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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for GRAMD1B |
 Gene summary |
| Gene information | Gene symbol | GRAMD1B | Gene ID | 57476 |
| Gene name | GRAM domain containing 1B | |
| Synonyms | LINC01059 | |
| Cytomap | 11q24.1 | |
| Type of gene | protein-coding | |
| Description | GRAM domain-containing protein 1Blong intergenic non-protein coding RNA 1059 | |
| Modification date | 20180519 | |
| UniProtAcc | Q3KR37 | |
| Context | PubMed: GRAMD1B [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 |
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Exon skipping events across known transcript of Ensembl for GRAMD1B 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. |
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Gene isoform structures and expression levels for GRAMD1B |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for GRAMD1B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_66149 | 11 | 123448074:123448285:123449117:123449138:123455019:123455040 | 123449117:123449138 | ENSG00000023171.10 | ENST00000456860.2 |
| exon_skip_66150 | 11 | 123464789:123464874:123465442:123465546:123466649:123466745 | 123465442:123465546 | ENSG00000023171.10 | ENST00000529750.1,ENST00000534764.1,ENST00000532581.1,ENST00000529432.1,ENST00000322282.7,ENST00000456860.2 |
| exon_skip_66152 | 11 | 123474133:123474249:123476029:123476186:123477316:123477506 | 123476029:123476186 | ENSG00000023171.10 | ENST00000529750.1,ENST00000534764.1,ENST00000532581.1,ENST00000529432.1,ENST00000322282.7,ENST00000456860.2 |
| exon_skip_66154 | 11 | 123479366:123479510:123480502:123480621:123480903:123481046 | 123480502:123480621 | ENSG00000023171.10 | ENST00000529750.1,ENST00000532581.1,ENST00000450171.2,ENST00000529432.1,ENST00000322282.7,ENST00000456860.2 |
| exon_skip_66157 | 11 | 123484162:123484366:123485452:123485543:123489400:123489508 | 123485452:123485543 | ENSG00000023171.10 | ENST00000532581.1,ENST00000525945.1,ENST00000450171.2 |
| exon_skip_66159 | 11 | 123485452:123485543:123489052:123489064:123489400:123489508 | 123489052:123489064 | ENSG00000023171.10 | ENST00000529750.1,ENST00000529432.1,ENST00000456860.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GRAMD1B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_66149 | 11 | 123448074:123448285:123449117:123449138:123455019:123455040 | 123449117:123449138 | ENSG00000023171.10 | ENST00000456860.2 |
| exon_skip_66150 | 11 | 123464789:123464874:123465442:123465546:123466649:123466745 | 123465442:123465546 | ENSG00000023171.10 | ENST00000456860.2,ENST00000322282.7,ENST00000529750.1,ENST00000532581.1,ENST00000529432.1,ENST00000534764.1 |
| exon_skip_66152 | 11 | 123474133:123474249:123476029:123476186:123477316:123477506 | 123476029:123476186 | ENSG00000023171.10 | ENST00000456860.2,ENST00000322282.7,ENST00000529750.1,ENST00000532581.1,ENST00000529432.1,ENST00000534764.1 |
| exon_skip_66154 | 11 | 123479366:123479510:123480502:123480621:123480903:123481046 | 123480502:123480621 | ENSG00000023171.10 | ENST00000456860.2,ENST00000322282.7,ENST00000529750.1,ENST00000532581.1,ENST00000529432.1,ENST00000450171.2 |
| exon_skip_66157 | 11 | 123484162:123484366:123485452:123485543:123489400:123489508 | 123485452:123485543 | ENSG00000023171.10 | ENST00000532581.1,ENST00000450171.2,ENST00000525945.1 |
| exon_skip_66159 | 11 | 123485452:123485543:123489052:123489064:123489400:123489508 | 123489052:123489064 | ENSG00000023171.10 | ENST00000456860.2,ENST00000529750.1,ENST00000529432.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for GRAMD1B |
| 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 |
| ENST00000529750 | 123465442 | 123465546 | Frame-shift |
| ENST00000529750 | 123476029 | 123476186 | Frame-shift |
| ENST00000529750 | 123480502 | 123480621 | Frame-shift |
| ENST00000529750 | 123489052 | 123489064 | 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 |
| ENST00000529750 | 123465442 | 123465546 | Frame-shift |
| ENST00000529750 | 123476029 | 123476186 | Frame-shift |
| ENST00000529750 | 123480502 | 123480621 | Frame-shift |
| ENST00000529750 | 123489052 | 123489064 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GRAMD1B |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| 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 |
| 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 |
| 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 |
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SNVs in the skipped exons for GRAMD1B |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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_66152 | 123476030 | 123476186 | 123476080 | 123476080 | Frame_Shift_Del | C | - | p.S263fs |
| LGG | TCGA-DB-5275-01 | exon_skip_66152 | 123476030 | 123476186 | 123476150 | 123476153 | Frame_Shift_Del | ACTA | - | p.286_287del |
| LGG | TCGA-DB-5275-01 | exon_skip_66152 | 123476030 | 123476186 | 123476150 | 123476153 | Frame_Shift_Del | ACTA | - | p.TL286fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_66154 | 123480503 | 123480621 | 123480523 | 123480523 | Frame_Shift_Del | A | - | p.K418fs |
| LIHC | TCGA-BC-A10T-01 | exon_skip_66154 | 123480503 | 123480621 | 123480598 | 123480599 | Frame_Shift_Ins | - | C | p.C442fs |
| ESCA | TCGA-IG-A97I-01 | exon_skip_66150 | 123465443 | 123465546 | 123465506 | 123465506 | Nonsense_Mutation | G | A | p.W135* |
| ESCA | TCGA-IG-A97I-01 | exon_skip_66150 | 123465443 | 123465546 | 123465506 | 123465506 | Nonsense_Mutation | G | A | p.W135X |
| LUSC | TCGA-46-3765-01 | exon_skip_66152 | 123476030 | 123476186 | 123476185 | 123476185 | Nonsense_Mutation | C | A | p.S305_splice |
| BRCA | TCGA-BH-A0BZ-01 | exon_skip_66152 | 123476030 | 123476186 | 123476187 | 123476187 | Splice_Site | G | A | e9+1 |
| - 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 |
| MM426_SKIN | 123476030 | 123476186 | 123476037 | 123476037 | Missense_Mutation | G | A | p.E249K |
| SW872_SOFT_TISSUE | 123476030 | 123476186 | 123476104 | 123476104 | Missense_Mutation | C | G | p.P271R |
| SW480_LARGE_INTESTINE | 123476030 | 123476186 | 123476139 | 123476139 | Missense_Mutation | A | T | p.T283S |
| LNCAPCLONEFGC_PROSTATE | 123480503 | 123480621 | 123480557 | 123480557 | Missense_Mutation | T | C | p.I428T |
| RH36_SOFT_TISSUE | 123480503 | 123480621 | 123480563 | 123480563 | Missense_Mutation | A | G | p.Y430C |
| C2BBE1_LARGE_INTESTINE | 123480503 | 123480621 | 123480563 | 123480563 | Missense_Mutation | A | G | p.Y430C |
| CACO2_LARGE_INTESTINE | 123480503 | 123480621 | 123480563 | 123480563 | Missense_Mutation | A | G | p.Y430C |
| JHUEM2_ENDOMETRIUM | 123480503 | 123480621 | 123480613 | 123480613 | Missense_Mutation | G | A | p.E447K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GRAMD1B |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GRAMD1B |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GRAMD1B |
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RelatedDrugs for GRAMD1B |
| 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 |
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RelatedDiseases for GRAMD1B |
| 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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