|
||||||
|
 | |
| |
| |
| |
| 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 CTDP1 |
 Gene summary |
| Gene information | Gene symbol | CTDP1 | Gene ID | 9150 |
| Gene name | CTD phosphatase subunit 1 | |
| Synonyms | CCFDN|FCP1 | |
| Cytomap | 18q23 | |
| Type of gene | protein-coding | |
| Description | RNA polymerase II subunit A C-terminal domain phosphataseCTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1CTD of POLR2A, phosphatase of, subunit 1TFIIF-associating CTD phosphatase 1serine phosphatase FCP1atranscri | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y5B0 | |
| Context | PubMed: CTDP1 [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 |
| CTDP1 | GO:0006470 | protein dephosphorylation | 9765293|22692537 |
| CTDP1 | GO:0043923 | positive regulation by host of viral transcription | 15723517 |
Top |
Exon skipping events across known transcript of Ensembl for CTDP1 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 CTDP1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CTDP1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_297563 | 18 | 77457859:77457988:77464766:77464917:77470345:77470436 | 77464766:77464917 | ENSG00000060069.12 | ENST00000075430.7,ENST00000299543.7,ENST00000591598.1 |
| exon_skip_297564 | 18 | 77464766:77464917:77470345:77470436:77472971:77473138 | 77470345:77470436 | ENSG00000060069.12 | ENST00000075430.7,ENST00000299543.7,ENST00000591598.1 |
| exon_skip_297567 | 18 | 77474490:77475528:77477534:77477676:77477809:77478016 | 77477534:77477676 | ENSG00000060069.12 | ENST00000075430.7,ENST00000299543.7,ENST00000591598.1 |
| exon_skip_297574 | 18 | 77477809:77478016:77488906:77489069:77496354:77496521 | 77488906:77489069 | ENSG00000060069.12 | ENST00000299543.7 |
| exon_skip_297575 | 18 | 77477809:77478016:77488906:77489069:77513651:77514501 | 77488906:77489069 | ENSG00000060069.12 | ENST00000591598.1 |
| exon_skip_297576 | 18 | 77477809:77478016:77496354:77496521:77513651:77514501 | 77496354:77496521 | ENSG00000060069.12 | ENST00000075430.7 |
| exon_skip_297582 | 18 | 77488906:77489069:77496354:77496521:77513651:77514501 | 77496354:77496521 | ENSG00000060069.12 | ENST00000299543.7 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CTDP1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_297563 | 18 | 77457859:77457988:77464766:77464917:77470345:77470436 | 77464766:77464917 | ENSG00000060069.12 | ENST00000299543.7,ENST00000075430.7,ENST00000591598.1 |
| exon_skip_297564 | 18 | 77464766:77464917:77470345:77470436:77472971:77473138 | 77470345:77470436 | ENSG00000060069.12 | ENST00000299543.7,ENST00000075430.7,ENST00000591598.1 |
| exon_skip_297567 | 18 | 77474490:77475528:77477534:77477676:77477809:77478016 | 77477534:77477676 | ENSG00000060069.12 | ENST00000299543.7,ENST00000075430.7,ENST00000591598.1 |
| exon_skip_297574 | 18 | 77477809:77478016:77488906:77489069:77496354:77496521 | 77488906:77489069 | ENSG00000060069.12 | ENST00000299543.7 |
| exon_skip_297575 | 18 | 77477809:77478016:77488906:77489069:77513651:77514501 | 77488906:77489069 | ENSG00000060069.12 | ENST00000591598.1 |
| exon_skip_297576 | 18 | 77477809:77478016:77496354:77496521:77513651:77514501 | 77496354:77496521 | ENSG00000060069.12 | ENST00000075430.7 |
| exon_skip_297582 | 18 | 77488906:77489069:77496354:77496521:77513651:77514501 | 77496354:77496521 | ENSG00000060069.12 | ENST00000299543.7 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CTDP1 |
| 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 |
Top |
Infer the effects of exon skipping event on protein functional features for CTDP1 |
| 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 |
| 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 |
Top |
SNVs in the skipped exons for CTDP1 |
| - 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-A39Y-01 | exon_skip_297564 | 77470346 | 77470436 | 77470348 | 77470348 | Frame_Shift_Del | T | - | p.F259fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_297564 | 77470346 | 77470436 | 77470348 | 77470348 | Frame_Shift_Del | T | - | p.F259fs |
| STAD | TCGA-B7-5816-01 | exon_skip_297564 | 77470346 | 77470436 | 77470348 | 77470348 | Frame_Shift_Del | T | - | p.G258fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_297564 | 77470346 | 77470436 | 77470370 | 77470370 | Frame_Shift_Del | T | - | p.L266fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_297564 | 77470346 | 77470436 | 77470370 | 77470370 | Frame_Shift_Del | T | - | p.L266fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_297564 | 77470346 | 77470436 | 77470370 | 77470370 | Frame_Shift_Del | T | - | p.L266fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_297564 | 77470346 | 77470436 | 77470370 | 77470370 | Frame_Shift_Del | T | - | p.L266fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_297564 | 77470346 | 77470436 | 77470369 | 77470370 | Frame_Shift_Ins | - | T | p.F266fs |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_297564 | 77470346 | 77470436 | 77470369 | 77470370 | Frame_Shift_Ins | - | T | p.F266fs |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_297564 | 77470346 | 77470436 | 77470369 | 77470370 | Frame_Shift_Ins | - | T | p.L266fs |
| SKCM | TCGA-ER-A194-01 | exon_skip_297575 exon_skip_297574 | 77488907 | 77489069 | 77488959 | 77488959 | Nonsense_Mutation | C | T | p.Q824* |
| SKCM | TCGA-ER-A194-01 | exon_skip_297575 exon_skip_297574 | 77488907 | 77489069 | 77488959 | 77488959 | Nonsense_Mutation | C | T | p.Q824X |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_297582 exon_skip_297576 | 77496355 | 77496521 | 77496373 | 77496373 | Nonsense_Mutation | G | T | p.E867* |
| ESCA | TCGA-L5-A4OI-01 | exon_skip_297582 exon_skip_297576 | 77496355 | 77496521 | 77496373 | 77496373 | Nonsense_Mutation | G | T | p.E867X |
| ESCA | TCGA-LN-A49X-01 | exon_skip_297582 exon_skip_297576 | 77496355 | 77496521 | 77496418 | 77496418 | Nonsense_Mutation | C | T | p.Q882* |
| ESCA | TCGA-LN-A49X-01 | exon_skip_297582 exon_skip_297576 | 77496355 | 77496521 | 77496418 | 77496418 | Nonsense_Mutation | C | T | p.Q882X |
| LUSC | TCGA-33-4586-01 | exon_skip_297564 | 77470346 | 77470436 | 77470345 | 77470345 | Splice_Site | G | T | p.G258_splice |
| KIRC | TCGA-3Z-A93Z-01 | exon_skip_297567 | 77477535 | 77477676 | 77477534 | 77477534 | Splice_Site | G | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-ER-A194-01 |
| Cancer type: SKCM | |
| ESID: exon_skip_297574 | |
| Skipped exon start: 77488907 | |
| Skipped exon end: 77489069 | |
| Mutation start: 77488959 | |
| Mutation end: 77488959 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: p.Q824X | |
| Sample: TCGA-ER-A194-01 |
| Cancer type: SKCM | |
| ESID: exon_skip_297574 | |
| Skipped exon start: 77488907 | |
| Skipped exon end: 77489069 | |
| Mutation start: 77488959 | |
| Mutation end: 77488959 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: p.Q824* | |
exon_skip_293285_SKCM_TCGA-ER-A194-01.png | |
exon_skip_297574_SKCM_TCGA-ER-A194-01.png | |
exon_skip_297575_SKCM_TCGA-ER-A194-01.png | |
exon_skip_385517_SKCM_TCGA-ER-A194-01.png | |
 | Sample: TCGA-ER-A194-01 |
| Cancer type: SKCM | |
| ESID: exon_skip_297574 | |
| Skipped exon start: 77488907 | |
| Skipped exon end: 77489069 | |
| Mutation start: 77488959 | |
| Mutation end: 77488959 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: p.Q824X | |
| Sample: TCGA-ER-A194-01 |
| Cancer type: SKCM | |
| ESID: exon_skip_297574 | |
| Skipped exon start: 77488907 | |
| Skipped exon end: 77489069 | |
| Mutation start: 77488959 | |
| Mutation end: 77488959 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: T | |
| AAchange: p.Q824* | |
| exon_skip_293285_SKCM_TCGA-ER-A194-01.png | |
| exon_skip_297574_SKCM_TCGA-ER-A194-01.png | |
| exon_skip_297575_SKCM_TCGA-ER-A194-01.png | |
| exon_skip_385517_SKCM_TCGA-ER-A194-01.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 |
| SCH_STOMACH | 77464767 | 77464917 | 77464854 | 77464854 | Missense_Mutation | G | A | p.A237T |
| SNU1040_LARGE_INTESTINE | 77464767 | 77464917 | 77464857 | 77464857 | Missense_Mutation | A | G | p.K238E |
| RI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 77464767 | 77464917 | 77464875 | 77464875 | Missense_Mutation | G | A | p.V244I |
| CHAGOK1_LUNG | 77464767 | 77464917 | 77464908 | 77464908 | Missense_Mutation | A | G | p.T255A |
| EMCBAC2_LUNG | 77464767 | 77464917 | 77464908 | 77464908 | Missense_Mutation | A | C | p.T255P |
| IPC298_SKIN | 77464767 | 77464917 | 77464908 | 77464908 | Missense_Mutation | A | C | p.T255P |
| FTC238_THYROID | 77464767 | 77464917 | 77464909 | 77464909 | Missense_Mutation | C | T | p.T255I |
| SKMEL5_SKIN | 77464767 | 77464917 | 77464914 | 77464914 | Missense_Mutation | G | A | p.A257T |
| NCIH513_PLEURA | 77477535 | 77477676 | 77477554 | 77477554 | Missense_Mutation | G | T | p.Q696H |
| SNUC4_LARGE_INTESTINE | 77477535 | 77477676 | 77477567 | 77477567 | Missense_Mutation | G | A | p.G701R |
| CW2_LARGE_INTESTINE | 77488907 | 77489069 | 77488915 | 77488915 | Missense_Mutation | C | T | p.P809L |
| SKOV3_OVARY | 77488907 | 77489069 | 77488935 | 77488935 | Missense_Mutation | T | C | p.F816L |
| KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 77488907 | 77489069 | 77488945 | 77488945 | Missense_Mutation | A | C | p.E819A |
| LCLC97TM1_LUNG | 77488907 | 77489069 | 77489056 | 77489056 | Missense_Mutation | G | C | p.S856T |
| TTC549_SOFT_TISSUE | 77488907 | 77489069 | 77489064 | 77489064 | Missense_Mutation | A | G | p.K859E |
| L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 77496355 | 77496521 | 77496412 | 77496412 | Missense_Mutation | G | A | p.E880K |
| 639V_URINARY_TRACT | 77496355 | 77496521 | 77496464 | 77496464 | Missense_Mutation | G | A | p.R897Q |
| HCC2450_LUNG | 77470346 | 77470436 | 77470360 | 77470360 | Nonsense_Mutation | G | T | p.E263* |
| KYSE410_OESOPHAGUS | 77496355 | 77496521 | 77496418 | 77496418 | Nonsense_Mutation | C | T | p.Q882* |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 77464767 | 77464917 | 77464768 | 77464768 | Splice_Site | G | A | p.G208D |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CTDP1 |
| 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 CTDP1 |
 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CTDP1 |
Top |
RelatedDrugs for CTDP1 |
| 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 CTDP1 |
| 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)
|