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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for GCFC2 |
 Gene summary |
| Gene information | Gene symbol | GCFC2 | Gene ID | 6936 |
| Gene name | GC-rich sequence DNA-binding factor 2 | |
| Synonyms | C2orf3|DNABF|GCF|TCF9 | |
| Cytomap | 2p12 | |
| Type of gene | protein-coding | |
| Description | GC-rich sequence DNA-binding factor 2GC binding factorGC bindng factorTCF-9transcription factor 9 (binds GC-rich sequences) | |
| Modification date | 20200320 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| GCFC2 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 9705290 |
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Gene structures and expression levels for GCFC2 |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000005436
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000442309.5 | GCFC2-204:protein_coding:GCFC2 | 3.169636e+00 | 1.231421e+00 | 1.286180e-05 | 1.302804e-04 |
| CB | DOWN | ENST00000492826.1 | GCFC2-210:protein_coding:GCFC2 | 4.627935e+00 | -1.227063e+00 | 1.456265e-02 | 4.710709e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GCFC2 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_10461 | chr2 | 75694241:75694427:75696200:75696315:75701190:75701287 | 75696200:75696315 |
| exon_skip_164098 | chr2 | 75690638:75690719:75691977:75692100:75694241:75694427 | 75691977:75692100 |
| exon_skip_168442 | chr2 | 75689969:75690081:75690638:75690719:75694241:75694427 | 75690638:75690719 |
| exon_skip_169939 | chr2 | 75687827:75687977:75689026:75689225:75689969:75690081 | 75689026:75689225 |
| exon_skip_174229 | chr2 | 75701190:75701287:75702313:75702423:75706523:75706644 | 75702313:75702423 |
| exon_skip_197601 | chr2 | 75665929:75666053:75670138:75670284:75671950:75672016 | 75670138:75670284 |
| exon_skip_215303 | chr2 | 75701190:75701287:75702313:75702423:75706523:75706651 | 75702313:75702423 |
| exon_skip_224536 | chr2 | 75673444:75673520:75680193:75680314:75687827:75687892 | 75680193:75680314 |
| exon_skip_244392 | chr2 | 75664645:75664783:75665929:75666053:75670138:75670214 | 75665929:75666053 |
| exon_skip_282698 | chr2 | 75671950:75672016:75673444:75673520:75680193:75680314 | 75673444:75673520 |
| exon_skip_29094 | chr2 | 75671950:75672016:75673444:75673520:75687827:75687892 | 75673444:75673520 |
| exon_skip_41823 | chr2 | 75701190:75701287:75702199:75702423:75706523:75706644 | 75702199:75702423 |
| exon_skip_5016 | chr2 | 75696252:75696315:75701190:75701287:75706523:75706651 | 75701190:75701287 |
| exon_skip_61857 | chr2 | 75664418:75664783:75665929:75666053:75670138:75670214 | 75665929:75666053 |
| exon_skip_81271 | chr2 | 75701190:75701287:75702199:75702423:75706523:75706651 | 75702199:75702423 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_224536 | Mayo_CB | 4.882927e-01 | 5.890789e-01 | -1.007863e-01 | 1.589640e-05 |
| exon_skip_164098 | Mayo_TC | 2.306757e-01 | 3.646774e-01 | -1.340017e-01 | 2.431295e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for GCFC2 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000321027 | 75665929 | 75666053 | Frame-shift |
| ENST00000321027 | 75673444 | 75673520 | Frame-shift |
| ENST00000321027 | 75680193 | 75680314 | Frame-shift |
| ENST00000321027 | 75689026 | 75689225 | Frame-shift |
| ENST00000321027 | 75691977 | 75692100 | Frame-shift |
| ENST00000321027 | 75696200 | 75696315 | Frame-shift |
| ENST00000321027 | 75670138 | 75670284 | In-frame |
| ENST00000321027 | 75702199 | 75702423 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000321027 | 75673444 | 75673520 | Frame-shift |
| ENST00000321027 | 75680193 | 75680314 | Frame-shift |
| ENST00000321027 | 75689026 | 75689225 | Frame-shift |
| ENST00000321027 | 75691977 | 75692100 | Frame-shift |
| ENST00000321027 | 75702199 | 75702423 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000321027 | 75665929 | 75666053 | Frame-shift |
| ENST00000321027 | 75673444 | 75673520 | Frame-shift |
| ENST00000321027 | 75680193 | 75680314 | Frame-shift |
| ENST00000321027 | 75689026 | 75689225 | Frame-shift |
| ENST00000321027 | 75691977 | 75692100 | Frame-shift |
| ENST00000321027 | 75696200 | 75696315 | Frame-shift |
| ENST00000321027 | 75702199 | 75702423 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GCFC2 |
p-ENSG00000005436_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000321027 | 4457 | 781 | 75702199 | 75702423 | 529 | 752 | 131 | 206 |
| ENST00000321027 | 4457 | 781 | 75670138 | 75670284 | 2091 | 2236 | 652 | 700 |
| Loci of skipped exons in MSBB 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 |
| ENST00000321027 | 4457 | 781 | 75702199 | 75702423 | 529 | 752 | 131 | 206 |
| Loci of skipped exons in Mayo 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 |
| ENST00000321027 | 4457 | 781 | 75702199 | 75702423 | 529 | 752 | 131 | 206 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| P16383 | 131 | 206 | 169 | 207 | Alternative sequence | ID=VSP_021798;Note=In isoform 2. GMKRESEDDPESEPDDHEKRIPFTLRPQTLRQRMAEESI->V;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:2556218;Dbxref=PMID:2556218 |
| P16383 | 131 | 206 | 1 | 781 | Chain | ID=PRO_0000087441;Note=GC-rich sequence DNA-binding factor 2 |
| P16383 | 131 | 206 | 174 | 174 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P16383 | 131 | 206 | 180 | 180 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P16383 | 652 | 700 | 214 | 779 | Alternative sequence | ID=VSP_054363;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17309879;Dbxref=PMID:17309879 |
| P16383 | 652 | 700 | 255 | 781 | Alternative sequence | ID=VSP_057399;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17309879;Dbxref=PMID:17309879 |
| P16383 | 652 | 700 | 1 | 781 | Chain | ID=PRO_0000087441;Note=GC-rich sequence DNA-binding factor 2 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| P16383 | 131 | 206 | 169 | 207 | Alternative sequence | ID=VSP_021798;Note=In isoform 2. GMKRESEDDPESEPDDHEKRIPFTLRPQTLRQRMAEESI->V;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:2556218;Dbxref=PMID:2556218 |
| P16383 | 131 | 206 | 1 | 781 | Chain | ID=PRO_0000087441;Note=GC-rich sequence DNA-binding factor 2 |
| P16383 | 131 | 206 | 174 | 174 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P16383 | 131 | 206 | 180 | 180 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| P16383 | 131 | 206 | 169 | 207 | Alternative sequence | ID=VSP_021798;Note=In isoform 2. GMKRESEDDPESEPDDHEKRIPFTLRPQTLRQRMAEESI->V;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:2556218;Dbxref=PMID:2556218 |
| P16383 | 131 | 206 | 1 | 781 | Chain | ID=PRO_0000087441;Note=GC-rich sequence DNA-binding factor 2 |
| P16383 | 131 | 206 | 174 | 174 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P16383 | 131 | 206 | 180 | 180 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
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3'-UTR located exon skipping events that lost miRNA binding sites in GCFC2 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for GCFC2 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for GCFC2 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GCFC2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_81271 | rs1990145 | chr2:75650524 | 3.037976e-05 | 6.487697e-03 |
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Correlation with RNA binding proteins (RBPs) for GCFC2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | CNOT4 | exon_skip_224536 | -4.002172e-01 | 1.887000e-07 |
| CB | TRA2A | exon_skip_224536 | -4.731448e-01 | 3.433123e-10 |
| CB | NUP42 | exon_skip_224536 | 4.106475e-01 | 8.365225e-08 |
| CB | RBM3 | exon_skip_164098 | 5.906766e-01 | 1.776099e-15 |
| CB | NUP42 | exon_skip_164098 | 4.800957e-01 | 5.073865e-10 |
| TC | RBM3 | exon_skip_164098 | 7.373218e-01 | 1.382503e-24 |
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RelatedDrugs for GCFC2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for GCFC2 |
| 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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