|
||||||
|
 | |
| |
| |
| |
| 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 SHOC2 |
 Gene summary |
| Gene information | Gene symbol | SHOC2 | Gene ID | 8036 |
| Gene name | SHOC2, leucine rich repeat scaffold protein | |
| Synonyms | SIAA0862|SOC2|SUR8 | |
| Cytomap | 10q25.2 | |
| Type of gene | protein-coding | |
| Description | leucine-rich repeat protein SHOC-2soc-2 suppressor of clear homolog | |
| Modification date | 20180523 | |
| UniProtAcc | Q9UQ13 | |
| Context | PubMed: SHOC2 [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 SHOC2 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 SHOC2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for SHOC2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_45069 | 10 | 112679360:112679415:112711365:112711550:112723882:112724282 | 112711365:112711550 | ENSG00000108061.7 | ENST00000480155.1 |
| exon_skip_45070 | 10 | 112679360:112679415:112723882:112724819:112745385:112745523 | 112723882:112724819 | ENSG00000108061.7 | ENST00000369452.4 |
| exon_skip_45074 | 10 | 112679360:112679415:112760172:112760303:112764363:112764552 | 112760172:112760303 | ENSG00000108061.7 | ENST00000489390.1 |
| exon_skip_45077 | 10 | 112724789:112724819:112745385:112745523:112760172:112760303 | 112745385:112745523 | ENSG00000108061.7 | ENST00000369452.4 |
| exon_skip_45078 | 10 | 112745385:112745523:112760172:112760303:112764363:112764552 | 112760172:112760303 | ENSG00000108061.7 | ENST00000369452.4 |
| exon_skip_45079 | 10 | 112769005:112769143:112769470:112769588:112771367:112771428 | 112769470:112769588 | ENSG00000108061.7 | ENST00000451838.1,ENST00000369452.4,ENST00000265277.5,ENST00000489390.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for SHOC2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_45069 | 10 | 112679360:112679415:112711365:112711550:112723882:112724282 | 112711365:112711550 | ENSG00000108061.7 | ENST00000480155.1 |
| exon_skip_45070 | 10 | 112679360:112679415:112723882:112724819:112745385:112745523 | 112723882:112724819 | ENSG00000108061.7 | ENST00000369452.4 |
| exon_skip_45074 | 10 | 112679360:112679415:112760172:112760303:112764363:112764552 | 112760172:112760303 | ENSG00000108061.7 | ENST00000489390.1 |
| exon_skip_45077 | 10 | 112724789:112724819:112745385:112745523:112760172:112760303 | 112745385:112745523 | ENSG00000108061.7 | ENST00000369452.4 |
| exon_skip_45078 | 10 | 112745385:112745523:112760172:112760303:112764363:112764552 | 112760172:112760303 | ENSG00000108061.7 | ENST00000369452.4 |
| exon_skip_45079 | 10 | 112769005:112769143:112769470:112769588:112771367:112771428 | 112769470:112769588 | ENSG00000108061.7 | ENST00000265277.5,ENST00000369452.4,ENST00000489390.1,ENST00000451838.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SHOC2 |
| 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 |
| ENST00000369452 | 112723882 | 112724819 | 5CDS-5UTR |
| ENST00000369452 | 112760172 | 112760303 | Frame-shift |
| ENST00000369452 | 112769470 | 112769588 | Frame-shift |
| ENST00000369452 | 112745385 | 112745523 | 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 |
| ENST00000369452 | 112723882 | 112724819 | 5CDS-5UTR |
| ENST00000369452 | 112760172 | 112760303 | Frame-shift |
| ENST00000369452 | 112769470 | 112769588 | Frame-shift |
| ENST00000369452 | 112745385 | 112745523 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SHOC2 |
| 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 |
| ENST00000369452 | 3960 | 582 | 112745385 | 112745523 | 1049 | 1186 | 234 | 280 |
| 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 |
| ENST00000369452 | 3960 | 582 | 112745385 | 112745523 | 1049 | 1186 | 234 | 280 |
| 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 |
| Q9UQ13 | 234 | 280 | 234 | 279 | Alternative sequence | ID=VSP_038188;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UQ13 | 234 | 280 | 1 | 582 | Chain | ID=PRO_0000097737;Note=Leucine-rich repeat protein SHOC-2 |
| Q9UQ13 | 234 | 280 | 216 | 237 | Repeat | Note=LRR 6 |
| Q9UQ13 | 234 | 280 | 239 | 260 | Repeat | Note=LRR 7 |
| Q9UQ13 | 234 | 280 | 262 | 283 | Repeat | Note=LRR 8 |
| 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 |
| Q9UQ13 | 234 | 280 | 234 | 279 | Alternative sequence | ID=VSP_038188;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9UQ13 | 234 | 280 | 1 | 582 | Chain | ID=PRO_0000097737;Note=Leucine-rich repeat protein SHOC-2 |
| Q9UQ13 | 234 | 280 | 216 | 237 | Repeat | Note=LRR 6 |
| Q9UQ13 | 234 | 280 | 239 | 260 | Repeat | Note=LRR 7 |
| Q9UQ13 | 234 | 280 | 262 | 283 | Repeat | Note=LRR 8 |
Top |
SNVs in the skipped exons for SHOC2 |
| - 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. |
SHOC2_COAD_exon_skip_45070_psi_boxplot.png |
SHOC2_HNSC_exon_skip_45070_psi_boxplot.png |
SHOC2_LIHC_exon_skip_45070_psi_boxplot.png |
SHOC2_LUAD_exon_skip_45070_psi_boxplot.png |
| - 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-CC-A7IH-01 | exon_skip_45070 | 112723883 | 112724819 | 112724768 | 112724768 | Frame_Shift_Del | A | - | p.L217fs |
| LIHC | TCGA-CC-A7IH-01 | exon_skip_45070 | 112723883 | 112724819 | 112724768 | 112724768 | Frame_Shift_Del | A | - | p.S218fs |
| COAD | TCGA-CA-6717-01 | exon_skip_45070 | 112723883 | 112724819 | 112724138 | 112724138 | Nonsense_Mutation | G | T | p.E8X |
| UCEC | TCGA-AX-A0J0-01 | exon_skip_45070 | 112723883 | 112724819 | 112724138 | 112724138 | Nonsense_Mutation | G | T | p.E8* |
| BLCA | TCGA-DK-AA75-01 | exon_skip_45070 | 112723883 | 112724819 | 112724252 | 112724252 | Nonsense_Mutation | A | T | p.K46* |
| HNSC | TCGA-CN-6023-01 | exon_skip_45070 | 112723883 | 112724819 | 112724421 | 112724421 | Nonsense_Mutation | C | G | p.S102* |
| HNSC | TCGA-CN-6021-01 | exon_skip_45070 | 112723883 | 112724819 | 112724466 | 112724466 | Nonsense_Mutation | C | G | p.S117* |
| HNSC | TCGA-MT-A67D-01 | exon_skip_45070 | 112723883 | 112724819 | 112724466 | 112724466 | Nonsense_Mutation | C | A | p.S117* |
| COAD | TCGA-AZ-4315-01 | exon_skip_45070 | 112723883 | 112724819 | 112724477 | 112724477 | Nonsense_Mutation | G | T | p.E121X |
| ESCA | TCGA-VR-AA7B-01 | exon_skip_45070 | 112723883 | 112724819 | 112724477 | 112724477 | Nonsense_Mutation | G | T | p.E121X |
| COAD | TCGA-AZ-4315-01 | exon_skip_45074 exon_skip_45078 | 112760173 | 112760303 | 112760262 | 112760262 | Nonsense_Mutation | G | T | p.E311X |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_45079 | 112769471 | 112769588 | 112769582 | 112769582 | Nonsense_Mutation | G | T | p.E512* |
| LUAD | TCGA-05-4402-01 | exon_skip_45070 | 112723883 | 112724819 | 112724821 | 112724821 | Splice_Site | T | A | p.G235_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-05-4402-01 |
| Cancer type: LUAD | |
| ESID: exon_skip_45070 | |
| Skipped exon start: 112723883 | |
| Skipped exon end: 112724819 | |
| Mutation start: 112724821 | |
| Mutation end: 112724821 | |
| Mutation type: Splice_Site | |
| Reference seq: T | |
| Mutation seq: A | |
| AAchange: p.G235_splice | |
exon_skip_45070_LUAD_TCGA-05-4402-01.png | |
| - 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 |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 112769471 | 112769588 | 112769542 | 112769547 | In_Frame_Del | TCTGGG | - | p.LG501del |
| HEC1_ENDOMETRIUM | 112723883 | 112724819 | 112724352 | 112724352 | Missense_Mutation | C | A | p.P79H |
| HEC1B_ENDOMETRIUM | 112723883 | 112724819 | 112724352 | 112724352 | Missense_Mutation | C | A | p.P79H |
| SNU81_LARGE_INTESTINE | 112723883 | 112724819 | 112724793 | 112724793 | Missense_Mutation | A | C | p.K226T |
| HS606T_FIBROBLAST | 112723883 | 112724819 | 112724801 | 112724801 | Missense_Mutation | C | A | p.Q229K |
| NCIH1666_LUNG | 112745386 | 112745523 | 112745434 | 112745434 | Missense_Mutation | A | G | p.E251G |
| TC205_BONE | 112745386 | 112745523 | 112745487 | 112745487 | Missense_Mutation | C | G | p.Q269E |
| CCK81_LARGE_INTESTINE | 112745386 | 112745523 | 112745521 | 112745521 | Missense_Mutation | T | C | p.I280T |
| CORL311_LUNG | 112760173 | 112760303 | 112760242 | 112760242 | Missense_Mutation | C | T | p.A304V |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 112769471 | 112769588 | 112769499 | 112769499 | Missense_Mutation | C | G | p.T484S |
| SNU81_LARGE_INTESTINE | 112723883 | 112724819 | 112724240 | 112724240 | Nonsense_Mutation | G | T | p.E42* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SHOC2 |
| 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 SHOC2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SHOC2 |
Top |
RelatedDrugs for SHOC2 |
| 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 SHOC2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SHOC2 | C1843181 | NOONAN SYNDROME-LIKE DISORDER WITH LOOSE ANAGEN HAIR | 2 | CTD_human;ORPHANET;UNIPROT |
| SHOC2 | C0018500 | Hair Diseases | 1 | CTD_human |
| SHOC2 | C0028326 | Noonan Syndrome | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|