|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for GFM2 |
 Gene summary |
| Gene information | Gene symbol | GFM2 | Gene ID | 84340 |
| Gene name | GTP dependent ribosome recycling factor mitochondrial 2 | |
| Synonyms | EF-G2mt|EFG2|MRRF2|MST027|MSTP027|RRF|RRF2|RRF2mt|hEFG2|mEF-G 2 | |
| Cytomap | 5q13.3 | |
| Type of gene | protein-coding | |
| Description | ribosome-releasing factor 2, mitochondrialG elongation factor mitochondrial 2mitochondrial elongation factor G2mitochondrial ribosome recycling factor 2ribosome releasing factor 2 | |
| Modification date | 20200313 | |
| 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 |
| GFM2 | GO:0032543 | mitochondrial translation | 19716793 |
| GFM2 | GO:0032790 | ribosome disassembly | 19716793 |
| GFM2 | GO:0070125 | mitochondrial translational elongation | 19716793 |
Top |
Gene structures and expression levels for GFM2 |
| 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. |
 |
ENSG00000164347
| 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 |
| CB | UP | ENST00000506778.1 | GFM2-205:protein_coding:GFM2 | 3.238557e+00 | 1.202249e+00 | 2.085553e-03 | 9.545693e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GFM2 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_14176 | chr5 | 74725941:74726126:74733022:74733098:74736796:74736963 | 74733022:74733098 |
| exon_skip_167010 | chr5 | 74760902:74760986:74763680:74763766:74766938:74767061 | 74763680:74763766 |
| exon_skip_174405 | chr5 | 74730260:74730398:74730602:74730775:74733022:74733098 | 74730602:74730775 |
| exon_skip_18016 | chr5 | 74763694:74763766:74765035:74765152:74766938:74767061 | 74765035:74765152 |
| exon_skip_196426 | chr5 | 74746105:74746165:74747692:74747780:74750579:74750667 | 74747692:74747780 |
| exon_skip_237730 | chr5 | 74747692:74747780:74750579:74750667:74751368:74751493 | 74750579:74750667 |
| exon_skip_239283 | chr5 | 74730260:74730398:74733022:74733098:74736796:74736963 | 74733022:74733098 |
| exon_skip_241282 | chr5 | 74747692:74747780:74750579:74750667:74758849:74758946 | 74750579:74750667 |
| exon_skip_246439 | chr5 | 74730602:74730775:74733022:74733098:74736796:74736963 | 74733022:74733098 |
| exon_skip_255097 | chr5 | 74760902:74760986:74763680:74763766:74766938:74767147 | 74763680:74763766 |
| exon_skip_277722 | chr5 | 74725941:74726126:74730260:74730398:74733022:74733098 | 74730260:74730398 |
| exon_skip_287211 | chr5 | 74738318:74738417:74738502:74738642:74739989:74740137 | 74738502:74738642 |
| exon_skip_33005 | chr5 | 74722379:74722561:74725640:74725755:74725941:74726126 | 74725640:74725755 |
| exon_skip_45909 | chr5 | 74750579:74750667:74751368:74751493:74758849:74758946 | 74751368:74751493 |
| exon_skip_60743 | chr5 | 74725941:74726126:74730260:74730398:74730602:74730775 | 74730260:74730398 |
| exon_skip_67093 | chr5 | 74763680:74763766:74765035:74765152:74766938:74767105 | 74765035:74765152 |
| exon_skip_6884 | chr5 | 74751379:74751493:74758849:74758946:74759369:74759426 | 74758849:74758946 |
| exon_skip_80210 | chr5 | 74745678:74745857:74746105:74746165:74747692:74747780 | 74746105:74746165 |
| 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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for GFM2 |
| 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 |
| ENST00000509430 | 74765035 | 74765152 | 3UTR-3UTR |
| ENST00000296805 | 74725640 | 74725755 | Frame-shift |
| ENST00000509430 | 74725640 | 74725755 | Frame-shift |
| ENST00000296805 | 74730260 | 74730398 | Frame-shift |
| ENST00000509430 | 74730260 | 74730398 | Frame-shift |
| ENST00000296805 | 74738502 | 74738642 | In-frame |
| ENST00000509430 | 74738502 | 74738642 | In-frame |
| ENST00000296805 | 74751368 | 74751493 | In-frame |
| ENST00000509430 | 74751368 | 74751493 | 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 |
| ENST00000296805 | 74730260 | 74730398 | Frame-shift |
| ENST00000509430 | 74730260 | 74730398 | Frame-shift |
| ENST00000296805 | 74738502 | 74738642 | In-frame |
| ENST00000509430 | 74738502 | 74738642 | In-frame |
| ENST00000296805 | 74751368 | 74751493 | In-frame |
| ENST00000509430 | 74751368 | 74751493 | 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 |
| ENST00000509430 | 74765035 | 74765152 | 3UTR-3UTR |
| ENST00000296805 | 74725640 | 74725755 | Frame-shift |
| ENST00000509430 | 74725640 | 74725755 | Frame-shift |
| ENST00000296805 | 74730260 | 74730398 | Frame-shift |
| ENST00000509430 | 74730260 | 74730398 | Frame-shift |
| ENST00000296805 | 74733022 | 74733098 | Frame-shift |
| ENST00000509430 | 74733022 | 74733098 | Frame-shift |
| ENST00000296805 | 74746105 | 74746165 | Frame-shift |
| ENST00000509430 | 74746105 | 74746165 | Frame-shift |
| ENST00000296805 | 74747692 | 74747780 | Frame-shift |
| ENST00000509430 | 74747692 | 74747780 | Frame-shift |
| ENST00000296805 | 74750579 | 74750667 | Frame-shift |
| ENST00000509430 | 74750579 | 74750667 | Frame-shift |
| ENST00000296805 | 74758849 | 74758946 | Frame-shift |
| ENST00000509430 | 74758849 | 74758946 | Frame-shift |
| ENST00000296805 | 74738502 | 74738642 | In-frame |
| ENST00000509430 | 74738502 | 74738642 | In-frame |
| ENST00000296805 | 74751368 | 74751493 | In-frame |
| ENST00000509430 | 74751368 | 74751493 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for GFM2 |
p-ENSG00000164347_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 |
| ENST00000296805 | 3266 | 779 | 74751368 | 74751493 | 763 | 887 | 101 | 143 |
| ENST00000509430 | 3064 | 779 | 74751368 | 74751493 | 615 | 739 | 101 | 143 |
| ENST00000296805 | 3266 | 779 | 74738502 | 74738642 | 1538 | 1677 | 360 | 406 |
| ENST00000509430 | 3064 | 779 | 74738502 | 74738642 | 1390 | 1529 | 360 | 406 |
| 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 |
| ENST00000296805 | 3266 | 779 | 74751368 | 74751493 | 763 | 887 | 101 | 143 |
| ENST00000509430 | 3064 | 779 | 74751368 | 74751493 | 615 | 739 | 101 | 143 |
| ENST00000296805 | 3266 | 779 | 74738502 | 74738642 | 1538 | 1677 | 360 | 406 |
| ENST00000509430 | 3064 | 779 | 74738502 | 74738642 | 1390 | 1529 | 360 | 406 |
| 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 |
| ENST00000296805 | 3266 | 779 | 74751368 | 74751493 | 763 | 887 | 101 | 143 |
| ENST00000509430 | 3064 | 779 | 74751368 | 74751493 | 615 | 739 | 101 | 143 |
| ENST00000296805 | 3266 | 779 | 74738502 | 74738642 | 1538 | 1677 | 360 | 406 |
| ENST00000509430 | 3064 | 779 | 74738502 | 74738642 | 1390 | 1529 | 360 | 406 |
| 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 |
| Q969S9 | 101 | 143 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 101 | 143 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 101 | 143 | 68 | 353 | Domain | Note=tr-type G |
| Q969S9 | 101 | 143 | 68 | 353 | Domain | Note=tr-type G |
| Q969S9 | 101 | 143 | 141 | 145 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_03059 |
| Q969S9 | 101 | 143 | 141 | 145 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_03059 |
| Q969S9 | 360 | 406 | 361 | 407 | Alternative sequence | ID=VSP_001363;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.4 |
| Q969S9 | 360 | 406 | 361 | 407 | Alternative sequence | ID=VSP_001363;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.4 |
| Q969S9 | 360 | 406 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 360 | 406 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| 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 |
| Q969S9 | 101 | 143 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 101 | 143 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 101 | 143 | 68 | 353 | Domain | Note=tr-type G |
| Q969S9 | 101 | 143 | 68 | 353 | Domain | Note=tr-type G |
| Q969S9 | 101 | 143 | 141 | 145 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_03059 |
| Q969S9 | 101 | 143 | 141 | 145 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_03059 |
| Q969S9 | 360 | 406 | 361 | 407 | Alternative sequence | ID=VSP_001363;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.4 |
| Q969S9 | 360 | 406 | 361 | 407 | Alternative sequence | ID=VSP_001363;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.4 |
| Q969S9 | 360 | 406 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 360 | 406 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| 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 |
| Q969S9 | 101 | 143 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 101 | 143 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 101 | 143 | 68 | 353 | Domain | Note=tr-type G |
| Q969S9 | 101 | 143 | 68 | 353 | Domain | Note=tr-type G |
| Q969S9 | 101 | 143 | 141 | 145 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_03059 |
| Q969S9 | 101 | 143 | 141 | 145 | Nucleotide binding | Note=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255|HAMAP-Rule:MF_03059 |
| Q969S9 | 360 | 406 | 361 | 407 | Alternative sequence | ID=VSP_001363;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.4 |
| Q969S9 | 360 | 406 | 361 | 407 | Alternative sequence | ID=VSP_001363;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.4 |
| Q969S9 | 360 | 406 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
| Q969S9 | 360 | 406 | 1 | 779 | Chain | ID=PRO_0000007450;Note=Ribosome-releasing factor 2%2C mitochondrial |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in GFM2 |
| 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 | ENST00000509430 | 74765035 | 74765152 | hsa-miR-5008-5p | chr5:74765125-74765132 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| Mayo | ENST00000509430 | 74765035 | 74765152 | hsa-miR-3922-5p | chr5:74765082-74765089 | 8mer-1a | chr5:74765081-74765100 | 161.00 | -27.34 |
| Mayo | ENST00000509430 | 74765035 | 74765152 | hsa-miR-4306 | chr5:74765136-74765143 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| Mayo | ENST00000509430 | 74765035 | 74765152 | hsa-miR-185-5p | chr5:74765136-74765143 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| Mayo | ENST00000509430 | 74765035 | 74765152 | hsa-miR-4644 | chr5:74765136-74765143 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| Mayo | ENST00000509430 | 74765035 | 74765152 | hsa-miR-4284 | chr5:74765066-74765073 | 8mer-1a | chr5:74765064-74765089 | 154.00 | -25.40 |
| ROSMAP | ENST00000509430 | 74765035 | 74765152 | hsa-miR-5008-5p | chr5:74765125-74765132 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| ROSMAP | ENST00000509430 | 74765035 | 74765152 | hsa-miR-3922-5p | chr5:74765082-74765089 | 8mer-1a | chr5:74765081-74765100 | 161.00 | -27.34 |
| ROSMAP | ENST00000509430 | 74765035 | 74765152 | hsa-miR-4306 | chr5:74765136-74765143 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| ROSMAP | ENST00000509430 | 74765035 | 74765152 | hsa-miR-185-5p | chr5:74765136-74765143 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| ROSMAP | ENST00000509430 | 74765035 | 74765152 | hsa-miR-4644 | chr5:74765136-74765143 | 8mer-1a | chr5:74765122-74765143 | 152.00 | -24.95 |
| ROSMAP | ENST00000509430 | 74765035 | 74765152 | hsa-miR-4284 | chr5:74765066-74765073 | 8mer-1a | chr5:74765064-74765089 | 154.00 | -25.40 |
Top |
SNVs in the skipped exons for GFM2 |
| - 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 |
Top |
AD stage-associated exon skippint events for GFM2 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GFM2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for GFM2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_167010 | -4.745938e-01 | 1.023401e-08 |
| CB | CNOT4 | exon_skip_167010 | -5.411899e-01 | 2.493635e-11 |
| CB | PCBP1 | exon_skip_167010 | -5.084626e-01 | 5.641289e-10 |
| CB | RBM45 | exon_skip_167010 | 5.022870e-01 | 9.800010e-10 |
| IFG | TARDBP | exon_skip_277722 | -4.201359e-01 | 2.911707e-02 |
| IFG | RBMS3 | exon_skip_277722 | -4.243316e-01 | 2.738437e-02 |
| IFG | ZNF638 | exon_skip_277722 | -5.976150e-01 | 9.958355e-04 |
| IFG | RBM6 | exon_skip_277722 | -5.287654e-01 | 4.573939e-03 |
| IFG | CNOT4 | exon_skip_277722 | -4.293595e-01 | 2.541894e-02 |
| IFG | RBM5 | exon_skip_277722 | -4.868436e-01 | 1.001549e-02 |
| IFG | RBM47 | exon_skip_277722 | -5.187629e-01 | 5.563812e-03 |
| IFG | PCBP2 | exon_skip_277722 | -5.976150e-01 | 9.958355e-04 |
| IFG | HNRNPD | exon_skip_277722 | -4.557013e-01 | 1.690425e-02 |
| IFG | SNRNP70 | exon_skip_277722 | -6.392308e-01 | 3.314519e-04 |
| PCC | SNRNP70 | exon_skip_277722 | -4.358779e-01 | 5.817050e-11 |
| PCC | ESRP2 | exon_skip_277722 | -4.705586e-01 | 9.538545e-13 |
Top |
RelatedDrugs for GFM2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for GFM2 |
| 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)
|