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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 PCIF1 |
 Gene summary |
| Gene information | Gene symbol | PCIF1 | Gene ID | 63935 |
| Gene name | PDX1 C-terminal inhibiting factor 1 | |
| Synonyms | C20orf67|PPP1R121 | |
| Cytomap | 20q13.12 | |
| Type of gene | protein-coding | |
| Description | phosphorylated CTD-interacting factor 1PDX-1 C terminus-interacting factor 1protein phosphatase 1, regulatory subunit 121 | |
| Modification date | 20180519 | |
| UniProtAcc | Q9H4Z3 | |
| Context | PubMed: PCIF1 [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 |
| PCIF1 | GO:0010923 | negative regulation of phosphatase activity | 19389623 |
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Exon skipping events across known transcript of Ensembl for PCIF1 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 PCIF1 |
| 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 PCIF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_352672 | 20 | 44567619:44567762:44567853:44567978:44569113:44569251 | 44567853:44567978 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352676 | 20 | 44567853:44567978:44569113:44569251:44569447:44569578 | 44569113:44569251 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352677 | 20 | 44571735:44571883:44571978:44572062:44572304:44572404 | 44571978:44572062 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352678 | 20 | 44571978:44572062:44572304:44572404:44573506:44573669 | 44572304:44572404 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352683 | 20 | 44573645:44573669:44574349:44574522:44574667:44574754 | 44574349:44574522 | ENSG00000100982.7 | ENST00000372409.3,ENST00000479348.1 |
| exon_skip_352689 | 20 | 44574687:44574754:44574838:44575023:44575711:44575805 | 44574838:44575023 | ENSG00000100982.7 | ENST00000372409.3,ENST00000479348.1 |
| exon_skip_352697 | 20 | 44574838:44575023:44575711:44575805:44575901:44576077 | 44575711:44575805 | ENSG00000100982.7 | ENST00000372409.3,ENST00000479348.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PCIF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_352672 | 20 | 44567619:44567762:44567853:44567978:44569113:44569251 | 44567853:44567978 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352676 | 20 | 44567853:44567978:44569113:44569251:44569447:44569578 | 44569113:44569251 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352677 | 20 | 44571735:44571883:44571978:44572062:44572304:44572404 | 44571978:44572062 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352678 | 20 | 44571978:44572062:44572304:44572404:44573506:44573669 | 44572304:44572404 | ENSG00000100982.7 | ENST00000372409.3 |
| exon_skip_352683 | 20 | 44573645:44573669:44574349:44574522:44574667:44574754 | 44574349:44574522 | ENSG00000100982.7 | ENST00000372409.3,ENST00000479348.1 |
| exon_skip_352689 | 20 | 44574687:44574754:44574838:44575023:44575711:44575805 | 44574838:44575023 | ENSG00000100982.7 | ENST00000372409.3,ENST00000479348.1 |
| exon_skip_352697 | 20 | 44574838:44575023:44575711:44575805:44575901:44576077 | 44575711:44575805 | ENSG00000100982.7 | ENST00000372409.3,ENST00000479348.1 |
| 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 PCIF1 |
| 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 |
| ENST00000372409 | 44567853 | 44567978 | Frame-shift |
| ENST00000372409 | 44572304 | 44572404 | Frame-shift |
| ENST00000372409 | 44574349 | 44574522 | Frame-shift |
| ENST00000372409 | 44574838 | 44575023 | Frame-shift |
| ENST00000372409 | 44575711 | 44575805 | Frame-shift |
| ENST00000372409 | 44569113 | 44569251 | In-frame |
| ENST00000372409 | 44571978 | 44572062 | 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 |
| ENST00000372409 | 44567853 | 44567978 | Frame-shift |
| ENST00000372409 | 44572304 | 44572404 | Frame-shift |
| ENST00000372409 | 44574349 | 44574522 | Frame-shift |
| ENST00000372409 | 44574838 | 44575023 | Frame-shift |
| ENST00000372409 | 44575711 | 44575805 | Frame-shift |
| ENST00000372409 | 44569113 | 44569251 | In-frame |
| ENST00000372409 | 44571978 | 44572062 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PCIF1 |
| 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 |
| ENST00000372409 | 2764 | 704 | 44569113 | 44569251 | 614 | 751 | 83 | 129 |
| ENST00000372409 | 2764 | 704 | 44571978 | 44572062 | 1186 | 1269 | 274 | 301 |
| 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 |
| ENST00000372409 | 2764 | 704 | 44569113 | 44569251 | 614 | 751 | 83 | 129 |
| ENST00000372409 | 2764 | 704 | 44571978 | 44572062 | 1186 | 1269 | 274 | 301 |
| 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 |
| Q9H4Z3 | 83 | 129 | 1 | 704 | Chain | ID=PRO_0000076087;Note=Phosphorylated CTD-interacting factor 1 |
| Q9H4Z3 | 83 | 129 | 116 | 116 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:21406692,PMID:23186163 |
| Q9H4Z3 | 83 | 129 | 109 | 113 | Motif | Note=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H4Z3 | 274 | 301 | 1 | 704 | Chain | ID=PRO_0000076087;Note=Phosphorylated CTD-interacting factor 1 |
| 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 |
| Q9H4Z3 | 83 | 129 | 1 | 704 | Chain | ID=PRO_0000076087;Note=Phosphorylated CTD-interacting factor 1 |
| Q9H4Z3 | 83 | 129 | 116 | 116 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:21406692,PMID:23186163 |
| Q9H4Z3 | 83 | 129 | 109 | 113 | Motif | Note=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9H4Z3 | 274 | 301 | 1 | 704 | Chain | ID=PRO_0000076087;Note=Phosphorylated CTD-interacting factor 1 |
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SNVs in the skipped exons for PCIF1 |
| - 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-G3-A3CJ-01 | exon_skip_352678 | 44572305 | 44572404 | 44572313 | 44572313 | Frame_Shift_Del | C | - | p.S305fs |
| STAD | TCGA-CD-A4MJ-01 | exon_skip_352683 | 44574350 | 44574522 | 44574482 | 44574483 | Frame_Shift_Del | GA | - | p.434_434del |
| KIRC | TCGA-CZ-4853-01 | exon_skip_352689 | 44574839 | 44575023 | 44575022 | 44575022 | Frame_Shift_Del | G | - | p.R537fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_352697 | 44575712 | 44575805 | 44575746 | 44575746 | Frame_Shift_Del | T | - | p.F550fs |
| COAD | TCGA-AA-3516-01 | exon_skip_352689 | 44574839 | 44575023 | 44574917 | 44574917 | Nonsense_Mutation | C | T | p.R503X |
| - 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 |
| SKMEL30_SKIN | 44567854 | 44567978 | 44567893 | 44567893 | Missense_Mutation | G | A | p.R55Q |
| SKMEL30_SKIN | 44567854 | 44567978 | 44567893 | 44567894 | Missense_Mutation | GG | AC | p.R55H |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44567854 | 44567978 | 44567902 | 44567903 | Missense_Mutation | AT | GC | p.N58S |
| DBTRG05MG_CENTRAL_NERVOUS_SYSTEM | 44567854 | 44567978 | 44567952 | 44567952 | Missense_Mutation | C | T | p.P75S |
| NCIBL2171_MATCHED_NORMAL_TISSUE | 44569114 | 44569251 | 44569136 | 44569136 | Missense_Mutation | C | T | p.A91V |
| NCIH630_LARGE_INTESTINE | 44569114 | 44569251 | 44569155 | 44569155 | Missense_Mutation | C | G | p.D97E |
| LIM1215_LARGE_INTESTINE | 44569114 | 44569251 | 44569171 | 44569171 | Missense_Mutation | A | G | p.T103A |
| HEC59_ENDOMETRIUM | 44569114 | 44569251 | 44569180 | 44569180 | Missense_Mutation | G | A | p.A106T |
| HEC59_ENDOMETRIUM | 44572305 | 44572404 | 44572307 | 44572307 | Missense_Mutation | G | A | p.S303N |
| SNU175_LARGE_INTESTINE | 44574350 | 44574522 | 44574388 | 44574388 | Missense_Mutation | T | C | p.Y403H |
| JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 44574350 | 44574522 | 44574404 | 44574404 | Missense_Mutation | G | A | p.R408Q |
| DV90_LUNG | 44574839 | 44575023 | 44574956 | 44574956 | Missense_Mutation | C | A | p.L516I |
| SNGM_ENDOMETRIUM | 44574839 | 44575023 | 44574965 | 44574965 | Missense_Mutation | T | C | p.Y519H |
| HCT15_LARGE_INTESTINE | 44574839 | 44575023 | 44574977 | 44574977 | Missense_Mutation | T | C | p.Y523H |
| T24_URINARY_TRACT | 44575712 | 44575805 | 44575753 | 44575753 | Missense_Mutation | C | G | p.A552G |
| SLR20_KIDNEY | 44575712 | 44575805 | 44575753 | 44575753 | Missense_Mutation | C | G | p.A552G |
| SKUT1_SOFT_TISSUE | 44575712 | 44575805 | 44575756 | 44575756 | Missense_Mutation | A | G | p.N553S |
| NCIH2882_LUNG | 44572305 | 44572404 | 44572393 | 44572393 | Nonsense_Mutation | G | T | p.E332* |
| CP50EBV_MATCHED_NORMAL_TISSUE | 44574839 | 44575023 | 44574839 | 44574839 | Splice_Site | A | T | p.M477L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PCIF1 |
| 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 PCIF1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PCIF1 |
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RelatedDrugs for PCIF1 |
| 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 PCIF1 |
| 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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