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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 RLIM |
Gene summary |
Gene information | Gene symbol | RLIM | Gene ID | 51132 |
Gene name | ring finger protein, LIM domain interacting | |
Synonyms | MRX61|NY-REN-43|RNF12|TOKAS | |
Cytomap | Xq13.2 | |
Type of gene | protein-coding | |
Description | E3 ubiquitin-protein ligase RLIME3 ubiquitin-protein ligase RNF12LIM domain-interacting RING finger proteinR-LIMRING finger LIM domain-binding proteinRING-type E3 ubiquitin transferase RLIMrenal carcinoma antigen NY-REN-43ring finger protein 12rin | |
Modification date | 20200313 | |
UniProtAcc | L0R533, Q9NVW2, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
RLIM | GO:0060816 | random inactivation of X chromosome | 19945382 |
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Gene structures and expression levels for RLIM |
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. |
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 | ENST00000349225.2 | RLIM-202:protein_coding:RLIM | 3.249996e+01 | 1.026928e+00 | 1.700644e-03 | 8.049672e-03 |
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 RLIM |
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_157692 | chrX | 74595809:74596000:74612582:74612643:74614422:74614617 | 74612582:74612643 |
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 RLIM |
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 |
ENST00000349225 | 74612582 | 74612643 | 3UTR-3UTR |
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 |
ENST00000349225 | 74612582 | 74612643 | 3UTR-3UTR |
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 |
ENST00000349225 | 74612582 | 74612643 | 3UTR-3UTR |
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Infer the effects of exon skipping event on protein functional features for RLIM |
p-ENSG00000131263_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 |
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 |
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 |
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 |
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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RLIM |
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 | ENST00000349225 | 74612582 | 74612643 | hsa-miR-4668-3p | chrX:74612619-74612626 | 8mer-1a | chrX:74612601-74612626 | 170.00 | -11.75 |
MSBB | ENST00000349225 | 74612582 | 74612643 | hsa-miR-4668-3p | chrX:74612619-74612626 | 8mer-1a | chrX:74612601-74612626 | 170.00 | -11.75 |
ROSMAP | ENST00000349225 | 74612582 | 74612643 | hsa-miR-4668-3p | chrX:74612619-74612626 | 8mer-1a | chrX:74612601-74612626 | 170.00 | -11.75 |
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SNVs in the skipped exons for RLIM |
- 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 RLIM |
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 RLIM |
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 RLIM |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
HCC | RBM3 | exon_skip_157692 | -4.916096e-01 | 3.638037e-17 |
IFG | RBM3 | exon_skip_157692 | -5.013154e-01 | 7.724608e-03 |
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RelatedDrugs for RLIM |
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 RLIM |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |