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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 SPATA5 |
 Gene summary |
| Gene information | Gene symbol | SPATA5 | Gene ID | 166378 |
| Gene name | spermatogenesis associated 5 | |
| Synonyms | AFG2|EHLMRS|SPAF | |
| Cytomap | 4q28.1 | |
| Type of gene | protein-coding | |
| Description | spermatogenesis-associated protein 5ATPase family gene 2 homologATPase family protein 2 homologspermatogenesis associated factor SPAFspermatogenesis-associated factor protein | |
| Modification date | 20180523 | |
| UniProtAcc | Q8NB90 | |
| Context | PubMed: SPATA5 [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 |
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Exon skipping events across known transcript of Ensembl for SPATA5 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 SPATA5 |
| 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 SPATA5 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_426011 | 4 | 123857254:123857311:123859280:123859404:123868387:123868643 | 123859280:123859404 | ENSG00000145375.7 | ENST00000422835.2,ENST00000274008.4 |
| exon_skip_426012 | 4 | 123868387:123868643:123900386:123900541:123949340:123949550 | 123900386:123900541 | ENSG00000145375.7 | ENST00000422835.2,ENST00000274008.4 |
| exon_skip_426014 | 4 | 123900386:123900541:123949340:123949550:123977541:123977595 | 123949340:123949550 | ENSG00000145375.7 | ENST00000422835.2,ENST00000274008.4 |
| exon_skip_426015 | 4 | 123949340:123949550:123977541:123977595:123978363:123978443 | 123977541:123977595 | ENSG00000145375.7 | ENST00000422835.2,ENST00000274008.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SPATA5 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_426011 | 4 | 123857254:123857311:123859280:123859404:123868387:123868643 | 123859280:123859404 | ENSG00000145375.7 | ENST00000274008.4,ENST00000422835.2 |
| exon_skip_426012 | 4 | 123868387:123868643:123900386:123900541:123949340:123949550 | 123900386:123900541 | ENSG00000145375.7 | ENST00000274008.4,ENST00000422835.2 |
| exon_skip_426014 | 4 | 123900386:123900541:123949340:123949550:123977541:123977595 | 123949340:123949550 | ENSG00000145375.7 | ENST00000274008.4,ENST00000422835.2 |
| exon_skip_426015 | 4 | 123949340:123949550:123977541:123977595:123978363:123978443 | 123977541:123977595 | ENSG00000145375.7 | ENST00000274008.4,ENST00000422835.2 |
| 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 SPATA5 |
| 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 |
| ENST00000274008 | 123859280 | 123859404 | Frame-shift |
| ENST00000274008 | 123900386 | 123900541 | Frame-shift |
| ENST00000274008 | 123949340 | 123949550 | In-frame |
| ENST00000274008 | 123977541 | 123977595 | 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 |
| ENST00000274008 | 123859280 | 123859404 | Frame-shift |
| ENST00000274008 | 123900386 | 123900541 | Frame-shift |
| ENST00000274008 | 123949340 | 123949550 | In-frame |
| ENST00000274008 | 123977541 | 123977595 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SPATA5 |
| 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 |
| ENST00000274008 | 8154 | 893 | 123949340 | 123949550 | 1939 | 2148 | 623 | 693 |
| ENST00000274008 | 8154 | 893 | 123977541 | 123977595 | 2149 | 2202 | 693 | 711 |
| 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 |
| ENST00000274008 | 8154 | 893 | 123949340 | 123949550 | 1939 | 2148 | 623 | 693 |
| ENST00000274008 | 8154 | 893 | 123977541 | 123977595 | 2149 | 2202 | 693 | 711 |
| 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 |
| Q8NB90 | 623 | 693 | 1 | 893 | Chain | ID=PRO_0000330583;Note=ATPase family protein 2 homolog |
| Q8NB90 | 623 | 693 | 626 | 626 | Natural variant | ID=VAR_075782;Note=In EHLMRS. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26299366;Dbxref=dbSNP:rs796052222,PMID:26299366 |
| Q8NB90 | 623 | 693 | 628 | 628 | Natural variant | ID=VAR_075783;Note=In EHLMRS. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26299366;Dbxref=dbSNP:rs768528444,PMID:26299366 |
| Q8NB90 | 623 | 693 | 673 | 673 | Natural variant | ID=VAR_042704;Note=S->Y;Dbxref=dbSNP:rs35133326 |
| Q8NB90 | 623 | 693 | 668 | 675 | Nucleotide binding | Note=ATP 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P32794 |
| Q8NB90 | 693 | 711 | 694 | 696 | Alternative sequence | ID=VSP_033046;Note=In isoform 3. GPE->VGC;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8NB90 | 693 | 711 | 697 | 893 | Alternative sequence | ID=VSP_033047;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8NB90 | 693 | 711 | 1 | 893 | Chain | ID=PRO_0000330583;Note=ATPase family protein 2 homolog |
| Q8NB90 | 693 | 711 | 695 | 695 | Sequence conflict | Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q8NB90 | 623 | 693 | 1 | 893 | Chain | ID=PRO_0000330583;Note=ATPase family protein 2 homolog |
| Q8NB90 | 623 | 693 | 626 | 626 | Natural variant | ID=VAR_075782;Note=In EHLMRS. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26299366;Dbxref=dbSNP:rs796052222,PMID:26299366 |
| Q8NB90 | 623 | 693 | 628 | 628 | Natural variant | ID=VAR_075783;Note=In EHLMRS. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26299366;Dbxref=dbSNP:rs768528444,PMID:26299366 |
| Q8NB90 | 623 | 693 | 673 | 673 | Natural variant | ID=VAR_042704;Note=S->Y;Dbxref=dbSNP:rs35133326 |
| Q8NB90 | 623 | 693 | 668 | 675 | Nucleotide binding | Note=ATP 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P32794 |
| Q8NB90 | 693 | 711 | 694 | 696 | Alternative sequence | ID=VSP_033046;Note=In isoform 3. GPE->VGC;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8NB90 | 693 | 711 | 697 | 893 | Alternative sequence | ID=VSP_033047;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8NB90 | 693 | 711 | 1 | 893 | Chain | ID=PRO_0000330583;Note=ATPase family protein 2 homolog |
| Q8NB90 | 693 | 711 | 695 | 695 | Sequence conflict | Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for SPATA5 |
| - 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 |
| STAD | TCGA-CG-4442-01 | exon_skip_426011 | 123859281 | 123859404 | 123859335 | 123859335 | Frame_Shift_Del | G | - | p.E463fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_426012 | 123900387 | 123900541 | 123900413 | 123900413 | Frame_Shift_Del | A | - | p.K582fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_426014 | 123949341 | 123949550 | 123949455 | 123949455 | Frame_Shift_Del | A | - | p.K662fs |
| COAD | TCGA-CK-5916-01 | exon_skip_426012 | 123900387 | 123900541 | 123900412 | 123900413 | Frame_Shift_Ins | - | A | p.L580fs |
| LUAD | TCGA-55-6970-01 | exon_skip_426011 | 123859281 | 123859404 | 123859323 | 123859323 | Nonsense_Mutation | T | A | p.C459* |
| COAD | TCGA-CA-6717-01 | exon_skip_426014 | 123949341 | 123949550 | 123949434 | 123949434 | Nonsense_Mutation | C | T | p.R655X |
| UCEC | TCGA-AP-A056-01 | exon_skip_426014 | 123949341 | 123949550 | 123949434 | 123949434 | Nonsense_Mutation | C | T | p.R655* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_426014 | 123949341 | 123949550 | 123949434 | 123949434 | Nonsense_Mutation | C | T | p.R655* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_426014 | 123949341 | 123949550 | 123949434 | 123949434 | Nonsense_Mutation | C | T | p.R655X |
| BLCA | TCGA-GV-A40E-01 | exon_skip_426012 | 123900387 | 123900541 | 123900543 | 123900543 | Splice_Site | T | G | p.N623_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 |
| EN_ENDOMETRIUM | 123859281 | 123859404 | 123859294 | 123859295 | Frame_Shift_Ins | - | T | p.I450fs |
| DV90_LUNG | 123900387 | 123900541 | 123900412 | 123900413 | Frame_Shift_Ins | - | A | p.K581fs |
| TC106_BONE | 123859281 | 123859404 | 123859339 | 123859339 | Missense_Mutation | G | T | p.A465S |
| GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 123859281 | 123859404 | 123859357 | 123859357 | Missense_Mutation | A | G | p.K471E |
| HCT15_LARGE_INTESTINE | 123900387 | 123900541 | 123900420 | 123900420 | Missense_Mutation | A | G | p.Q583R |
| SNU1040_LARGE_INTESTINE | 123900387 | 123900541 | 123900446 | 123900446 | Missense_Mutation | G | A | p.A592T |
| COLO741_SKIN | 123949341 | 123949550 | 123949464 | 123949464 | Missense_Mutation | C | T | p.L665F |
| SNUC2B_LARGE_INTESTINE | 123949341 | 123949550 | 123949485 | 123949485 | Missense_Mutation | T | C | p.C672R |
| IGR1_SKIN | 123949341 | 123949550 | 123949519 | 123949519 | Missense_Mutation | A | G | p.N683S |
| HCC2998_LARGE_INTESTINE | 123977542 | 123977595 | 123977561 | 123977561 | Missense_Mutation | A | C | p.K700T |
| NCIH513_PLEURA | 123977542 | 123977595 | 123977584 | 123977584 | Missense_Mutation | G | C | p.A708P |
| NCIH2170_LUNG | 123859281 | 123859404 | 123859306 | 123859306 | Nonsense_Mutation | G | T | p.E454* |
| HEC151_ENDOMETRIUM | 123859281 | 123859404 | 123859282 | 123859282 | Splice_Site | C | T | p.H446Y |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPATA5 |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPATA5 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPATA5 |
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RelatedDrugs for SPATA5 |
| 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 SPATA5 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SPATA5 | C0036341 | Schizophrenia | 1 | CTD_human |
| SPATA5 | C4225276 | EPILEPSY, HEARING LOSS, AND MENTAL RETARDATION SYNDROME | 1 | ORPHANET;UNIPROT |
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