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Translation Factor: RCC1L (NCBI Gene ID:81554) |
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 Gene Summary |
| Gene Information | Gene Name: RCC1L | Gene ID: 81554 | Gene Symbol | RCC1L | Gene ID | 81554 |
| Gene Name | RCC1 like | |
| Synonyms | WBSCR16 | |
| Cytomap | 7q11.23 | |
| Type of Gene | protein-coding | |
| Description | RCC1-like G exchanging factor-like proteinWilliams-Beuren syndrome chromosomal region 16 proteinWilliams-Beuren syndrome chromosome region 16 | |
| Modification date | 20200313 | |
| UniProtAcc | Q96I51 | |
| Child GO biological process term(s) under GO:0006412 |
| GO ID | GO term |
| GO:0006417 | Regulation of translation |
| GO:0032543 | Mitochondrial translation |
| GO:0045727 | Positive regulation of translation |
| GO:0006412 | Translation |
| Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Inferred gene age of translation factor. |
| Gene | Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25 |
| RCC1L | >1119.25 |
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| We searched PubMed using 'RCC1L[title] AND translation [title] AND human.' |
| Gene | Title | PMID |
| RCC1L | . | . |
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| 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. For more annotations, please visit our ExonSkipDB. |
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| Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ENST | Exon skip start (DNA) | Exon Skip end (DNA) | ORF |
| Exon skipping position in the amino acid sequence. |
| ENST | Exon skip start (DNA) | Exon Skip end (DNA) | Len(transcript seq) | Exon skip start (mRNA) | Exon Skip end (mRNA) | Len(amino acid seq) | Exon skip start (AA) | Exon Skip end (AA) |
| Potentially (partially) lost protein functional features of UniProt. |
| UniProtAcc | Exon skip start (AA) | Exon Skip end (AA) | Function feature start (AA) | Function feature end (AA) | Functional feature type | Functional feature desc. |
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| Gene expression level across TCGA pancancer |
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| Gene expression level across GTEx pantissue |
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| Expression level of gene isoforms across TCGA pancancer |
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| Expression level of gene isoforms across GTEx pantissue |
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| Cancer(tissue) type-specific expression level of Translation factor using z-score distriution |
| Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples) |
| Cancer type | Translation factor | FC | adj.pval |
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| Translation factor expression regulation through miRNA binding |
| Cancer type | Gene | miRNA | TargetScan binding score (Context++ score percentile) | Coefficient | Pvalue |
| Translation factor expression regulation through methylation in the promoter of Translation factor |
| Cancer type | Gene | methyl group b | methyl group a | DEG pval | avg methyl in b | avg methyl in a | avg exp in b | avg exp in a |
| Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation) |
| Cancer type | Gene | methyl group b | methyl group a | DEG pval | avg methyl in b | avg methyl in a | avg exp in b | avg exp in a |
| Translation factor expression regulation through copy number variation of Translation factor |
| Cancer type | Gene | Coefficient | Pvalue |
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| Strongly correlated genes belong to cellular important gene groups with RCC1L (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green) |
| Cancer type | Gene group | Translation factor | Correlated gene | Coefficient | Pvalue |
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| Protein 3D structure Visit iCn3D. |
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| Protein-protein interaction networks * Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P)) |
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| Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P)) |
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 * Edge colors based on TCGA cancer types. |
| * Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P)) |
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| Cancer type | Translation factor | Interacting protein coding gene | FC | adj.pval |
| KICH | RCC1L | WBSCR16 | 1.5230976821616 | 0.000162303447723389 |
| KICH | RCC1L | UBE3B | 1.48046532601591 | 0.000187873840332031 |
| STAD | RCC1L | WBSCR16 | -1.13833861108984 | 0.000433447770774365 |
| KIRC | RCC1L | CEP290 | 2.01274993761606 | 0.00050811011383314 |
| PRAD | RCC1L | CEP290 | 1.12609973856799 | 0.00539979031822387 |
| STAD | RCC1L | RAN | -1.27021088526323 | 0.00647870777174831 |
| KICH | RCC1L | TRUB2 | -2.06154942711577 | 0.00882232189178467 |
| STAD | RCC1L | RPUSD4 | -1.77759628022672 | 0.0148032568395138 |
| ESCA | RCC1L | TRUB2 | -1.63055491619549 | 0.0185546875 |
| LUSC | RCC1L | PDE6D | -1.80270759082532 | 0.0193520018513058 |
| LIHC | RCC1L | FASTKD2 | -2.17426498508978 | 0.0264015241133303 |
| CHOL | RCC1L | TRUB2 | -2.3070167517537 | 0.02734375 |
| HNSC | RCC1L | UBE3B | -7.33002785622862 | 0.038631391710851 |
| HNSC | RCC1L | FASTKD2 | -1.72219345188751 | 0.0410440647583528 |
| ESCA | RCC1L | RAN | -1.60475857712189 | 0.0419921875 |
| UCEC | RCC1L | CEP290 | -2.35798420010899 | 0.046875 |
| KIRC | RCC1L | RPUSD3 | 1.03010103400179 | 1.09375608261512e-08 |
| BRCA | RCC1L | PDE6D | -1.63708541356331 | 1.19549556846834e-14 |
| HNSC | RCC1L | RPUSD4 | -3.64823171256213 | 1.42088565553422e-05 |
| THCA | RCC1L | CEP290 | -1.40035509707833 | 1.44893111105687e-05 |
| BRCA | RCC1L | TRUB2 | -2.53279756068983 | 1.7326162077773e-13 |
| LUSC | RCC1L | WBSCR16 | -2.87043544276894 | 1.86041017272598e-07 |
| LUSC | RCC1L | TRUB2 | -3.50473378801546 | 1.91629083762368e-08 |
| HNSC | RCC1L | RAN | 2.26649469099398 | 2.97245203455532e-05 |
| LUAD | RCC1L | WBSCR16 | -2.84505915400831 | 3.09848396407815e-08 |
| BRCA | RCC1L | RAN | -3.8324290184836 | 3.15616171635324e-25 |
| PRAD | RCC1L | NGRN | -1.95446330682921 | 3.16187259327918e-07 |
| LIHC | RCC1L | PDE6D | -1.02375714851873 | 3.27330247270532e-06 |
| HNSC | RCC1L | CEP290 | -1.50219778925446 | 3.30502848555626e-06 |
| LUAD | RCC1L | PDE6D | -2.99122861667671 | 3.32622703073417e-05 |
| LUAD | RCC1L | TRUB2 | -1.92983802030623 | 3.47524877088934e-09 |
| BRCA | RCC1L | FASTKD2 | -1.95659368089906 | 4.12639478109604e-08 |
| KIRP | RCC1L | RAN | -1.52465218388642 | 4.5965425670147e-06 |
| LIHC | RCC1L | RAN | -1.18561048767513 | 4.92124311953285e-07 |
| KIRC | RCC1L | RPUSD4 | -3.43456748913004 | 9.61177113723533e-08 |
| Protein-protein interactors with this translation factor (BIOGRID-3.4.160) |
| PPI interactors with RCC1L |
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| Clinically associated variants from ClinVar. |
| Gene | Chr | Position | RefSeq | VarSeq | RefSeeq | VarType | Pathogenic | Disease | VarInfo |
| RCC1L | chr7 | 74470190 | C | A | single_nucleotide_variant | Benign | not_provided | SO:0001627|intron_variant | SO:0001627|intron_variant |
| nsSNVs with sample frequency (size of circle) from TCGA 33 cancers. |
| SNVs and Indels |
| Gene | Cancer type | Chromosome | Start | End | RefSeeq | MutSeq | Mutation type | AAchange | # samples |
| Copy number variation (CNV) of RCC1L * Click on the image to open the original image in a new window. |
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| Fusion gene breakpoints (product of the structural variants (SVs)) across RCC1L * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion genes with this translation factor from FusionGDB2.0. |
| FusionGDB2 ID | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
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| Kaplan-Meier plots with logrank tests of overall survival (OS) |
| Cancer type | Translation factor | Coefficent | Hazard ratio | Wald test pval | Likelihool ratio pval | Logrank test pval | # samples |
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| Differential gene expression between female and male. (Wilcoxon test, pval<0.05) |
| Cancer type | Translation factor | pval | adj.p |
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| Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05) |
| Cancer type | Translation factor | pval | adj.p |
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| Drugs targeting genes involved in this translation factor. (DrugBank Version 5.1.8 2021-05-08) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| Diseases associated with this translation factor. (DisGeNet 4.0) |
| Disease ID | Disease Name | # PubMeds | Disease source |
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