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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 PRPF40A |
 Gene summary |
| Gene information | Gene symbol | PRPF40A | Gene ID | 55660 |
| Gene name | pre-mRNA processing factor 40 homolog A | |
| Synonyms | FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40 | |
| Cytomap | 2q23.3 | |
| Type of gene | protein-coding | |
| Description | pre-mRNA-processing factor 40 homolog AFas-ligand associated factor 1Huntingtin-interacting protein ANY-REN-6 antigenPRP40 pre-mRNA processing factor 40 homolog Afas ligand-associated factor 1formin binding protein 3formin-binding protein 11huntin | |
| Modification date | 20180523 | |
| UniProtAcc | O75400 | |
| Context | PubMed: PRPF40A [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 PRPF40A 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 PRPF40A |
| 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 PRPF40A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_344066 | 2 | 153515461:153515523:153515606:153515703:153515783:153515870 | 153515606:153515703 | ENSG00000196504.11 | ENST00000471167.1,ENST00000410080.1 |
| exon_skip_344067 | 2 | 153520651:153520766:153525650:153525784:153526744:153526895 | 153525650:153525784 | ENSG00000196504.11 | ENST00000410080.1 |
| exon_skip_344069 | 2 | 153530111:153530220:153532918:153533293:153533964:153533989 | 153532918:153533293 | ENSG00000196504.11 | ENST00000545856.1,ENST00000410080.1,ENST00000354363.6 |
| exon_skip_344070 | 2 | 153532918:153533293:153533964:153533989:153535865:153535986 | 153533964:153533989 | ENSG00000196504.11 | ENST00000493468.2 |
| exon_skip_344071 | 2 | 153533964:153533989:153535569:153535623:153535865:153535986 | 153535569:153535623 | ENSG00000196504.11 | ENST00000545856.1,ENST00000410080.1,ENST00000354363.6 |
| exon_skip_344075 | 2 | 153537739:153537850:153547475:153547492:153549551:153549582 | 153547475:153547492 | ENSG00000196504.11 | ENST00000467114.2,ENST00000493468.2,ENST00000545856.1,ENST00000410080.1,ENST00000354363.6 |
| exon_skip_344079 | 2 | 153549551:153549582:153549671:153549990:153551055:153551136 | 153549671:153549990 | ENSG00000196504.11 | ENST00000354363.6 |
| exon_skip_344085 | 2 | 153551055:153551136:153571063:153571143:153572508:153572640 | 153571063:153571143 | ENSG00000196504.11 | ENST00000489741.1 |
| exon_skip_344087 | 2 | 153551055:153551136:153572508:153572640:153573869:153573945 | 153572508:153572640 | ENSG00000196504.11 | ENST00000448428.1,ENST00000450303.2,ENST00000354363.6 |
| exon_skip_344091 | 2 | 153572508:153572640:153573869:153573945:153574344:153574446 | 153573869:153573945 | ENSG00000196504.11 | ENST00000450303.2 |
| exon_skip_344093 | 2 | 153572508:153572640:153573869:153574139:153574344:153574446 | 153573869:153574139 | ENSG00000196504.11 | ENST00000486100.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PRPF40A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_344066 | 2 | 153515461:153515523:153515606:153515703:153515783:153515870 | 153515606:153515703 | ENSG00000196504.11 | ENST00000410080.1,ENST00000471167.1 |
| exon_skip_344067 | 2 | 153520651:153520766:153525650:153525784:153526744:153526895 | 153525650:153525784 | ENSG00000196504.11 | ENST00000410080.1 |
| exon_skip_344069 | 2 | 153530111:153530220:153532918:153533293:153533964:153533989 | 153532918:153533293 | ENSG00000196504.11 | ENST00000410080.1,ENST00000354363.6,ENST00000545856.1 |
| exon_skip_344070 | 2 | 153532918:153533293:153533964:153533989:153535865:153535986 | 153533964:153533989 | ENSG00000196504.11 | ENST00000493468.2 |
| exon_skip_344071 | 2 | 153533964:153533989:153535569:153535623:153535865:153535986 | 153535569:153535623 | ENSG00000196504.11 | ENST00000410080.1,ENST00000354363.6,ENST00000545856.1 |
| exon_skip_344075 | 2 | 153537739:153537850:153547475:153547492:153549551:153549582 | 153547475:153547492 | ENSG00000196504.11 | ENST00000410080.1,ENST00000354363.6,ENST00000545856.1,ENST00000493468.2,ENST00000467114.2 |
| exon_skip_344079 | 2 | 153549551:153549582:153549671:153549990:153551055:153551136 | 153549671:153549990 | ENSG00000196504.11 | ENST00000354363.6 |
| exon_skip_344085 | 2 | 153551055:153551136:153571063:153571143:153572508:153572640 | 153571063:153571143 | ENSG00000196504.11 | ENST00000489741.1 |
| exon_skip_344087 | 2 | 153551055:153551136:153572508:153572640:153573869:153573945 | 153572508:153572640 | ENSG00000196504.11 | ENST00000354363.6,ENST00000448428.1,ENST00000450303.2 |
| exon_skip_344091 | 2 | 153572508:153572640:153573869:153573945:153574344:153574446 | 153573869:153573945 | ENSG00000196504.11 | ENST00000450303.2 |
| exon_skip_344093 | 2 | 153572508:153572640:153573869:153574139:153574344:153574446 | 153573869:153574139 | ENSG00000196504.11 | ENST00000486100.1 |
| 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 PRPF40A |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for PRPF40A |
| 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 |
| 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 |
| 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 |
| 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 |
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SNVs in the skipped exons for PRPF40A |
| - 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. |
PRPF40A_LUSC_exon_skip_344069_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-G3-A3CJ-01 | exon_skip_344066 | 153515607 | 153515703 | 153515661 | 153515661 | Frame_Shift_Del | T | - | p.R818fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_344069 | 153532919 | 153533293 | 153533252 | 153533252 | Frame_Shift_Del | G | - | p.P233fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_344087 | 153572509 | 153572640 | 153572534 | 153572534 | Frame_Shift_Del | G | - | p.P64fs |
| STAD | TCGA-BR-6452-01 | exon_skip_344087 | 153572509 | 153572640 | 153572534 | 153572534 | Frame_Shift_Del | G | - | p.P64fs |
| BRCA | TCGA-D8-A1JG-01 | exon_skip_344067 | 153525651 | 153525784 | 153525674 | 153525674 | Nonsense_Mutation | G | A | p.R581* |
| LUSC | TCGA-85-6561-01 | exon_skip_344069 | 153532919 | 153533293 | 153532918 | 153532918 | Splice_Site | C | G | p.D371_splice |
| CESC | TCGA-C5-A1BQ-01 | exon_skip_344070 | 153533965 | 153533989 | 153533990 | 153533990 | Splice_Site | C | T | e9-1 |
| LUAD | TCGA-55-6981-01 | exon_skip_344075 | 153547476 | 153547492 | 153547493 | 153547494 | Splice_Site | - | A | p.G137_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-85-6561-01 |
| Cancer type: LUSC | |
| ESID: exon_skip_344069 | |
| Skipped exon start: 153532919 | |
| Skipped exon end: 153533293 | |
| Mutation start: 153532918 | |
| Mutation end: 153532918 | |
| Mutation type: Splice_Site | |
| Reference seq: C | |
| Mutation seq: G | |
| AAchange: p.D371_splice | |
exon_skip_104683_LUSC_TCGA-85-6561-01.png | |
exon_skip_315479_LUSC_TCGA-85-6561-01.png | |
exon_skip_344069_LUSC_TCGA-85-6561-01.png | |
exon_skip_354387_LUSC_TCGA-85-6561-01.png | |
exon_skip_367235_LUSC_TCGA-85-6561-01.png | |
exon_skip_371719_LUSC_TCGA-85-6561-01.png | |
exon_skip_91283_LUSC_TCGA-85-6561-01.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 |
| OC316_OVARY | 153515607 | 153515703 | 153515660 | 153515661 | Frame_Shift_Ins | - | T | p.R818fs |
| OC314_OVARY | 153515607 | 153515703 | 153515660 | 153515661 | Frame_Shift_Ins | - | T | p.R818fs |
| RMGI_OVARY | 153532919 | 153533293 | 153533174 | 153533176 | In_Frame_Del | GCT | - | p.258_259AA>A |
| AN3CA_ENDOMETRIUM | 153532919 | 153533293 | 153533173 | 153533174 | In_Frame_Ins | - | GCT | p.259_259A>AA |
| CAL148_BREAST | 153515607 | 153515703 | 153515613 | 153515613 | Missense_Mutation | C | T | p.E834K |
| EWS502_BONE | 153515607 | 153515703 | 153515643 | 153515643 | Missense_Mutation | G | A | p.R824C |
| FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153515607 | 153515703 | 153515643 | 153515643 | Missense_Mutation | G | A | p.R824C |
| NCIH720_LUNG | 153515607 | 153515703 | 153515682 | 153515682 | Missense_Mutation | C | T | p.D811N |
| SKUT1_SOFT_TISSUE | 153525651 | 153525784 | 153525679 | 153525679 | Missense_Mutation | C | T | p.R579Q |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153525651 | 153525784 | 153525739 | 153525739 | Missense_Mutation | C | T | p.R559Q |
| RH28_SOFT_TISSUE | 153525651 | 153525784 | 153525740 | 153525740 | Missense_Mutation | G | C | p.R559G |
| JHUEM7_ENDOMETRIUM | 153525651 | 153525784 | 153525781 | 153525781 | Missense_Mutation | A | G | p.M545T |
| SW480_LARGE_INTESTINE | 153532919 | 153533293 | 153532940 | 153532940 | Missense_Mutation | G | C | p.S337C |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153532919 | 153533293 | 153532978 | 153532978 | Missense_Mutation | T | A | p.Q324H |
| HT55_LARGE_INTESTINE | 153532919 | 153533293 | 153532992 | 153532992 | Missense_Mutation | C | T | p.A320T |
| AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153532919 | 153533293 | 153532998 | 153532998 | Missense_Mutation | T | C | p.T318A |
| TC138_BONE | 153532919 | 153533293 | 153533024 | 153533024 | Missense_Mutation | G | C | p.T309S |
| NUGC3_STOMACH | 153532919 | 153533293 | 153533249 | 153533249 | Missense_Mutation | G | A | p.T234I |
| HCC1359_LUNG | 153532919 | 153533293 | 153533258 | 153533258 | Missense_Mutation | G | A | p.P231L |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 153535570 | 153535623 | 153535597 | 153535597 | Missense_Mutation | T | C | p.S202G |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153535570 | 153535623 | 153535597 | 153535597 | Missense_Mutation | T | C | p.S202G |
| OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153535570 | 153535623 | 153535597 | 153535597 | Missense_Mutation | T | C | p.S202G |
| S117_SOFT_TISSUE | 153535570 | 153535623 | 153535597 | 153535597 | Missense_Mutation | T | C | p.S202G |
| GP2D_LARGE_INTESTINE | 153547476 | 153547492 | 153547490 | 153547490 | Missense_Mutation | T | C | p.T111A |
| GP5D_LARGE_INTESTINE | 153547476 | 153547492 | 153547490 | 153547490 | Missense_Mutation | T | C | p.T111A |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRPF40A |
| 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 PRPF40A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PRPF40A |
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RelatedDrugs for PRPF40A |
| 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 PRPF40A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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