|
||||||
|
 | |
| |
| |
| |
| 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 CXXC1 |
 Gene summary |
| Gene information | Gene symbol | CXXC1 | Gene ID | 30827 |
| Gene name | CXXC finger protein 1 | |
| Synonyms | 2410002I16Rik|5830420C16Rik|CFP1|CGBP|HsT2645|PCCX1|PHF18|SPP1|ZCGPC1|hCGBP | |
| Cytomap | 18q21.1 | |
| Type of gene | protein-coding | |
| Description | CXXC-type zinc finger protein 1CXXC finger 1 (PHD domain)CpG binding proteinDNA-binding protein with PHD finger and CXXC domainPHD finger and CXXC domain-containing protein 1cpG-binding proteinzinc finger, CpG binding-type containing 1 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9P0U4 | |
| Context | PubMed: CXXC1 [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 |
| CXXC1 | GO:0006355 | regulation of transcription, DNA-templated | 10688657 |
| CXXC1 | GO:0045893 | positive regulation of transcription, DNA-templated | 10688657 |
| CXXC1 | GO:0051568 | histone H3-K4 methylation | 17355966 |
Top |
Exon skipping events across known transcript of Ensembl for CXXC1 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 CXXC1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CXXC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_299318 | 18 | 47809276:47809376:47809634:47809694:47809884:47809934 | 47809634:47809694 | ENSG00000154832.10 | ENST00000589940.1 |
| exon_skip_299319 | 18 | 47809276:47809376:47809634:47809731:47809884:47809934 | 47809634:47809731 | ENSG00000154832.10 | ENST00000590901.1,ENST00000412036.2,ENST00000285106.6,ENST00000586144.1 |
| exon_skip_299325 | 18 | 47809884:47809934:47810074:47810185:47810263:47810393 | 47810074:47810185 | ENSG00000154832.10 | ENST00000590901.1,ENST00000412036.2,ENST00000285106.6,ENST00000589940.1 |
| exon_skip_299326 | 18 | 47810798:47810932:47811089:47811209:47811371:47811413 | 47811089:47811209 | ENSG00000154832.10 | ENST00000412036.2,ENST00000591474.1 |
| exon_skip_299327 | 18 | 47810798:47810932:47811101:47811209:47811371:47811413 | 47811101:47811209 | ENSG00000154832.10 | ENST00000590901.1,ENST00000285106.6,ENST00000590234.1,ENST00000591190.1,ENST00000589940.1,ENST00000592078.1 |
| exon_skip_299328 | 18 | 47811101:47811209:47811371:47811617:47812118:47812298 | 47811371:47811617 | ENSG00000154832.10 | ENST00000591190.1 |
| exon_skip_299330 | 18 | 47811590:47811617:47811694:47811721:47812118:47812298 | 47811694:47811721 | ENSG00000154832.10 | ENST00000590901.1,ENST00000412036.2,ENST00000285106.6,ENST00000586837.1,ENST00000589940.1,ENST00000591474.1 |
| exon_skip_299331 | 18 | 47812118:47812298:47812391:47812627:47812908:47813009 | 47812391:47812627 | ENSG00000154832.10 | ENST00000412036.2,ENST00000285106.6,ENST00000589548.1,ENST00000586837.1,ENST00000589940.1 |
| exon_skip_299334 | 18 | 47813109:47813228:47813792:47813878:47813956:47814006 | 47813792:47813878 | ENSG00000154832.10 | ENST00000587396.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CXXC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_299318 | 18 | 47809276:47809376:47809634:47809694:47809884:47809934 | 47809634:47809694 | ENSG00000154832.10 | ENST00000589940.1 |
| exon_skip_299319 | 18 | 47809276:47809376:47809634:47809731:47809884:47809934 | 47809634:47809731 | ENSG00000154832.10 | ENST00000412036.2,ENST00000285106.6,ENST00000590901.1,ENST00000586144.1 |
| exon_skip_299325 | 18 | 47809884:47809934:47810074:47810185:47810263:47810393 | 47810074:47810185 | ENSG00000154832.10 | ENST00000412036.2,ENST00000285106.6,ENST00000589940.1,ENST00000590901.1 |
| exon_skip_299326 | 18 | 47810798:47810932:47811089:47811209:47811371:47811413 | 47811089:47811209 | ENSG00000154832.10 | ENST00000412036.2,ENST00000591474.1 |
| exon_skip_299327 | 18 | 47810798:47810932:47811101:47811209:47811371:47811413 | 47811101:47811209 | ENSG00000154832.10 | ENST00000285106.6,ENST00000589940.1,ENST00000590901.1,ENST00000590234.1,ENST00000591190.1,ENST00000592078.1 |
| exon_skip_299328 | 18 | 47811101:47811209:47811371:47811617:47812118:47812298 | 47811371:47811617 | ENSG00000154832.10 | ENST00000591190.1 |
| exon_skip_299330 | 18 | 47811590:47811617:47811694:47811721:47812118:47812298 | 47811694:47811721 | ENSG00000154832.10 | ENST00000412036.2,ENST00000285106.6,ENST00000589940.1,ENST00000590901.1,ENST00000591474.1,ENST00000586837.1 |
| exon_skip_299331 | 18 | 47812118:47812298:47812391:47812627:47812908:47813009 | 47812391:47812627 | ENSG00000154832.10 | ENST00000412036.2,ENST00000285106.6,ENST00000589940.1,ENST00000589548.1,ENST00000586837.1 |
| exon_skip_299334 | 18 | 47813109:47813228:47813792:47813878:47813956:47814006 | 47813792:47813878 | ENSG00000154832.10 | ENST00000587396.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CXXC1 |
| 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 |
| ENST00000285106 | 47809634 | 47809731 | Frame-shift |
| ENST00000285106 | 47812391 | 47812627 | Frame-shift |
| ENST00000285106 | 47810074 | 47810185 | In-frame |
| ENST00000285106 | 47811101 | 47811209 | In-frame |
| ENST00000285106 | 47811694 | 47811721 | 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 |
| ENST00000285106 | 47809634 | 47809731 | Frame-shift |
| ENST00000285106 | 47812391 | 47812627 | Frame-shift |
| ENST00000285106 | 47810074 | 47810185 | In-frame |
| ENST00000285106 | 47811101 | 47811209 | In-frame |
| ENST00000285106 | 47811694 | 47811721 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for CXXC1 |
| 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 |
| ENST00000285106 | 2953 | 656 | 47811101 | 47811209 | 1628 | 1735 | 304 | 340 |
| ENST00000285106 | 2953 | 656 | 47810074 | 47810185 | 2129 | 2239 | 471 | 508 |
| 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 |
| ENST00000285106 | 2953 | 656 | 47811101 | 47811209 | 1628 | 1735 | 304 | 340 |
| ENST00000285106 | 2953 | 656 | 47810074 | 47810185 | 2129 | 2239 | 471 | 508 |
| 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 |
| Q9P0U4 | 304 | 340 | 340 | 340 | Alternative sequence | ID=VSP_040132;Note=In isoform 2. K->KVMER;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9P0U4 | 304 | 340 | 1 | 656 | Chain | ID=PRO_0000079743;Note=CXXC-type zinc finger protein 1 |
| Q9P0U4 | 304 | 340 | 256 | 317 | Compositional bias | Note=Asp/Glu-rich (acidic) |
| Q9P0U4 | 304 | 340 | 321 | 359 | Compositional bias | Note=Arg/Lys-rich (basic) |
| Q9P0U4 | 471 | 508 | 1 | 656 | Chain | ID=PRO_0000079743;Note=CXXC-type zinc finger protein 1 |
| Q9P0U4 | 471 | 508 | 422 | 474 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9P0U4 | 304 | 340 | 340 | 340 | Alternative sequence | ID=VSP_040132;Note=In isoform 2. K->KVMER;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9P0U4 | 304 | 340 | 1 | 656 | Chain | ID=PRO_0000079743;Note=CXXC-type zinc finger protein 1 |
| Q9P0U4 | 304 | 340 | 256 | 317 | Compositional bias | Note=Asp/Glu-rich (acidic) |
| Q9P0U4 | 304 | 340 | 321 | 359 | Compositional bias | Note=Arg/Lys-rich (basic) |
| Q9P0U4 | 471 | 508 | 1 | 656 | Chain | ID=PRO_0000079743;Note=CXXC-type zinc finger protein 1 |
| Q9P0U4 | 471 | 508 | 422 | 474 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for CXXC1 |
| - 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-A1EG-01 | exon_skip_299328 | 47811372 | 47811617 | 47811506 | 47811506 | Frame_Shift_Del | C | - | p.A260fs |
| BLCA | TCGA-GC-A3RC-01 | exon_skip_299331 | 47812392 | 47812627 | 47812527 | 47812533 | Frame_Shift_Del | CCCTCCA | - | p.G106fs |
| BLCA | TCGA-GC-A3RC-01 | exon_skip_299331 | 47812392 | 47812627 | 47812527 | 47812533 | Frame_Shift_Del | CCCTCCA | - | p.GGG106fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_299331 | 47812392 | 47812627 | 47812544 | 47812544 | Frame_Shift_Del | G | - | p.R103fs |
| CESC | TCGA-LP-A7HU-01 | exon_skip_299325 | 47810075 | 47810185 | 47810186 | 47810186 | Splice_Site | C | G | e11-1 |
| LUAD | TCGA-64-1678-01 | exon_skip_299325 | 47810075 | 47810185 | 47810186 | 47810186 | Splice_Site | C | T | p.S472_splice |
| UCS | TCGA-N7-A4Y0-01 | exon_skip_299330 | 47811695 | 47811721 | 47811722 | 47811722 | Splice_Site | C | A | . |
| - 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 |
| NCIH2347_LUNG | 47809635 | 47809694 | 47809655 | 47809655 | Missense_Mutation | C | T | p.E551K |
| NCIH2347_LUNG | 47809635 | 47809731 | 47809655 | 47809655 | Missense_Mutation | C | T | p.E551K |
| SNU1040_LARGE_INTESTINE | 47809635 | 47809731 | 47809723 | 47809723 | Missense_Mutation | C | T | p.R528Q |
| EFO21_OVARY | 47810075 | 47810185 | 47810086 | 47810086 | Missense_Mutation | A | C | p.C505G |
| SF172_CENTRAL_NERVOUS_SYSTEM | 47810075 | 47810185 | 47810130 | 47810130 | Missense_Mutation | C | A | p.G490V |
| BB49HNC_UPPER_AERODIGESTIVE_TRACT | 47810075 | 47810185 | 47810179 | 47810179 | Missense_Mutation | C | T | p.E474K |
| SKMEL24_SKIN | 47811102 | 47811209 | 47811160 | 47811160 | Missense_Mutation | C | T | p.R321Q |
| SKMEL24_SKIN | 47811090 | 47811209 | 47811160 | 47811160 | Missense_Mutation | C | T | p.R321Q |
| SNU175_LARGE_INTESTINE | 47811372 | 47811617 | 47811397 | 47811397 | Missense_Mutation | G | A | p.A296V |
| CAL148_BREAST | 47811372 | 47811617 | 47811419 | 47811419 | Missense_Mutation | C | T | p.D289N |
| SNU201_CENTRAL_NERVOUS_SYSTEM | 47811372 | 47811617 | 47811431 | 47811431 | Missense_Mutation | G | A | p.P285S |
| LS513_LARGE_INTESTINE | 47811372 | 47811617 | 47811466 | 47811466 | Missense_Mutation | G | T | p.T273K |
| BCPAP_THYROID | 47811372 | 47811617 | 47811473 | 47811473 | Missense_Mutation | C | T | p.E271K |
| GIMEN_AUTONOMIC_GANGLIA | 47811372 | 47811617 | 47811538 | 47811538 | Missense_Mutation | T | A | p.Q249L |
| MEWO_SKIN | 47812392 | 47812627 | 47812438 | 47812438 | Missense_Mutation | G | A | p.S138L |
| TTC466_BONE | 47812392 | 47812627 | 47812453 | 47812453 | Missense_Mutation | G | A | p.A133V |
| SNU175_LARGE_INTESTINE | 47812392 | 47812627 | 47812526 | 47812526 | Missense_Mutation | G | A | p.R109C |
| LOVO_LARGE_INTESTINE | 47812392 | 47812627 | 47812562 | 47812562 | Missense_Mutation | G | A | p.R97W |
| MEWO_SKIN | 47812392 | 47812627 | 47812604 | 47812604 | Missense_Mutation | G | A | p.R83C |
| HUCCT1_BILIARY_TRACT | 47811372 | 47811617 | 47811371 | 47811375 | Splice_Site | CCAGG | - | p.LA304fs |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CXXC1 |
| 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 CXXC1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CXXC1 |
Top |
RelatedDrugs for CXXC1 |
| 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 CXXC1 |
| 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)
|