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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 SKA3 |
 Gene summary |
| Gene information | Gene symbol | SKA3 | Gene ID | 221150 |
| Gene name | spindle and kinetochore associated complex subunit 3 | |
| Synonyms | C13orf3|RAMA1 | |
| Cytomap | 13q12.11 | |
| Type of gene | protein-coding | |
| Description | spindle and kinetochore-associated protein 3 | |
| Modification date | 20180523 | |
| UniProtAcc | Q8IX90 | |
| Context | PubMed: SKA3 [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 |
| SKA3 | GO:0031110 | regulation of microtubule polymerization or depolymerization | 19289083 |
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Exon skipping events across known transcript of Ensembl for SKA3 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 SKA3 |
| 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 SKA3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_102334 | 13 | 21728835:21729289:21729831:21729950:21732060:21732264 | 21729831:21729950 | ENSG00000165480.11 | ENST00000314759.5,ENST00000298260.4 |
| exon_skip_102337 | 13 | 21728835:21729289:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENSG00000165480.11 | ENST00000400018.3 |
| exon_skip_102339 | 13 | 21729831:21729950:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENSG00000165480.11 | ENST00000314759.5,ENST00000298260.4 |
| exon_skip_102347 | 13 | 21734040:21734126:21735928:21736014:21742126:21742538 | 21735928:21736014 | ENSG00000165480.11 | ENST00000314759.5,ENST00000298260.4,ENST00000400018.3 |
| exon_skip_102353 | 13 | 21735928:21736014:21742126:21742538:21746477:21746643 | 21742126:21742538 | ENSG00000165480.11 | ENST00000314759.5,ENST00000465471.1,ENST00000298260.4,ENST00000400018.3 |
| exon_skip_102356 | 13 | 21742360:21742538:21746477:21746643:21746758:21746820 | 21746477:21746643 | ENSG00000165480.11 | ENST00000314759.5,ENST00000536239.1,ENST00000465471.1,ENST00000400018.3 |
| exon_skip_102357 | 13 | 21742360:21742538:21746477:21746643:21750513:21750612 | 21746477:21746643 | ENSG00000165480.11 | ENST00000298260.4 |
| exon_skip_102359 | 13 | 21746477:21746643:21746758:21746820:21750486:21750690 | 21746758:21746820 | ENSG00000165480.11 | ENST00000465471.1 |
| exon_skip_102360 | 13 | 21746477:21746643:21746758:21746820:21750513:21750612 | 21746758:21746820 | ENSG00000165480.11 | ENST00000475251.1,ENST00000314759.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SKA3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_102334 | 13 | 21728835:21729289:21729831:21729950:21732060:21732264 | 21729831:21729950 | ENSG00000165480.11 | ENST00000298260.4,ENST00000314759.5 |
| exon_skip_102339 | 13 | 21729831:21729950:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENSG00000165480.11 | ENST00000298260.4,ENST00000314759.5 |
| exon_skip_102347 | 13 | 21734040:21734126:21735928:21736014:21742126:21742538 | 21735928:21736014 | ENSG00000165480.11 | ENST00000400018.3,ENST00000298260.4,ENST00000314759.5 |
| exon_skip_102356 | 13 | 21742360:21742538:21746477:21746643:21746758:21746820 | 21746477:21746643 | ENSG00000165480.11 | ENST00000400018.3,ENST00000314759.5,ENST00000465471.1,ENST00000536239.1 |
| exon_skip_102359 | 13 | 21746477:21746643:21746758:21746820:21750486:21750690 | 21746758:21746820 | ENSG00000165480.11 | ENST00000465471.1 |
| exon_skip_102360 | 13 | 21746477:21746643:21746758:21746820:21750513:21750612 | 21746758:21746820 | ENSG00000165480.11 | ENST00000314759.5,ENST00000475251.1 |
| 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 SKA3 |
| 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 |
| ENST00000314759 | 21729831 | 21729950 | Frame-shift |
| ENST00000314759 | 21735928 | 21736014 | Frame-shift |
| ENST00000314759 | 21742126 | 21742538 | Frame-shift |
| ENST00000314759 | 21746477 | 21746643 | Frame-shift |
| ENST00000314759 | 21746758 | 21746820 | Frame-shift |
| ENST00000314759 | 21732060 | 21732264 | 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 |
| ENST00000314759 | 21729831 | 21729950 | Frame-shift |
| ENST00000314759 | 21735928 | 21736014 | Frame-shift |
| ENST00000314759 | 21746477 | 21746643 | Frame-shift |
| ENST00000314759 | 21746758 | 21746820 | Frame-shift |
| ENST00000314759 | 21732060 | 21732264 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SKA3 |
| 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 |
| ENST00000314759 | 2936 | 412 | 21732060 | 21732264 | 1041 | 1244 | 305 | 373 |
| 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 |
| ENST00000314759 | 2936 | 412 | 21732060 | 21732264 | 1041 | 1244 | 305 | 373 |
| 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 |
| Q8IX90 | 305 | 373 | 36 | 412 | Alternative sequence | ID=VSP_040528;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8IX90 | 305 | 373 | 1 | 412 | Chain | ID=PRO_0000089878;Note=Spindle and kinetochore-associated protein 3 |
| Q8IX90 | 305 | 373 | 318 | 318 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332 |
| Q8IX90 | 305 | 373 | 335 | 335 | Natural variant | ID=VAR_057832;Note=D->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.1;Dbxref=dbSNP:rs17279819 |
| 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 |
| Q8IX90 | 305 | 373 | 36 | 412 | Alternative sequence | ID=VSP_040528;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8IX90 | 305 | 373 | 1 | 412 | Chain | ID=PRO_0000089878;Note=Spindle and kinetochore-associated protein 3 |
| Q8IX90 | 305 | 373 | 318 | 318 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332 |
| Q8IX90 | 305 | 373 | 335 | 335 | Natural variant | ID=VAR_057832;Note=D->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.1;Dbxref=dbSNP:rs17279819 |
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SNVs in the skipped exons for SKA3 |
| - 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 |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_102337 exon_skip_102339 | 21732061 | 21732264 | 21732185 | 21732185 | Frame_Shift_Del | A | - | p.L332fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_102337 exon_skip_102339 | 21732061 | 21732264 | 21732185 | 21732185 | Frame_Shift_Del | A | - | p.L332fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_102356 exon_skip_102357 | 21746478 | 21746643 | 21746552 | 21746552 | Frame_Shift_Del | T | - | p.N86fs |
| HNSC | TCGA-CN-4723-01 | exon_skip_102334 | 21729832 | 21729950 | 21729931 | 21729931 | Nonsense_Mutation | G | C | p.S380* |
| MESO | TCGA-ZN-A9VW-01 | exon_skip_102334 | 21729832 | 21729950 | 21729936 | 21729936 | Nonsense_Mutation | G | T | p.Y378* |
| BLCA | TCGA-UY-A9PH-01 | exon_skip_102337 exon_skip_102339 | 21732061 | 21732264 | 21732242 | 21732242 | Nonsense_Mutation | G | C | p.S313* |
| UVM | TCGA-VD-A8KH-01 | exon_skip_102360 exon_skip_102359 | 21746759 | 21746820 | 21746793 | 21746793 | Nonsense_Mutation | A | T | p.L44* |
| UVM | TCGA-VD-A8KH-01 | exon_skip_102360 exon_skip_102359 | 21746759 | 21746820 | 21746793 | 21746793 | Nonsense_Mutation | A | T | p.L44X |
| PAAD | TCGA-HZ-A49H-01 | exon_skip_102337 exon_skip_102339 | 21732061 | 21732264 | 21732266 | 21732266 | Splice_Site | T | A | . |
| KIRP | TCGA-IZ-8196-01 | exon_skip_102347 | 21735929 | 21736014 | 21735928 | 21735928 | Splice_Site | C | T | . |
| LGG | TCGA-DU-7294-01 | exon_skip_102353 | 21742127 | 21742538 | 21742125 | 21742125 | Splice_Site | A | C | . |
| PCPG | TCGA-RW-A68A-01 | exon_skip_102353 | 21742127 | 21742538 | 21742125 | 21742125 | Splice_Site | A | C | . |
| KICH | TCGA-KL-8345-01 | exon_skip_102353 | 21742127 | 21742538 | 21742126 | 21742126 | Splice_Site | C | A | . |
| KICH | TCGA-KN-8430-01 | exon_skip_102353 | 21742127 | 21742538 | 21742126 | 21742126 | Splice_Site | C | A | . |
| LIHC | TCGA-DD-A119-01 | exon_skip_102353 | 21742127 | 21742538 | 21742126 | 21742126 | Splice_Site | C | A | . |
| LIHC | TCGA-DD-AADY-01 | exon_skip_102353 | 21742127 | 21742538 | 21742126 | 21742126 | Splice_Site | C | A | . |
| LIHC | TCGA-G3-A25Y-01 | exon_skip_102353 | 21742127 | 21742538 | 21742126 | 21742126 | Splice_Site | C | A | . |
| KIRC | TCGA-BP-5180-01 | exon_skip_102356 exon_skip_102357 | 21746478 | 21746643 | 21746645 | 21746645 | Splice_Site | T | G | . |
| PAAD | TCGA-IB-A6UF-01 | exon_skip_102356 exon_skip_102357 | 21746478 | 21746643 | 21746645 | 21746645 | Splice_Site | T | G | . |
| - 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 |
| C33A_CERVIX | 21735929 | 21736014 | 21735969 | 21735969 | Frame_Shift_Del | A | - | p.F263fs |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 21742127 | 21742538 | 21742242 | 21742242 | Frame_Shift_Del | T | - | p.M210fs |
| ES6_BONE | 21742127 | 21742538 | 21742487 | 21742487 | Frame_Shift_Del | T | - | p.N128fs |
| SW48_LARGE_INTESTINE | 21746478 | 21746643 | 21746552 | 21746552 | Frame_Shift_Del | T | - | p.N86fs |
| CAL51_BREAST | 21735929 | 21736014 | 21735931 | 21735932 | Frame_Shift_Ins | - | T | p.S276fs |
| OCUBM_BREAST | 21729832 | 21729950 | 21729938 | 21729938 | Missense_Mutation | A | G | p.Y378H |
| NCIH1437_LUNG | 21732061 | 21732264 | 21732086 | 21732086 | Missense_Mutation | G | T | p.T365N |
| NCIBL1437_MATCHED_NORMAL_TISSUE | 21732061 | 21732264 | 21732086 | 21732086 | Missense_Mutation | G | T | p.T365N |
| SW684_SOFT_TISSUE | 21732061 | 21732264 | 21732128 | 21732128 | Missense_Mutation | G | A | p.S351F |
| HDQP1_BREAST | 21732061 | 21732264 | 21732152 | 21732152 | Missense_Mutation | T | G | p.D343A |
| HCE4_OESOPHAGUS | 21732061 | 21732264 | 21732165 | 21732165 | Missense_Mutation | C | G | p.E339Q |
| NCIBL2126_MATCHED_NORMAL_TISSUE | 21732061 | 21732264 | 21732194 | 21732194 | Missense_Mutation | G | A | p.S329L |
| NCIH2126_LUNG | 21732061 | 21732264 | 21732194 | 21732194 | Missense_Mutation | G | A | p.S329L |
| HCC2935_LUNG | 21742127 | 21742538 | 21742142 | 21742142 | Missense_Mutation | G | A | p.A243V |
| SNU1040_LARGE_INTESTINE | 21742127 | 21742538 | 21742160 | 21742160 | Missense_Mutation | G | A | p.T237I |
| IMR5_AUTONOMIC_GANGLIA | 21742127 | 21742538 | 21742203 | 21742203 | Missense_Mutation | A | T | p.F223I |
| COLO824_BREAST | 21742127 | 21742538 | 21742255 | 21742255 | Missense_Mutation | T | A | p.K205N |
| UWB1289_OVARY | 21742127 | 21742538 | 21742380 | 21742380 | Missense_Mutation | C | G | p.E164Q |
| WM88_SKIN | 21742127 | 21742538 | 21742413 | 21742413 | Missense_Mutation | G | A | p.P153S |
| EFO21_OVARY | 21742127 | 21742538 | 21742448 | 21742448 | Missense_Mutation | G | T | p.P141H |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 21742127 | 21742538 | 21742461 | 21742461 | Missense_Mutation | C | T | p.D137N |
| L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 21746478 | 21746643 | 21746516 | 21746516 | Missense_Mutation | T | A | p.Q98L |
| HEC251_ENDOMETRIUM | 21746478 | 21746643 | 21746534 | 21746534 | Missense_Mutation | T | G | p.K92T |
| HEC108_ENDOMETRIUM | 21746478 | 21746643 | 21746543 | 21746543 | Missense_Mutation | T | C | p.D89G |
| K2_SKIN | 21735929 | 21736014 | 21735947 | 21735947 | Nonsense_Mutation | G | A | p.Q271* |
| KELLY_AUTONOMIC_GANGLIA | 21746478 | 21746643 | 21746508 | 21746508 | Nonsense_Mutation | C | A | p.G101* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SKA3 |
| 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 |
| exon_skip_102337 | 13 | 21728835:21729289:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000400018.3 | ESCA | rs17279819 | chr13:21732175 | G/T | 3.55e-06 |
| exon_skip_102337 | 13 | 21728835:21729289:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000400018.3 | ESCA | rs17345571 | chr13:21732193 | C/T | 3.55e-06 |
| exon_skip_102337 | 13 | 21728835:21729289:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000400018.3 | STAD | rs17279819 | chr13:21732175 | G/T | 9.41e-08 |
| exon_skip_102337 | 13 | 21728835:21729289:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000400018.3 | STAD | rs17345571 | chr13:21732193 | C/T | 9.41e-08 |
| exon_skip_102339 | 13 | 21729831:21729950:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000314759.5,ENST00000298260.4 | ESCA | rs17279819 | chr13:21732175 | G/T | 3.55e-06 |
| exon_skip_102339 | 13 | 21729831:21729950:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000314759.5,ENST00000298260.4 | ESCA | rs17345571 | chr13:21732193 | C/T | 3.55e-06 |
| exon_skip_102339 | 13 | 21729831:21729950:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000314759.5,ENST00000298260.4 | STAD | rs17279819 | chr13:21732175 | G/T | 9.41e-08 |
| exon_skip_102339 | 13 | 21729831:21729950:21732060:21732264:21734040:21734126 | 21732060:21732264 | ENST00000314759.5,ENST00000298260.4 | STAD | rs17345571 | chr13:21732193 | C/T | 9.41e-08 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SKA3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SKA3 |
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RelatedDrugs for SKA3 |
| 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 SKA3 |
| 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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