|
||||||
|
 | |
| |
| |
| |
| 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 SERAC1 |
 Gene summary |
| Gene information | Gene symbol | SERAC1 | Gene ID | 84947 |
| Gene name | serine active site containing 1 | |
| Synonyms | - | |
| Cytomap | 6q25.3 | |
| Type of gene | protein-coding | |
| Description | protein SERAC1serine active site-containing protein 1 | |
| Modification date | 20180519 | |
| UniProtAcc | Q96JX3 | |
| Context | PubMed: SERAC1 [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 SERAC1 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 SERAC1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for SERAC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_463069 | 6 | 158537216:158537314:158538563:158538607:158538758:158538853 | 158538563:158538607 | ENSG00000122335.9 | ENST00000367101.1,ENST00000367102.2 |
| exon_skip_463071 | 6 | 158537216:158537314:158538758:158538853:158540060:158540093 | 158538758:158538853 | ENSG00000122335.9 | ENST00000435180.1,ENST00000367104.3,ENST00000607071.1 |
| exon_skip_463073 | 6 | 158541456:158541607:158549139:158549302:158551404:158551518 | 158549139:158549302 | ENSG00000122335.9 | ENST00000607742.1,ENST00000367104.3,ENST00000607071.1,ENST00000367101.1,ENST00000367102.2 |
| exon_skip_463074 | 6 | 158541456:158541607:158549139:158549302:158564087:158564216 | 158549139:158549302 | ENSG00000122335.9 | ENST00000606965.1 |
| exon_skip_463076 | 6 | 158549139:158549302:158551404:158551518:158564087:158564216 | 158551404:158551518 | ENSG00000122335.9 | ENST00000607742.1,ENST00000367104.3,ENST00000607071.1,ENST00000367101.1,ENST00000367102.2 |
| exon_skip_463077 | 6 | 158565330:158565452:158566295:158566395:158567813:158567945 | 158566295:158566395 | ENSG00000122335.9 | ENST00000607071.1 |
| exon_skip_463078 | 6 | 158565330:158565452:158567813:158567945:158569896:158569986 | 158567813:158567945 | ENSG00000122335.9 | ENST00000607742.1,ENST00000367104.3,ENST00000367101.1,ENST00000367102.2,ENST00000606965.1 |
| exon_skip_463079 | 6 | 158567813:158567945:158569896:158569986:158571484:158571621 | 158569896:158569986 | ENSG00000122335.9 | ENST00000607742.1,ENST00000607000.1,ENST00000367104.3,ENST00000607071.1,ENST00000367101.1,ENST00000367102.2,ENST00000606965.1 |
| exon_skip_463084 | 6 | 158569896:158569986:158571484:158571621:158579304:158579396 | 158571484:158571621 | ENSG00000122335.9 | ENST00000607742.1,ENST00000607071.1 |
| exon_skip_463087 | 6 | 158571484:158571621:158576346:158576383:158579304:158579396 | 158576346:158576383 | ENSG00000122335.9 | ENST00000607000.1,ENST00000367104.3,ENST00000367101.1,ENST00000367102.2,ENST00000606965.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for SERAC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_463069 | 6 | 158537216:158537314:158538563:158538607:158538758:158538853 | 158538563:158538607 | ENSG00000122335.9 | ENST00000367102.2,ENST00000367101.1 |
| exon_skip_463071 | 6 | 158537216:158537314:158538758:158538853:158540060:158540093 | 158538758:158538853 | ENSG00000122335.9 | ENST00000367104.3,ENST00000607071.1,ENST00000435180.1 |
| exon_skip_463073 | 6 | 158541456:158541607:158549139:158549302:158551404:158551518 | 158549139:158549302 | ENSG00000122335.9 | ENST00000367102.2,ENST00000367104.3,ENST00000607742.1,ENST00000607071.1,ENST00000367101.1 |
| exon_skip_463074 | 6 | 158541456:158541607:158549139:158549302:158564087:158564216 | 158549139:158549302 | ENSG00000122335.9 | ENST00000606965.1 |
| exon_skip_463076 | 6 | 158549139:158549302:158551404:158551518:158564087:158564216 | 158551404:158551518 | ENSG00000122335.9 | ENST00000367102.2,ENST00000367104.3,ENST00000607742.1,ENST00000607071.1,ENST00000367101.1 |
| exon_skip_463077 | 6 | 158565330:158565452:158566295:158566395:158567813:158567945 | 158566295:158566395 | ENSG00000122335.9 | ENST00000607071.1 |
| exon_skip_463078 | 6 | 158565330:158565452:158567813:158567945:158569896:158569986 | 158567813:158567945 | ENSG00000122335.9 | ENST00000367102.2,ENST00000367104.3,ENST00000607742.1,ENST00000606965.1,ENST00000367101.1 |
| exon_skip_463079 | 6 | 158567813:158567945:158569896:158569986:158571484:158571621 | 158569896:158569986 | ENSG00000122335.9 | ENST00000367102.2,ENST00000367104.3,ENST00000607742.1,ENST00000607071.1,ENST00000606965.1,ENST00000367101.1,ENST00000607000.1 |
| exon_skip_463084 | 6 | 158569896:158569986:158571484:158571621:158579304:158579396 | 158571484:158571621 | ENSG00000122335.9 | ENST00000607742.1,ENST00000607071.1 |
| exon_skip_463087 | 6 | 158571484:158571621:158576346:158576383:158579304:158579396 | 158576346:158576383 | ENSG00000122335.9 | ENST00000367102.2,ENST00000367104.3,ENST00000606965.1,ENST00000367101.1,ENST00000607000.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SERAC1 |
| 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 |
| ENST00000367104 | 158538758 | 158538853 | Frame-shift |
| ENST00000367104 | 158549139 | 158549302 | Frame-shift |
| ENST00000367104 | 158576346 | 158576383 | Frame-shift |
| ENST00000367104 | 158551404 | 158551518 | In-frame |
| ENST00000367104 | 158567813 | 158567945 | In-frame |
| ENST00000367104 | 158569896 | 158569986 | 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 |
| ENST00000367104 | 158538758 | 158538853 | Frame-shift |
| ENST00000367104 | 158549139 | 158549302 | Frame-shift |
| ENST00000367104 | 158576346 | 158576383 | Frame-shift |
| ENST00000367104 | 158551404 | 158551518 | In-frame |
| ENST00000367104 | 158567813 | 158567945 | In-frame |
| ENST00000367104 | 158569896 | 158569986 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SERAC1 |
| 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 |
| ENST00000367104 | 3965 | 654 | 158569896 | 158569986 | 398 | 487 | 88 | 118 |
| ENST00000367104 | 3965 | 654 | 158567813 | 158567945 | 488 | 619 | 118 | 162 |
| ENST00000367104 | 3965 | 654 | 158551404 | 158551518 | 871 | 984 | 246 | 284 |
| 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 |
| ENST00000367104 | 3965 | 654 | 158569896 | 158569986 | 398 | 487 | 88 | 118 |
| ENST00000367104 | 3965 | 654 | 158567813 | 158567945 | 488 | 619 | 118 | 162 |
| ENST00000367104 | 3965 | 654 | 158551404 | 158551518 | 871 | 984 | 246 | 284 |
| 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 |
| Q96JX3 | 88 | 118 | 1 | 654 | Chain | ID=PRO_0000274671;Note=Protein SERAC1 |
| Q96JX3 | 118 | 162 | 1 | 654 | Chain | ID=PRO_0000274671;Note=Protein SERAC1 |
| Q96JX3 | 246 | 284 | 168 | 654 | Alternative sequence | ID=VSP_022858;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96JX3 | 246 | 284 | 1 | 654 | Chain | ID=PRO_0000274671;Note=Protein SERAC1 |
| 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 |
| Q96JX3 | 88 | 118 | 1 | 654 | Chain | ID=PRO_0000274671;Note=Protein SERAC1 |
| Q96JX3 | 118 | 162 | 1 | 654 | Chain | ID=PRO_0000274671;Note=Protein SERAC1 |
| Q96JX3 | 246 | 284 | 168 | 654 | Alternative sequence | ID=VSP_022858;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96JX3 | 246 | 284 | 1 | 654 | Chain | ID=PRO_0000274671;Note=Protein SERAC1 |
Top |
SNVs in the skipped exons for SERAC1 |
| - 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_463071 | 158538759 | 158538853 | 158538839 | 158538839 | Frame_Shift_Del | T | - | p.K441fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_463076 | 158551405 | 158551518 | 158551468 | 158551468 | Frame_Shift_Del | A | - | p.F263fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_463076 | 158551405 | 158551518 | 158551473 | 158551473 | Frame_Shift_Del | T | - | p.S262fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_463076 | 158551405 | 158551518 | 158551473 | 158551473 | Frame_Shift_Del | T | - | p.S262fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_463076 | 158551405 | 158551518 | 158551473 | 158551473 | Frame_Shift_Del | T | - | p.S262fs |
| LUAD | TCGA-05-4398-01 | exon_skip_463084 | 158571485 | 158571621 | 158571537 | 158571537 | Frame_Shift_Del | C | - | p.M71fs |
| LGG | TCGA-P5-A780-01 | exon_skip_463087 | 158576347 | 158576383 | 158576366 | 158576366 | Frame_Shift_Del | T | - | p.T37fs |
| UCEC | TCGA-AP-A0LE-01 | exon_skip_463084 | 158571485 | 158571621 | 158571521 | 158571522 | Frame_Shift_Ins | - | AT | p.Y76fs |
| LUSC | TCGA-39-5036-01 | exon_skip_463071 | 158538759 | 158538853 | 158538849 | 158538849 | Nonsense_Mutation | C | T | p.W438* |
| BLCA | TCGA-GC-A6I3-01 | exon_skip_463078 | 158567814 | 158567945 | 158567876 | 158567876 | Nonsense_Mutation | G | C | p.S142* |
| HNSC | TCGA-CR-7402-01 | exon_skip_463079 | 158569897 | 158569986 | 158569896 | 158569896 | Splice_Site | C | G | p.D119_splice |
| - 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 |
| HCC2998_LARGE_INTESTINE | 158538759 | 158538853 | 158538822 | 158538822 | Missense_Mutation | C | T | p.R447Q |
| HCC1500_BREAST | 158549140 | 158549302 | 158549154 | 158549154 | Missense_Mutation | G | A | p.S334F |
| COGN305_AUTONOMIC_GANGLIA | 158551405 | 158551518 | 158551435 | 158551435 | Missense_Mutation | G | T | p.F274L |
| DU145_PROSTATE | 158571485 | 158571621 | 158571537 | 158571537 | Missense_Mutation | C | A | p.M71I |
| JHH2_LIVER | 158551405 | 158551518 | 158551507 | 158551507 | Nonsense_Mutation | C | T | p.W250* |
| HCC2998_LARGE_INTESTINE | 158569897 | 158569986 | 158569963 | 158569963 | Nonsense_Mutation | C | A | p.E97* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SERAC1 |
| 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 SERAC1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SERAC1 |
Top |
RelatedDrugs for SERAC1 |
| 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 SERAC1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SERAC1 | C0011053 | Deafness | 1 | CTD_human |
| SERAC1 | C0013421 | Dystonia | 1 | CTD_human |
| SERAC1 | C0023772 | Lipid Metabolism, Inborn Errors | 1 | CTD_human |
| SERAC1 | C3553597 | 3-METHYLGLUTACONIC ACIDURIA WITH DEAFNESS, ENCEPHALOPATHY, AND LEIGH-LIKE SYNDROME | 1 | ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|