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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 GTF2H2 |
 Gene summary |
| Gene information | Gene symbol | GTF2H2 | Gene ID | 2966 |
| Gene name | general transcription factor IIH subunit 2 | |
| Synonyms | BTF2|BTF2P44|T-BTF2P44|TFIIH|p44 | |
| Cytomap | 5q13.2 | |
| Type of gene | protein-coding | |
| Description | general transcription factor IIH subunit 2BTF2 p44TFIIH basal transcription factor complex p44 subunitbasic transcription factor 2 44 kDa subunitgeneral transcription factor IIH polypeptide 2general transcription factor IIH, polypeptide 2, 44kD subun | |
| Modification date | 20200327 | |
| 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 |
| GTF2H2 | GO:0006366 | transcription by RNA polymerase II | 9852112|27193682 |
| GTF2H2 | GO:1905776 | positive regulation of DNA helicase activity | 11445587 |
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Gene structures and expression levels for GTF2H2 |
| 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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ENSG00000145736
| 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. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| 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 GTF2H2 |
| 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_100422 | chr5 | 71060844:71060930:71061272:71061308:71061688:71061703 | 71061272:71061308 |
| exon_skip_120120 | chr5 | 71042181:71042284:71045444:71045507:71048006:71048113 | 71045444:71045507 |
| exon_skip_128236 | chr5 | 71060844:71060930:71061272:71061308:71061688:71061765 | 71061272:71061308 |
| exon_skip_133247 | chr5 | 71041522:71041624:71042181:71042284:71045444:71045507 | 71042181:71042284 |
| exon_skip_137153 | chr5 | 71048089:71048113:71048762:71048849:71049068:71049158 | 71048762:71048849 |
| exon_skip_143405 | chr5 | 71049068:71049158:71055352:71055457:71059690:71059744 | 71055352:71055457 |
| exon_skip_14768 | chr5 | 71059690:71059744:71060120:71060170:71060844:71060930 | 71060120:71060170 |
| exon_skip_182895 | chr5 | 71062752:71062796:71065125:71065222:71067494:71067601 | 71065125:71065222 |
| exon_skip_291003 | chr5 | 71035329:71035796:71037507:71037546:71041522:71041624 | 71037507:71037546 |
| exon_skip_35062 | chr5 | 71049068:71049158:71050217:71050305:71055352:71055457 | 71050217:71050305 |
| exon_skip_64417 | chr5 | 71045444:71045507:71048006:71048113:71048762:71048849 | 71048006:71048113 |
| exon_skip_99299 | chr5 | 71062752:71062796:71065125:71065222:71067296:71067638 | 71065125:71065222 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for GTF2H2 |
| 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 |
| ENST00000330280 | 71065125 | 71065222 | 3UTR-3UTR |
| ENST00000274400 | 71037507 | 71037546 | Frame-shift |
| ENST00000330280 | 71037507 | 71037546 | Frame-shift |
| ENST00000274400 | 71042181 | 71042284 | Frame-shift |
| ENST00000330280 | 71042181 | 71042284 | Frame-shift |
| ENST00000274400 | 71045444 | 71045507 | Frame-shift |
| ENST00000330280 | 71045444 | 71045507 | Frame-shift |
| ENST00000274400 | 71048762 | 71048849 | Frame-shift |
| ENST00000330280 | 71048762 | 71048849 | Frame-shift |
| ENST00000274400 | 71055352 | 71055457 | Frame-shift |
| ENST00000330280 | 71055352 | 71055457 | Frame-shift |
| ENST00000274400 | 71061272 | 71061308 | Frame-shift |
| ENST00000330280 | 71061272 | 71061308 | Frame-shift |
| ENST00000274400 | 71060120 | 71060170 | In-frame |
| ENST00000330280 | 71060120 | 71060170 | 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 |
| ENST00000330280 | 71065125 | 71065222 | 3UTR-3UTR |
| ENST00000274400 | 71037507 | 71037546 | Frame-shift |
| ENST00000330280 | 71037507 | 71037546 | Frame-shift |
| ENST00000274400 | 71042181 | 71042284 | Frame-shift |
| ENST00000330280 | 71042181 | 71042284 | Frame-shift |
| ENST00000274400 | 71045444 | 71045507 | Frame-shift |
| ENST00000330280 | 71045444 | 71045507 | Frame-shift |
| ENST00000274400 | 71048762 | 71048849 | Frame-shift |
| ENST00000330280 | 71048762 | 71048849 | Frame-shift |
| ENST00000274400 | 71055352 | 71055457 | Frame-shift |
| ENST00000330280 | 71055352 | 71055457 | Frame-shift |
| ENST00000274400 | 71061272 | 71061308 | Frame-shift |
| ENST00000330280 | 71061272 | 71061308 | Frame-shift |
| ENST00000274400 | 71048006 | 71048113 | In-frame |
| ENST00000330280 | 71048006 | 71048113 | 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 |
| ENST00000330280 | 71065125 | 71065222 | 3UTR-3UTR |
| ENST00000274400 | 71037507 | 71037546 | Frame-shift |
| ENST00000330280 | 71037507 | 71037546 | Frame-shift |
| ENST00000274400 | 71045444 | 71045507 | Frame-shift |
| ENST00000330280 | 71045444 | 71045507 | Frame-shift |
| ENST00000274400 | 71048762 | 71048849 | Frame-shift |
| ENST00000330280 | 71048762 | 71048849 | Frame-shift |
| ENST00000274400 | 71061272 | 71061308 | Frame-shift |
| ENST00000330280 | 71061272 | 71061308 | Frame-shift |
| ENST00000274400 | 71048006 | 71048113 | In-frame |
| ENST00000330280 | 71048006 | 71048113 | In-frame |
| ENST00000274400 | 71060120 | 71060170 | In-frame |
| ENST00000330280 | 71060120 | 71060170 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GTF2H2 |
p-ENSG00000145736_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 |
| ENST00000274400 | 4353 | 395 | 71060120 | 71060170 | 400 | 449 | 86 | 102 |
| ENST00000330280 | 2094 | 395 | 71060120 | 71060170 | 547 | 596 | 86 | 102 |
| 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 |
| ENST00000274400 | 4353 | 395 | 71048006 | 71048113 | 791 | 897 | 216 | 252 |
| ENST00000330280 | 2094 | 395 | 71048006 | 71048113 | 938 | 1044 | 216 | 252 |
| 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 |
| ENST00000274400 | 4353 | 395 | 71060120 | 71060170 | 400 | 449 | 86 | 102 |
| ENST00000330280 | 2094 | 395 | 71060120 | 71060170 | 547 | 596 | 86 | 102 |
| ENST00000274400 | 4353 | 395 | 71048006 | 71048113 | 791 | 897 | 216 | 252 |
| ENST00000330280 | 2094 | 395 | 71048006 | 71048113 | 938 | 1044 | 216 | 252 |
| 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 |
| Q13888 | 86 | 102 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 86 | 102 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 86 | 102 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 86 | 102 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 86 | 102 | 95 | 95 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:A0JN27 |
| Q13888 | 86 | 102 | 95 | 95 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:A0JN27 |
| 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 |
| Q13888 | 216 | 252 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 216 | 252 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 216 | 252 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 216 | 252 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 216 | 252 | 236 | 236 | Natural variant | ID=VAR_011665;Note=V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9063743;Dbxref=dbSNP:rs201102513,PMID:9063743 |
| Q13888 | 216 | 252 | 236 | 236 | Natural variant | ID=VAR_011665;Note=V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9063743;Dbxref=dbSNP:rs201102513,PMID:9063743 |
| 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 |
| Q13888 | 86 | 102 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 86 | 102 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 86 | 102 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 86 | 102 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 86 | 102 | 95 | 95 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:A0JN27 |
| Q13888 | 86 | 102 | 95 | 95 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:A0JN27 |
| Q13888 | 216 | 252 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 216 | 252 | 1 | 395 | Chain | ID=PRO_0000119248;Note=General transcription factor IIH subunit 2 |
| Q13888 | 216 | 252 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 216 | 252 | 60 | 236 | Domain | Note=VWFA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00219 |
| Q13888 | 216 | 252 | 236 | 236 | Natural variant | ID=VAR_011665;Note=V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9063743;Dbxref=dbSNP:rs201102513,PMID:9063743 |
| Q13888 | 216 | 252 | 236 | 236 | Natural variant | ID=VAR_011665;Note=V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9063743;Dbxref=dbSNP:rs201102513,PMID:9063743 |
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3'-UTR located exon skipping events that lost miRNA binding sites in GTF2H2 |
| 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 |
| Mayo | ENST00000330280 | 71065125 | 71065222 | hsa-miR-1976 | chr5:71065154-71065161 | 8mer-1a | chr5:71065141-71065161 | 149.00 | -24.39 |
| Mayo | ENST00000330280 | 71065125 | 71065222 | hsa-miR-199a-5p | chr5:71065184-71065191 | 8mer-1a | chr5:71065179-71065203 | 156.00 | -22.65 |
| Mayo | ENST00000330280 | 71065125 | 71065222 | hsa-miR-199b-5p | chr5:71065184-71065191 | 8mer-1a | chr5:71065179-71065203 | 156.00 | -22.65 |
| Mayo | ENST00000330280 | 71065125 | 71065222 | hsa-miR-504-3p | chr5:71065213-71065220 | 8mer-1a | chr5:71065199-71065220 | 162.00 | -30.67 |
| MSBB | ENST00000330280 | 71065125 | 71065222 | hsa-miR-1976 | chr5:71065154-71065161 | 8mer-1a | chr5:71065141-71065161 | 149.00 | -24.39 |
| MSBB | ENST00000330280 | 71065125 | 71065222 | hsa-miR-199a-5p | chr5:71065184-71065191 | 8mer-1a | chr5:71065179-71065203 | 156.00 | -22.65 |
| MSBB | ENST00000330280 | 71065125 | 71065222 | hsa-miR-199b-5p | chr5:71065184-71065191 | 8mer-1a | chr5:71065179-71065203 | 156.00 | -22.65 |
| MSBB | ENST00000330280 | 71065125 | 71065222 | hsa-miR-504-3p | chr5:71065213-71065220 | 8mer-1a | chr5:71065199-71065220 | 162.00 | -30.67 |
| ROSMAP | ENST00000330280 | 71065125 | 71065222 | hsa-miR-1976 | chr5:71065154-71065161 | 8mer-1a | chr5:71065141-71065161 | 149.00 | -24.39 |
| ROSMAP | ENST00000330280 | 71065125 | 71065222 | hsa-miR-199a-5p | chr5:71065184-71065191 | 8mer-1a | chr5:71065179-71065203 | 156.00 | -22.65 |
| ROSMAP | ENST00000330280 | 71065125 | 71065222 | hsa-miR-199b-5p | chr5:71065184-71065191 | 8mer-1a | chr5:71065179-71065203 | 156.00 | -22.65 |
| ROSMAP | ENST00000330280 | 71065125 | 71065222 | hsa-miR-504-3p | chr5:71065213-71065220 | 8mer-1a | chr5:71065199-71065220 | 162.00 | -30.67 |
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SNVs in the skipped exons for GTF2H2 |
| - 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 GTF2H2 |
| 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 GTF2H2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for GTF2H2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | FUBP1 | exon_skip_120120 | -4.041675e-01 | 6.096606e-07 |
| CB | PCBP4 | exon_skip_14768 | 4.872754e-01 | 1.937847e-10 |
| CB | RC3H1 | exon_skip_14768 | -4.106125e-01 | 1.486891e-07 |
| CB | FUBP1 | exon_skip_14768 | -4.161726e-01 | 9.687923e-08 |
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RelatedDrugs for GTF2H2 |
| 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 GTF2H2 |
| 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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