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Translation Factor: COA3 (NCBI Gene ID:28958) |
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 Gene Summary |
| Gene Information | Gene Name: COA3 | Gene ID: 28958 | Gene Symbol | COA3 | Gene ID | 28958 |
| Gene Name | cytochrome c oxidase assembly factor 3 | |
| Synonyms | CCDC56|COX25|HSPC009|MITRAC12 | |
| Cytomap | 17q21.2 | |
| Type of Gene | protein-coding | |
| Description | cytochrome c oxidase assembly factor 3 homolog, mitochondrialcoiled-coil domain-containing protein 56cytochrome C oxidase assembly factor 3 homolog, mitochondrialcytochrome c oxidase assembly protein 3 homolog, mitochondrialmitochondrial translation r | |
| Modification date | 20200313 | |
| UniProtAcc | Q9Y2R0 | |
| 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 |
| COA3 | (733 - 1119.25] |
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| We searched PubMed using 'COA3[title] AND translation [title] AND human.' |
| Gene | Title | PMID |
| COA3 | . | . |
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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 COA3 (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 |
| PRAD | COA3 | COX5A | -1.50957833695125 | 0.00032729612581089 |
| KIRP | COA3 | COX4I1 | 1.43810228138948 | 0.000713176093995571 |
| COAD | COA3 | COX15 | -2.5974345550705 | 0.00197160243988037 |
| HNSC | COA3 | SURF1 | 2.02861077453821 | 0.00302236390302824 |
| CHOL | COA3 | TACO1 | -8.87050800605738 | 0.00390625 |
| CHOL | COA3 | SURF1 | -4.66180670817039 | 0.0078125 |
| BRCA | COA3 | COX5A | -1.1228309402962 | 1.10165204902036e-07 |
| COAD | COA3 | COX5A | -1.28758365707444 | 1.1056661605835e-05 |
| LUAD | COA3 | COX5A | -1.19611349201209 | 1.55866533367651e-05 |
| KICH | COA3 | COX5A | 1.89560737971351 | 1.78813934326172e-07 |
| COAD | COA3 | COX4I1 | -1.19884063606806 | 2.62260437011719e-06 |
| KICH | COA3 | COX4I1 | 1.48645262483204 | 6.36577606201172e-05 |
| BRCA | COA3 | TACO1 | -2.33803140550261 | 7.20141361596004e-14 |
| LUAD | COA3 | TACO1 | -4.94497725815155 | 9.56799412915172e-10 |
| Protein-protein interactors with this translation factor (BIOGRID-3.4.160) |
| PPI interactors with COA3 |
| MOV10, Smc3, COQ9, NDUFA4, C15orf48, CHCHD10, COX1, COX2, COX3, COX4I1, COX4I2, COX5A, NDUFA9, NDUFV1, TUFM, SLIRP, LRPPRC, EGFR, K8.1, SGTA, AFG3L2, COA3, CTNNBL1, FAM208A, MBTPS2, PPCS, TAZ, MAD2L2, PHB, PHB2, SLC25A24, ATP5O, NIPSNAP1, ATP5H, CYB5A, NDUFB10, MGST1, ATP5F1, HADHB, VAPB, COX7C, NDUFB1, SCCPDH, OCIAD1, NDUFA8, MTCH2, ATP5B, ATP5C1, ATP6V1A, C20orf24, CANX, COX7A2, CYC1, HADHA, MGST3, MINOS1, NDUFB8, NDUFS1, NDUFS2, NDUFS3, NDUFS7, NDUFS8, OGDH, PCCB, PDHA1, PDHB, TOMM40, TOMM5, UQCRC1, UQCRC2, UQCRQ, VDAC2, VDAC3, LMBR1L, Hsp22, SURF1, TMEM70, COPS5, DNAJA3, CXCL2, SNX25, CMC1, COX5B, CUX1, SLC9A1, COX14, |
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| Clinically associated variants from ClinVar. |
| Gene | Chr | Position | RefSeq | VarSeq | RefSeeq | VarType | Pathogenic | Disease | VarInfo |
| COA3 | chr17 | 40950185 | T | C | single_nucleotide_variant | Pathogenic | Mitochondrial_complex_IV_deficiency | SO:0001583|missense_variant | SO:0001583|missense_variant |
| COA3 | chr17 | 40950500 | A | AG | Duplication | Pathogenic | Mitochondrial_complex_IV_deficiency | SO:0001589|frameshift_variant | SO:0001589|frameshift_variant |
| nsSNVs with sample frequency (size of circle) from TCGA 33 cancers. |
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| SNVs and Indels |
| Gene | Cancer type | Chromosome | Start | End | RefSeeq | MutSeq | Mutation type | AAchange | # samples |
| COA3 | CESC | chr17 | 40950669 | 40950669 | C | G | Missense_Mutation | 2 | |
| COA3 | SARC | chr17 | 40950489 | 40950489 | T | C | Missense_Mutation | 2 | |
| COA3 | SARC | chr17 | 40950489 | 40950489 | T | C | Missense_Mutation | p.I71V | 2 |
| COA3 | SKCM | chr17 | 40950543 | 40950543 | G | A | Missense_Mutation | p.R53W | 1 |
| COA3 | BLCA | chr17 | 40950643 | 40950643 | G | A | Silent | p.F19F | 1 |
| COA3 | TGCT | chr17 | 40950543 | 40950543 | G | T | Silent | p.R53R | 1 |
| COA3 | THYM | chr17 | 40950616 | 40950616 | C | T | Silent | 1 | |
| COA3 | CESC | chr17 | 40950669 | 40950669 | C | G | Missense_Mutation | p.D11H | 1 |
| COA3 | THYM | chr17 | 40950616 | 40950616 | C | T | Silent | p.E28E | 1 |
| COA3 | ESCA | chr17 | 40950176 | 40950176 | G | T | Missense_Mutation | p.T75N | 1 |
| COA3 | HNSC | chr17 | 40950578 | 40950578 | G | C | Missense_Mutation | 1 | |
| COA3 | LGG | chr17 | 40950138 | 40950138 | G | A | Silent | p.L88L | 1 |
| COA3 | LGG | chr17 | 40950138 | 40950138 | G | A | Silent | 1 | |
| COA3 | SARC | chr17 | 40950600 | 40950600 | G | T | Missense_Mutation | 1 | |
| COA3 | BLCA | chr17 | 40950665 | 40950665 | G | A | Missense_Mutation | 1 | |
| COA3 | BLCA | chr17 | 40950643 | 40950643 | G | A | Silent | 1 |
| Copy number variation (CNV) of COA3 * 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 COA3 * 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 |
| 23460 | STAD | TCGA-BR-8364-01A | DNAJC14 | chr12 | 56223297 | - | COA3 | chr17 | 40950715 | - |
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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 |
| C0268237 | Cytochrome-c Oxidase Deficiency | 1 | ORPHANET |
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