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Open reading frame (ORF) annotation in the exon skipping event | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon | |
Gene summary for RGPD1 |
Gene summary |
Gene information | Gene symbol | RGPD1 | Gene ID | 400966 |
Gene name | RANBP2-like and GRIP domain containing 1 | |
Synonyms | RGP1|RGPD2|RanBP2L2 | |
Cytomap | 2p11.2 | |
Type of gene | protein-coding | |
Description | RANBP2-like and GRIP domain-containing protein 1RANBP2-like and GRIP domain-containing protein 1/2ran-binding protein 2-like 2/6ran-binding protein 2-like 6ranBP2-like 2/6ranBP2-like 6ranBP2L6 | |
Modification date | 20180523 | |
UniProtAcc | P0DJD0 | |
Context | PubMed: RGPD1 [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 RGPD1 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 RGPD1 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for RGPD1 |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_327485 | 2 | 87184828:87185059:87185404:87185550:87190151:87190347 | 87185404:87185550 | ENSG00000187627.10 | ENST00000559485.1,ENST00000409776.2,ENST00000398193.3 |
exon_skip_327486 | 2 | 87211876:87211971:87212698:87214922:87221963:87222103 | 87212698:87214922 | ENSG00000187627.10 | ENST00000559485.1,ENST00000409776.2,ENST00000398193.3,ENST00000428128.1 |
exon_skip_327487 | 2 | 87212698:87214922:87221963:87222103:87224685:87224881 | 87221963:87222103 | ENSG00000187627.10 | ENST00000559485.1,ENST00000409776.2,ENST00000398193.3,ENST00000428128.1 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RGPD1 |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for RGPD1 |
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 |
ENST00000409776 | 87185404 | 87185550 | Frame-shift |
ENST00000559485 | 87185404 | 87185550 | Frame-shift |
ENST00000409776 | 87212698 | 87214922 | Frame-shift |
ENST00000559485 | 87212698 | 87214922 | Frame-shift |
ENST00000409776 | 87221963 | 87222103 | Frame-shift |
ENST00000559485 | 87221963 | 87222103 | Frame-shift |
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 |
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Infer the effects of exon skipping event on protein functional features for RGPD1 |
Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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 RGPD1 |
- Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
- 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 |
LUSC | TCGA-66-2794-01 | exon_skip_327486 | 87212699 | 87214922 | 87214094 | 87214094 | Nonsense_Mutation | A | T | p.R1358* |
- 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 |
MET2B | 87212699 | 87214922 | 87213901 | 87213904 | Frame_Shift_Del | TCTA | - | p.SL1285fs |
HUPT3_PANCREAS | 87212699 | 87214922 | 87214212 | 87214213 | Frame_Shift_Del | TT | - | p.L1389fs |
ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 87212699 | 87214922 | 87212781 | 87212781 | Missense_Mutation | C | T | p.S912L |
MDAMB468_BREAST | 87212699 | 87214922 | 87213849 | 87213849 | Missense_Mutation | G | A | p.R1268H |
CH157MN_CENTRAL_NERVOUS_SYSTEM | 87212699 | 87214922 | 87213873 | 87213873 | Missense_Mutation | T | C | p.F1276S |
SCC9_UPPER_AERODIGESTIVE_TRACT | 87212699 | 87214922 | 87213873 | 87213873 | Missense_Mutation | T | C | p.F1276S |
MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 87212699 | 87214922 | 87214178 | 87214178 | Missense_Mutation | C | T | p.R1378C |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RGPD1 |
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 RGPD1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RGPD1 |
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RelatedDrugs for RGPD1 |
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 RGPD1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |