11 | 11 | Sequence conflict | Note=K->M;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9H169 | 106 | 170 | 1 | 189 | Chain | ID=PRO_0000182406;Note=Stathmin-4 |
| Q9H169 | 106 | 170 | 90 | 188 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H169 | 106 | 170 | 48 | 189 | Domain | Note=SLD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00998 |
| Q9H169 | 106 | 170 | 91 | 182 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6BR1 |
Top |
SNVs in the skipped exons for STMN4 |
| - 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 |
| KIRP | TCGA-EV-5902-01 | exon_skip_488850 | 27097488 | 27097679 | 27097566 | 27097566 | Frame_Shift_Del | T | - | p.K171fs |
| KIRP | TCGA-EV-5902-01 | exon_skip_488850 | 27097488 | 27097679 | 27097566 | 27097566 | Frame_Shift_Del | T | - | p.L172fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_488850 | 27097488 | 27097679 | 27097612 | 27097612 | Frame_Shift_Del | T | - | p.K156fs |
| KIRP | TCGA-AT-A5NU-01 | exon_skip_488850 | 27097488 | 27097679 | 27097616 | 27097616 | Frame_Shift_Del | G | - | p.Q155fs |
| UCEC | TCGA-DI-A0WH-01 | exon_skip_488850 | 27097488 | 27097679 | 27097623 | 27097624 | Frame_Shift_Del | CT | - | p.E152fs |
| BRCA | TCGA-BH-A18V-01 | exon_skip_488852 exon_skip_488853 | 27099194 | 27099274 | 27099197 | 27099197 | Nonsense_Mutation | G | A | p.Q63* |
| READ | TCGA-AG-A002-01 | exon_skip_488852 exon_skip_488853 | 27099194 | 27099274 | 27099209 | 27099209 | Nonsense_Mutation | C | A | p.E59X |
| - 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 |
| HCT116_LARGE_INTESTINE | 27097488 | 27097679 | 27097623 | 27097624 | Frame_Shift_Del | CT | - | p.E125fs |
| JHUEM1_ENDOMETRIUM | 27097488 | 27097679 | 27097623 | 27097624 | Frame_Shift_Del | CT | - | p.E125fs |
| EN_ENDOMETRIUM | 27097488 | 27097679 | 27097562 | 27097562 | Missense_Mutation | C | T | p.A146T |
| GCT_SOFT_TISSUE | 27097488 | 27097679 | 27097571 | 27097571 | Missense_Mutation | C | T | p.E143K |
| SMSCTR_SOFT_TISSUE | 27097488 | 27097679 | 27097577 | 27097577 | Missense_Mutation | C | A | p.A141S |
| SAS_UPPER_AERODIGESTIVE_TRACT | 27097488 | 27097679 | 27097627 | 27097627 | Missense_Mutation | C | T | p.R124K |
| TT_OESOPHAGUS | 27097488 | 27097679 | 27097490 | 27097490 | Nonsense_Mutation | T | A | p.K170* |
| CHP126_AUTONOMIC_GANGLIA | 27097488 | 27097679 | 27097493 | 27097493 | Nonsense_Mutation | C | A | p.E169* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for STMN4 |
| 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 STMN4 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for STMN4 |
Top |
RelatedDrugs for STMN4 |
| 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 |
| Q9H169 | DB01206 | Lomustine | Stathmin-4 | small molecule | approved|investigational |
Top |
RelatedDiseases for STMN4 |
| 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)
|