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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 SMG7 |
 Gene summary |
| Gene information | Gene symbol | SMG7 | Gene ID | 9887 |
| Gene name | SMG7 nonsense mediated mRNA decay factor | |
| Synonyms | C1orf16|EST1C|SGA56M | |
| Cytomap | 1q25.3 | |
| Type of gene | protein-coding | |
| Description | protein SMG7EST1 telomerase component homolog CEST1-like protein Cbreast cancer-associated antigen SGA-56Mever shorter telomeres 1Csmg-7 homolog, nonsense mediated mRNA decay factor | |
| 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 |
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Gene structures and expression levels for SMG7 |
| 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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ENSG00000116698
| 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 |
| STG | UP | ENST00000508461.5 | SMG7-214:protein_coding:SMG7 | 4.474520e+01 | 2.962512e+00 | 2.859107e-04 | 2.002212e-02 |
| CB | UP | ENST00000444547.6 | SMG7-206:nonsense_mediated_decay:SMG7 | 1.758397e+01 | 1.238816e+00 | 3.597981e-11 | 2.730821e-09 |
| CB | DOWN | ENST00000507469.5 | SMG7-212:protein_coding:SMG7 | 5.170944e+02 | -8.907571e-01 | 6.800404e-07 | 1.080297e-05 |
| CB | DOWN | ENST00000515829.6 | SMG7-215:protein_coding:SMG7 | 8.029687e+02 | -1.373657e+00 | 1.329230e-03 | 6.561885e-03 |
| TC | UP | ENST00000444547.6 | SMG7-206:nonsense_mediated_decay:SMG7 | 6.722707e+00 | 8.378202e-01 | 2.811497e-07 | 1.441977e-05 |
| 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 SMG7 |
| 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_114906 | chr1 | 183545966:183546337:183547103:183547252:183549208:183549288 | 183547103:183547252 |
| exon_skip_14539 | chr1 | 183546254:183546337:183547103:183547252:183549208:183549288 | 183547103:183547252 |
| exon_skip_146704 | chr1 | 183472621:183472649:183515874:183515991:183517688:183517820 | 183515874:183515991 |
| exon_skip_193271 | chr1 | 183526596:183526767:183527626:183527731:183527956:183528027 | 183527626:183527731 |
| exon_skip_207579 | chr1 | 183472621:183472649:183512837:183512868:183515874:183515894 | 183512837:183512868 |
| exon_skip_254236 | chr1 | 183545020:183545312:183545966:183546337:183549208:183549288 | 183545966:183546337 |
| exon_skip_280652 | chr1 | 183472621:183472649:183501131:183501267:183502253:183502391 | 183501131:183501267 |
| exon_skip_28087 | chr1 | 183547103:183547252:183549208:183549288:183549764:183549923 | 183549208:183549288 |
| exon_skip_31014 | chr1 | 183544930:183545312:183545966:183546337:183549208:183549288 | 183545966:183546337 |
| exon_skip_38564 | chr1 | 183472621:183472649:183502253:183502391:183512837:183512868 | 183502253:183502391 |
| exon_skip_41093 | chr1 | 183545966:183546337:183549208:183549288:183549764:183549923 | 183549208:183549288 |
| exon_skip_61042 | chr1 | 183545020:183545312:183545966:183546337:183547103:183547252 | 183545966:183546337 |
| exon_skip_74954 | chr1 | 183545188:183545312:183545966:183546337:183549208:183549288 | 183545966:183546337 |
| exon_skip_75959 | chr1 | 183544987:183545312:183545966:183546337:183549208:183549288 | 183545966:183546337 |
| 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_14539 | Mayo_TC | 4.591463e-01 | 5.652000e-01 | -1.060537e-01 | 7.720074e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for SMG7 |
| 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 |
| ENST00000347615 | 183512837 | 183512868 | Frame-shift |
| ENST00000347615 | 183545966 | 183546337 | 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 |
| ENST00000347615 | 183512837 | 183512868 | Frame-shift |
| ENST00000347615 | 183545966 | 183546337 | 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 |
| ENST00000347615 | 183512837 | 183512868 | Frame-shift |
| ENST00000347615 | 183545966 | 183546337 | In-frame |
| ENST00000347615 | 183549208 | 183549288 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMG7 |
p-ENSG00000116698_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 |
| ENST00000347615 | 5805 | 1137 | 183545966 | 183546337 | 2491 | 2861 | 790 | 914 |
| 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 |
| ENST00000347615 | 5805 | 1137 | 183545966 | 183546337 | 2491 | 2861 | 790 | 914 |
| 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 |
| ENST00000347615 | 5805 | 1137 | 183545966 | 183546337 | 2491 | 2861 | 790 | 914 |
| ENST00000347615 | 5805 | 1137 | 183549208 | 183549288 | 2863 | 2942 | 914 | 941 |
| 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 |
| Q92540 | 790 | 914 | 914 | 914 | Alternative sequence | ID=VSP_016575;Note=In isoform 4 and isoform 5. E->EDPKSSPLLPPDLLKSLAALEEEEELIFSNPPDLYPALLGPLASLPGRSLF;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q92540 | 790 | 914 | 2 | 1137 | Chain | ID=PRO_0000076324;Note=Protein SMG7 |
| Q92540 | 790 | 914 | 648 | 843 | Compositional bias | Note=Gln/Pro-rich |
| Q92540 | 790 | 914 | 897 | 897 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92540 | 790 | 914 | 900 | 900 | Natural variant | ID=VAR_051364;Note=V->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9039502;Dbxref=dbSNP:rs2298083,PMID:15489334,PMID:9039502 |
| 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 |
| Q92540 | 790 | 914 | 914 | 914 | Alternative sequence | ID=VSP_016575;Note=In isoform 4 and isoform 5. E->EDPKSSPLLPPDLLKSLAALEEEEELIFSNPPDLYPALLGPLASLPGRSLF;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q92540 | 790 | 914 | 2 | 1137 | Chain | ID=PRO_0000076324;Note=Protein SMG7 |
| Q92540 | 790 | 914 | 648 | 843 | Compositional bias | Note=Gln/Pro-rich |
| Q92540 | 790 | 914 | 897 | 897 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92540 | 790 | 914 | 900 | 900 | Natural variant | ID=VAR_051364;Note=V->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9039502;Dbxref=dbSNP:rs2298083,PMID:15489334,PMID:9039502 |
| 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 |
| Q92540 | 790 | 914 | 914 | 914 | Alternative sequence | ID=VSP_016575;Note=In isoform 4 and isoform 5. E->EDPKSSPLLPPDLLKSLAALEEEEELIFSNPPDLYPALLGPLASLPGRSLF;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q92540 | 790 | 914 | 2 | 1137 | Chain | ID=PRO_0000076324;Note=Protein SMG7 |
| Q92540 | 790 | 914 | 648 | 843 | Compositional bias | Note=Gln/Pro-rich |
| Q92540 | 790 | 914 | 897 | 897 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92540 | 790 | 914 | 900 | 900 | Natural variant | ID=VAR_051364;Note=V->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9039502;Dbxref=dbSNP:rs2298083,PMID:15489334,PMID:9039502 |
| Q92540 | 914 | 941 | 914 | 914 | Alternative sequence | ID=VSP_016575;Note=In isoform 4 and isoform 5. E->EDPKSSPLLPPDLLKSLAALEEEEELIFSNPPDLYPALLGPLASLPGRSLF;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334 |
| Q92540 | 914 | 941 | 2 | 1137 | Chain | ID=PRO_0000076324;Note=Protein SMG7 |
| Q92540 | 914 | 941 | 922 | 1015 | Compositional bias | Note=Ser-rich |
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3'-UTR located exon skipping events that lost miRNA binding sites in SMG7 |
| 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 SMG7 |
| - 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 SMG7 |
| 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 SMG7 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_207579 | rs2702185 | chr1:183532215 | 6.681888e-04 | 4.263516e-02 |
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Correlation with RNA binding proteins (RBPs) for SMG7 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | HNRNPK | exon_skip_114906 | 4.233695e-01 | 3.659287e-08 |
| CB | PCBP2 | exon_skip_114906 | 4.183523e-01 | 5.493735e-08 |
| CB | RALYL | exon_skip_114906 | 5.628360e-01 | 2.052266e-14 |
| CB | SRSF9 | exon_skip_114906 | 4.298029e-01 | 2.152118e-08 |
| DLPFC | KHDRBS2 | exon_skip_114906 | 7.066857e-01 | 3.092332e-46 |
| DLPFC | CPEB1 | exon_skip_114906 | 5.240074e-01 | 2.399758e-22 |
| HCC | U2AF2 | exon_skip_114906 | -5.114478e-01 | 1.562127e-19 |
| HCC | CNOT4 | exon_skip_114906 | -4.063513e-01 | 3.078733e-12 |
| HCC | TIA1 | exon_skip_114906 | -5.087712e-01 | 2.584352e-19 |
| HCC | TRNAU1AP | exon_skip_114906 | -4.767144e-01 | 7.710709e-17 |
| HCC | TRA2A | exon_skip_114906 | -4.203535e-01 | 4.525311e-13 |
| HCC | KHDRBS2 | exon_skip_114906 | 4.531731e-01 | 3.517173e-15 |
| HCC | SF1 | exon_skip_114906 | -5.078877e-01 | 3.048560e-19 |
| HCC | KHDRBS3 | exon_skip_114906 | -4.913804e-01 | 6.124396e-18 |
| HCC | FUBP1 | exon_skip_114906 | -4.980899e-01 | 1.844817e-18 |
| HCC | RALY | exon_skip_114906 | -6.108272e-01 | 3.297162e-29 |
| HCC | PTBP1 | exon_skip_114906 | -7.238914e-01 | 1.992355e-45 |
| HCC | SRSF1 | exon_skip_114906 | -4.562052e-01 | 2.185754e-15 |
| IFG | SRSF2 | exon_skip_38564 | 4.997190e-01 | 7.953417e-03 |
| IFG | ILF2 | exon_skip_38564 | 5.253219e-01 | 4.896300e-03 |
| IFG | KHDRBS3 | exon_skip_38564 | 4.306221e-01 | 2.494382e-02 |
| IFG | HNRNPA0 | exon_skip_38564 | 4.737696e-01 | 1.254831e-02 |
| IFG | HNRNPAB | exon_skip_38564 | 4.485645e-01 | 1.893674e-02 |
| IFG | NUP42 | exon_skip_38564 | 5.404369e-01 | 3.611833e-03 |
| IFG | PABPC5 | exon_skip_38564 | 6.392087e-01 | 3.316595e-04 |
| IFG | EWSR1 | exon_skip_38564 | 5.037291e-01 | 7.389173e-03 |
| IFG | SRSF1 | exon_skip_38564 | 4.503641e-01 | 1.840625e-02 |
| IFG | HNRNPH2 | exon_skip_38564 | 5.725176e-01 | 1.803890e-03 |
| IFG | ZCRB1 | exon_skip_38564 | 5.046545e-01 | 7.263859e-03 |
| IFG | HNRNPF | exon_skip_38564 | 4.830617e-01 | 1.069980e-02 |
| IFG | SART3 | exon_skip_38564 | 5.265558e-01 | 4.778643e-03 |
| IFG | CNOT4 | exon_skip_207579 | -4.742402e-01 | 1.244870e-02 |
| IFG | TRA2A | exon_skip_207579 | -4.417629e-01 | 2.105618e-02 |
| IFG | PTBP1 | exon_skip_114906 | -4.462092e-01 | 3.282539e-02 |
| PCC | RALYL | exon_skip_114906 | 4.192442e-01 | 2.398705e-10 |
| PCC | PTBP1 | exon_skip_114906 | -6.405545e-01 | 1.196125e-25 |
| PCC | CPEB1 | exon_skip_114906 | 5.354844e-01 | 5.574364e-17 |
| TC | FXR2 | exon_skip_14539 | 4.701559e-01 | 5.208509e-10 |
| TC | HNRNPK | exon_skip_14539 | 4.634247e-01 | 9.842097e-10 |
| TC | KHDRBS2 | exon_skip_14539 | 7.916978e-01 | 5.403453e-35 |
| TC | KHDRBS3 | exon_skip_14539 | 6.970146e-01 | 3.721879e-24 |
| TC | RALYL | exon_skip_14539 | 8.005729e-01 | 2.683753e-36 |
| TC | PTBP1 | exon_skip_14539 | -4.856407e-01 | 1.142067e-10 |
| TC | PTBP3 | exon_skip_14539 | 4.656145e-01 | 8.013718e-10 |
| TC | CPEB1 | exon_skip_14539 | 6.147780e-01 | 1.082106e-17 |
| TC | SRSF9 | exon_skip_14539 | 4.048976e-01 | 1.441861e-07 |
| TC | SRSF5 | exon_skip_14539 | 4.933571e-01 | 5.209335e-11 |
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RelatedDrugs for SMG7 |
| 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 SMG7 |
| 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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