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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 PLOD3 |
 Gene summary |
| Gene information | Gene symbol | PLOD3 | Gene ID | 8985 |
| Gene name | procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | |
| Synonyms | LH3 | |
| Cytomap | 7q22.1 | |
| Type of gene | protein-coding | |
| Description | procollagen-lysine,2-oxoglutarate 5-dioxygenase 3lysine hydroxylase 3lysyl hydroxlase 3lysyl hydroxylase 3 | |
| Modification date | 20180523 | |
| UniProtAcc | O60568 | |
| Context | PubMed: PLOD3 [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 |
| PLOD3 | GO:0017185 | peptidyl-lysine hydroxylation | 9582318|9724729 |
| PLOD3 | GO:0046947 | hydroxylysine biosynthetic process | 9582318|9724729 |
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Exon skipping events across known transcript of Ensembl for PLOD3 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 PLOD3 |
| 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 PLOD3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_478421 | 7 | 100849257:100849717:100850059:100850185:100850858:100850948 | 100850059:100850185 | ENSG00000106397.7 | ENST00000223127.3 |
| exon_skip_478428 | 7 | 100850059:100850185:100850858:100851005:100852133:100852238 | 100850858:100851005 | ENSG00000106397.7 | ENST00000223127.3 |
| exon_skip_478443 | 7 | 100853636:100853725:100853812:100853954:100854871:100854953 | 100853812:100853954 | ENSG00000106397.7 | ENST00000223127.3 |
| exon_skip_478451 | 7 | 100855555:100855655:100855810:100855936:100856122:100856224 | 100855810:100855936 | ENSG00000106397.7 | ENST00000478082.1,ENST00000223127.3 |
| exon_skip_478453 | 7 | 100855533:100855655:100856122:100856224:100856387:100856485 | 100856122:100856224 | ENSG00000106397.7 | ENST00000421736.1 |
| exon_skip_478458 | 7 | 100856387:100856485:100858369:100858433:100859188:100859301 | 100858369:100858433 | ENSG00000106397.7 | ENST00000424135.1,ENST00000478082.1,ENST00000223127.3,ENST00000421736.1 |
| exon_skip_478459 | 7 | 100859975:100860067:100860446:100860699:100861129:100861180 | 100860446:100860699 | ENSG00000106397.7 | ENST00000456079.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PLOD3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_478421 | 7 | 100849257:100849717:100850059:100850185:100850858:100850948 | 100850059:100850185 | ENSG00000106397.7 | ENST00000223127.3 |
| exon_skip_478428 | 7 | 100850059:100850185:100850858:100851005:100852133:100852238 | 100850858:100851005 | ENSG00000106397.7 | ENST00000223127.3 |
| exon_skip_478443 | 7 | 100853636:100853725:100853812:100853954:100854871:100854953 | 100853812:100853954 | ENSG00000106397.7 | ENST00000223127.3 |
| exon_skip_478451 | 7 | 100855555:100855655:100855810:100855936:100856122:100856224 | 100855810:100855936 | ENSG00000106397.7 | ENST00000223127.3,ENST00000478082.1 |
| exon_skip_478453 | 7 | 100855533:100855655:100856122:100856224:100856387:100856485 | 100856122:100856224 | ENSG00000106397.7 | ENST00000421736.1 |
| exon_skip_478458 | 7 | 100856387:100856485:100858369:100858433:100859188:100859301 | 100858369:100858433 | ENSG00000106397.7 | ENST00000223127.3,ENST00000421736.1,ENST00000478082.1,ENST00000424135.1 |
| exon_skip_478459 | 7 | 100859975:100860067:100860446:100860699:100861129:100861180 | 100860446:100860699 | ENSG00000106397.7 | ENST00000456079.1 |
| 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 PLOD3 |
| 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 |
| ENST00000223127 | 100853812 | 100853954 | Frame-shift |
| ENST00000223127 | 100858369 | 100858433 | Frame-shift |
| ENST00000223127 | 100850059 | 100850185 | In-frame |
| ENST00000223127 | 100850858 | 100851005 | In-frame |
| ENST00000223127 | 100855810 | 100855936 | 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 |
| ENST00000223127 | 100853812 | 100853954 | Frame-shift |
| ENST00000223127 | 100858369 | 100858433 | Frame-shift |
| ENST00000223127 | 100850059 | 100850185 | In-frame |
| ENST00000223127 | 100850858 | 100851005 | In-frame |
| ENST00000223127 | 100855810 | 100855936 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PLOD3 |
| 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 |
| ENST00000223127 | 2937 | 738 | 100855810 | 100855936 | 1279 | 1404 | 293 | 335 |
| ENST00000223127 | 2937 | 738 | 100850858 | 100851005 | 2188 | 2334 | 596 | 645 |
| ENST00000223127 | 2937 | 738 | 100850059 | 100850185 | 2335 | 2460 | 645 | 687 |
| 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 |
| ENST00000223127 | 2937 | 738 | 100855810 | 100855936 | 1279 | 1404 | 293 | 335 |
| ENST00000223127 | 2937 | 738 | 100850858 | 100851005 | 2188 | 2334 | 596 | 645 |
| ENST00000223127 | 2937 | 738 | 100850059 | 100850185 | 2335 | 2460 | 645 | 687 |
| 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 |
| O60568 | 293 | 335 | 25 | 738 | Chain | ID=PRO_0000024686;Note=Procollagen-lysine%2C2-oxoglutarate 5-dioxygenase 3 |
| O60568 | 596 | 645 | 25 | 738 | Chain | ID=PRO_0000024686;Note=Procollagen-lysine%2C2-oxoglutarate 5-dioxygenase 3 |
| O60568 | 645 | 687 | 25 | 738 | Chain | ID=PRO_0000024686;Note=Procollagen-lysine%2C2-oxoglutarate 5-dioxygenase 3 |
| O60568 | 645 | 687 | 647 | 738 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| O60568 | 645 | 687 | 667 | 667 | Metal binding | Note=Iron;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| O60568 | 645 | 687 | 669 | 669 | Metal binding | Note=Iron;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| 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 |
| O60568 | 293 | 335 | 25 | 738 | Chain | ID=PRO_0000024686;Note=Procollagen-lysine%2C2-oxoglutarate 5-dioxygenase 3 |
| O60568 | 596 | 645 | 25 | 738 | Chain | ID=PRO_0000024686;Note=Procollagen-lysine%2C2-oxoglutarate 5-dioxygenase 3 |
| O60568 | 645 | 687 | 25 | 738 | Chain | ID=PRO_0000024686;Note=Procollagen-lysine%2C2-oxoglutarate 5-dioxygenase 3 |
| O60568 | 645 | 687 | 647 | 738 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| O60568 | 645 | 687 | 667 | 667 | Metal binding | Note=Iron;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
| O60568 | 645 | 687 | 669 | 669 | Metal binding | Note=Iron;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
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SNVs in the skipped exons for PLOD3 |
| - 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. |
PLOD3_LIHC_exon_skip_478451_psi_boxplot.png |
PLOD3_LUSC_exon_skip_478451_psi_boxplot.png |
PLOD3_STAD_exon_skip_478451_psi_boxplot.png |
| - 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-G3-A3CJ-01 | exon_skip_478421 | 100850060 | 100850185 | 100850179 | 100850179 | Frame_Shift_Del | C | - | p.A648fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_478428 | 100850859 | 100851005 | 100850940 | 100850940 | Frame_Shift_Del | C | - | p.G618fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_478443 | 100853813 | 100853954 | 100853921 | 100853921 | Frame_Shift_Del | G | - | p.A464fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_478451 | 100855811 | 100855936 | 100855824 | 100855824 | Frame_Shift_Del | A | - | p.F331fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_478451 | 100855811 | 100855936 | 100855841 | 100855841 | Frame_Shift_Del | G | - | p.P325fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_478451 | 100855811 | 100855936 | 100855879 | 100855879 | Frame_Shift_Del | G | - | p.R313fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| PRAD | TCGA-HC-7078-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| STAD | TCGA-BR-8368-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| STAD | TCGA-CG-4465-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| STAD | TCGA-CG-5723-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| UCEC | TCGA-AP-A0LG-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| UCEC | TCGA-BS-A0TE-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| LIHC | TCGA-4R-AA8I-01 | exon_skip_478453 | 100856123 | 100856224 | 100856126 | 100856126 | Frame_Shift_Del | C | - | p.Q293fs |
| UCEC | TCGA-B5-A0JZ-01 | exon_skip_478453 | 100856123 | 100856224 | 100856126 | 100856126 | Frame_Shift_Del | C | - | p.G292fs |
| UCEC | TCGA-DI-A0WH-01 | exon_skip_478453 | 100856123 | 100856224 | 100856126 | 100856126 | Frame_Shift_Del | C | - | p.G292fs |
| LUAD | TCGA-17-Z041-01 | exon_skip_478451 | 100855811 | 100855936 | 100855926 | 100855927 | Frame_Shift_Ins | - | G | p.G297fs |
| SKCM | TCGA-FS-A1Z3-06 | exon_skip_478451 | 100855811 | 100855936 | 100855926 | 100855927 | Frame_Shift_Ins | - | G | p.R297fs |
| STAD | TCGA-BR-8363-01 | exon_skip_478451 | 100855811 | 100855936 | 100855926 | 100855927 | Frame_Shift_Ins | - | G | p.R297fs |
| STAD | TCGA-FP-A4BE-01 | exon_skip_478451 | 100855811 | 100855936 | 100855926 | 100855927 | Frame_Shift_Ins | - | G | p.R297fs |
| STAD | TCGA-HU-A4GX-01 | exon_skip_478451 | 100855811 | 100855936 | 100855926 | 100855927 | Frame_Shift_Ins | - | G | p.R297fs |
| UCEC | TCGA-D1-A17B-01 | exon_skip_478451 | 100855811 | 100855936 | 100855926 | 100855927 | Frame_Shift_Ins | - | G | p.R297fs |
| STAD | TCGA-BR-8363-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855928 | Frame_Shift_Ins | - | G | p.R297fs |
| STAD | TCGA-FP-A4BE-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855928 | Frame_Shift_Ins | - | G | p.R297fs |
| STAD | TCGA-HU-A4GX-01 | exon_skip_478451 | 100855811 | 100855936 | 100855927 | 100855928 | Frame_Shift_Ins | - | G | p.R297fs |
| KIRC | TCGA-A3-3313-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| KIRC | TCGA-A3-3363-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| KIRC | TCGA-A3-3372-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| KIRC | TCGA-A3-3378-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| KIRC | TCGA-A3-3380-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| KIRC | TCGA-AK-3427-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| KIRC | TCGA-AS-3778-01 | exon_skip_478453 | 100856123 | 100856224 | 100856125 | 100856126 | Frame_Shift_Ins | - | C | p.A293fs |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_478443 | 100853813 | 100853954 | 100853821 | 100853821 | Nonsense_Mutation | G | A | p.R498* |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_478451 | 100855811 | 100855936 | 100855870 | 100855870 | Nonsense_Mutation | G | A | p.Q316* |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_478451 | 100855811 | 100855936 | 100855870 | 100855870 | Nonsense_Mutation | G | A | p.Q316X |
| LUSC | TCGA-21-5784-01 | exon_skip_478451 | 100855811 | 100855936 | 100855937 | 100855937 | Splice_Site | C | G | p.P294_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-21-5784-01 |
| Cancer type: LUSC | |
| ESID: exon_skip_478451 | |
| Skipped exon start: 100855811 | |
| Skipped exon end: 100855936 | |
| Mutation start: 100855937 | |
| Mutation end: 100855937 | |
| Mutation type: Splice_Site | |
| Reference seq: C | |
| Mutation seq: G | |
| AAchange: p.P294_splice | |
exon_skip_286384_LUSC_TCGA-21-5784-01.png | |
exon_skip_478451_LUSC_TCGA-21-5784-01.png | |
| - 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 |
| DOV13_OVARY | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| TOV21G_OVARY | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| RKO_LARGE_INTESTINE | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| CCK81_LARGE_INTESTINE | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| IGROV1_OVARY | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| KM12_LARGE_INTESTINE | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100855811 | 100855936 | 100855927 | 100855927 | Frame_Shift_Del | G | - | p.R297fs |
| SNUC4_LARGE_INTESTINE | 100856123 | 100856224 | 100856126 | 100856126 | Frame_Shift_Del | C | - | p.G292fs |
| SNU61_LARGE_INTESTINE | 100860447 | 100860699 | 100860503 | 100860504 | In_Frame_Ins | - | GCAGCAGCG | p.17_18insPLL |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100850859 | 100851005 | 100850873 | 100850873 | Missense_Mutation | C | T | p.G641S |
| EN_ENDOMETRIUM | 100850859 | 100851005 | 100850969 | 100850969 | Missense_Mutation | T | C | p.T609A |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100853813 | 100853954 | 100853840 | 100853840 | Missense_Mutation | C | A | p.M491I |
| MLMA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100853813 | 100853954 | 100853853 | 100853853 | Missense_Mutation | G | C | p.T487R |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100853813 | 100853954 | 100853916 | 100853916 | Missense_Mutation | A | G | p.V466A |
| RCM1_LARGE_INTESTINE | 100853813 | 100853954 | 100853919 | 100853919 | Missense_Mutation | T | C | p.Y465C |
| SNU1040_LARGE_INTESTINE | 100853813 | 100853954 | 100853935 | 100853935 | Missense_Mutation | A | T | p.Y460N |
| MYLA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100856123 | 100856224 | 100856133 | 100856133 | Missense_Mutation | G | C | p.P290R |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 100856123 | 100856224 | 100856145 | 100856145 | Missense_Mutation | C | A | p.R286L |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 100856123 | 100856224 | 100856148 | 100856148 | Missense_Mutation | T | G | p.D285A |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 100856123 | 100856224 | 100856149 | 100856149 | Missense_Mutation | C | T | p.D285N |
| PACADD137_PANCREAS | 100856123 | 100856224 | 100856199 | 100856199 | Missense_Mutation | T | C | p.Y268C |
| FTC238_THYROID | 100858370 | 100858433 | 100858379 | 100858379 | Missense_Mutation | C | T | p.G224R |
| COLO824_BREAST | 100858370 | 100858433 | 100858408 | 100858408 | Missense_Mutation | T | A | p.H214L |
| NCIH1648_LUNG | 100858370 | 100858433 | 100858409 | 100858409 | Missense_Mutation | G | A | p.H214Y |
| ASH3_THYROID | 100850859 | 100851005 | 100850904 | 100850904 | Nonsense_Mutation | A | C | p.Y630* |
| NCIH508_LARGE_INTESTINE | 100855811 | 100855936 | 100855870 | 100855870 | Nonsense_Mutation | G | A | p.Q316* |
| SAS_UPPER_AERODIGESTIVE_TRACT | 100856123 | 100856224 | 100856184 | 100856184 | Nonsense_Mutation | C | T | p.W273* |
| MCIXC_AUTONOMIC_GANGLIA | 100850060 | 100850185 | 100850184 | 100850184 | Splice_Site | G | A | p.A646V |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLOD3 |
| 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 PLOD3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLOD3 |
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RelatedDrugs for PLOD3 |
| 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 |
| O60568 | DB00126 | Ascorbic acid | Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | small molecule | approved|nutraceutical |
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RelatedDiseases for PLOD3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PLOD3 | C2676285 | Bone Fragility with Contractures, Arterial Rupture, and Deafness | 1 | CTD_human;ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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