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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 DDX54 |
 Gene summary |
| Gene information | Gene symbol | DDX54 | Gene ID | 79039 |
| Gene name | DEAD-box helicase 54 | |
| Synonyms | DP97 | |
| Cytomap | 12q24.13 | |
| Type of gene | protein-coding | |
| Description | ATP-dependent RNA helicase DDX54ATP-dependent RNA helicase DP97DEAD (Asp-Glu-Ala-Asp) box polypeptide 54DEAD box RNA helicase 97 kDaDEAD box helicase 97 KDaDEAD box protein 54 | |
| Modification date | 20180522 | |
| UniProtAcc | Q8TDD1 | |
| Context | PubMed: DDX54 [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 |
| DDX54 | GO:0006396 | RNA processing | 12466272 |
| DDX54 | GO:0016070 | RNA metabolic process | 12466272 |
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Exon skipping events across known transcript of Ensembl for DDX54 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 DDX54 |
| 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 DDX54 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_96808 | 12 | 113600736:113600850:113600936:113601079:113601871:113601898 | 113600936:113601079 | ENSG00000123064.8 | ENST00000314045.7,ENST00000548786.1,ENST00000306014.5,ENST00000550016.1 |
| exon_skip_96812 | 12 | 113600936:113601079:113601871:113602090:113603448:113603483 | 113601871:113602090 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5,ENST00000550016.1 |
| exon_skip_96818 | 12 | 113603448:113603522:113603606:113603837:113607574:113607709 | 113603606:113603837 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96820 | 12 | 113603606:113603837:113607574:113607709:113610157:113610368 | 113607574:113607709 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96821 | 12 | 113607574:113607709:113610157:113610368:113612444:113612576 | 113610157:113610368 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96822 | 12 | 113610157:113610368:113612444:113612576:113612679:113612741 | 113612444:113612576 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96825 | 12 | 113614856:113614898:113616781:113616831:113616947:113617136 | 113616781:113616831 | ENSG00000123064.8 | ENST00000314045.7,ENST00000551344.1,ENST00000306014.5,ENST00000552375.1 |
| exon_skip_96827 | 12 | 113616947:113617136:113617739:113617810:113618733:113618863 | 113617739:113617810 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5,ENST00000552375.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for DDX54 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_96808 | 12 | 113600736:113600850:113600936:113601079:113601871:113601898 | 113600936:113601079 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5,ENST00000550016.1,ENST00000548786.1 |
| exon_skip_96812 | 12 | 113600936:113601079:113601871:113602090:113603448:113603483 | 113601871:113602090 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5,ENST00000550016.1 |
| exon_skip_96818 | 12 | 113603448:113603522:113603606:113603837:113607574:113607709 | 113603606:113603837 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96820 | 12 | 113603606:113603837:113607574:113607709:113610157:113610368 | 113607574:113607709 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96821 | 12 | 113607574:113607709:113610157:113610368:113612444:113612576 | 113610157:113610368 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96822 | 12 | 113610157:113610368:113612444:113612576:113612679:113612741 | 113612444:113612576 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5 |
| exon_skip_96825 | 12 | 113614856:113614898:113616781:113616831:113616947:113617136 | 113616781:113616831 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5,ENST00000551344.1,ENST00000552375.1 |
| exon_skip_96827 | 12 | 113616947:113617136:113617739:113617810:113618733:113618863 | 113617739:113617810 | ENSG00000123064.8 | ENST00000314045.7,ENST00000306014.5,ENST00000552375.1 |
| 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 DDX54 |
| 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 |
| ENST00000306014 | 113600936 | 113601079 | Frame-shift |
| ENST00000306014 | 113610157 | 113610368 | Frame-shift |
| ENST00000306014 | 113616781 | 113616831 | Frame-shift |
| ENST00000306014 | 113617739 | 113617810 | Frame-shift |
| ENST00000306014 | 113601871 | 113602090 | In-frame |
| ENST00000306014 | 113603606 | 113603837 | In-frame |
| ENST00000306014 | 113607574 | 113607709 | In-frame |
| ENST00000306014 | 113612444 | 113612576 | 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 |
| ENST00000306014 | 113600936 | 113601079 | Frame-shift |
| ENST00000306014 | 113610157 | 113610368 | Frame-shift |
| ENST00000306014 | 113616781 | 113616831 | Frame-shift |
| ENST00000306014 | 113617739 | 113617810 | Frame-shift |
| ENST00000306014 | 113601871 | 113602090 | In-frame |
| ENST00000306014 | 113603606 | 113603837 | In-frame |
| ENST00000306014 | 113607574 | 113607709 | In-frame |
| ENST00000306014 | 113612444 | 113612576 | In-frame |
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Infer the effects of exon skipping event on protein functional features for DDX54 |
| 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 |
| ENST00000306014 | 4394 | 881 | 113612444 | 113612576 | 965 | 1096 | 312 | 356 |
| ENST00000306014 | 4394 | 881 | 113607574 | 113607709 | 1308 | 1442 | 426 | 471 |
| ENST00000306014 | 4394 | 881 | 113603606 | 113603837 | 1443 | 1673 | 471 | 548 |
| ENST00000306014 | 4394 | 881 | 113601871 | 113602090 | 1748 | 1966 | 573 | 646 |
| 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 |
| ENST00000306014 | 4394 | 881 | 113612444 | 113612576 | 965 | 1096 | 312 | 356 |
| ENST00000306014 | 4394 | 881 | 113607574 | 113607709 | 1308 | 1442 | 426 | 471 |
| ENST00000306014 | 4394 | 881 | 113603606 | 113603837 | 1443 | 1673 | 471 | 548 |
| ENST00000306014 | 4394 | 881 | 113601871 | 113602090 | 1748 | 1966 | 573 | 646 |
| 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 |
| Q8TDD1 | 312 | 356 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 312 | 356 | 326 | 473 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q8TDD1 | 426 | 471 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 426 | 471 | 326 | 473 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q8TDD1 | 471 | 548 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 471 | 548 | 326 | 473 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q8TDD1 | 573 | 646 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 573 | 646 | 644 | 644 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| Q8TDD1 | 573 | 646 | 605 | 647 | Region | Note=Interaction with nuclear receptors |
| 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 |
| Q8TDD1 | 312 | 356 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 312 | 356 | 326 | 473 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q8TDD1 | 426 | 471 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 426 | 471 | 326 | 473 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q8TDD1 | 471 | 548 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 471 | 548 | 326 | 473 | Domain | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 |
| Q8TDD1 | 573 | 646 | 1 | 881 | Chain | ID=PRO_0000055056;Note=ATP-dependent RNA helicase DDX54 |
| Q8TDD1 | 573 | 646 | 644 | 644 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| Q8TDD1 | 573 | 646 | 605 | 647 | Region | Note=Interaction with nuclear receptors |
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SNVs in the skipped exons for DDX54 |
| - 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. |
| - 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-DD-A39Y-01 | exon_skip_96818 | 113603607 | 113603837 | 113603629 | 113603629 | Frame_Shift_Del | C | - | p.G541fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_96818 | 113603607 | 113603837 | 113603629 | 113603629 | Frame_Shift_Del | C | - | p.G541fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_96818 | 113603607 | 113603837 | 113603732 | 113603732 | Frame_Shift_Del | C | - | p.G507fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_96818 | 113603607 | 113603837 | 113603732 | 113603732 | Frame_Shift_Del | C | - | p.G507fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_96821 | 113610158 | 113610368 | 113610189 | 113610189 | Frame_Shift_Del | G | - | p.P416fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_96827 | 113617740 | 113617810 | 113617788 | 113617788 | Frame_Shift_Del | T | - | p.K109fs |
| LUSC | TCGA-34-2596-01 | exon_skip_96812 | 113601872 | 113602090 | 113601994 | 113601994 | Nonsense_Mutation | G | A | p.Q606* |
| STAD | TCGA-BR-8591-01 | exon_skip_96808 | 113600937 | 113601079 | 113600936 | 113600936 | Splice_Site | C | - | . |
| STAD | TCGA-BR-8591-01 | exon_skip_96808 | 113600937 | 113601079 | 113600936 | 113600936 | Splice_Site | C | - | p.G694_splice |
| - 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 |
| CAPAN2_PANCREAS | 113601872 | 113602090 | 113601959 | 113601960 | Frame_Shift_Ins | - | C | p.G617fs |
| MEL202_EYE | 113600937 | 113601079 | 113600980 | 113600980 | Missense_Mutation | A | G | p.F680L |
| MFE319_ENDOMETRIUM | 113600937 | 113601079 | 113601012 | 113601012 | Missense_Mutation | C | T | p.R669Q |
| NCIH1618_LUNG | 113600937 | 113601079 | 113601030 | 113601030 | Missense_Mutation | T | G | p.N663T |
| SNGM_ENDOMETRIUM | 113600937 | 113601079 | 113601069 | 113601069 | Missense_Mutation | G | A | p.S650L |
| 201T_LUNG | 113601872 | 113602090 | 113601960 | 113601960 | Missense_Mutation | C | T | p.G617D |
| HEC108_ENDOMETRIUM | 113601872 | 113602090 | 113601979 | 113601979 | Missense_Mutation | G | A | p.R611W |
| MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 113601872 | 113602090 | 113602002 | 113602002 | Missense_Mutation | C | T | p.R603H |
| CP66MEL_SKIN | 113603607 | 113603837 | 113603616 | 113603616 | Missense_Mutation | G | A | p.P546S |
| RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 113603607 | 113603837 | 113603697 | 113603697 | Missense_Mutation | A | G | p.Y519H |
| HEC59_ENDOMETRIUM | 113603607 | 113603837 | 113603822 | 113603822 | Missense_Mutation | T | C | p.D477G |
| GP2D_LARGE_INTESTINE | 113603607 | 113603837 | 113603822 | 113603822 | Missense_Mutation | T | C | p.D477G |
| JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 113607575 | 113607709 | 113607599 | 113607599 | Missense_Mutation | C | T | p.A464T |
| EN_ENDOMETRIUM | 113607575 | 113607709 | 113607634 | 113607634 | Missense_Mutation | T | C | p.D452G |
| NUGC3_STOMACH | 113610158 | 113610368 | 113610163 | 113610163 | Missense_Mutation | C | T | p.R425H |
| MEWO_SKIN | 113610158 | 113610368 | 113610287 | 113610287 | Missense_Mutation | A | T | p.F384I |
| NCIH2081_LUNG | 113610158 | 113610368 | 113610314 | 113610314 | Missense_Mutation | T | C | p.T375A |
| C33A_CERVIX | 113612445 | 113612576 | 113612537 | 113612537 | Missense_Mutation | C | T | p.V326M |
| LOVO_LARGE_INTESTINE | 113612445 | 113612576 | 113612564 | 113612564 | Missense_Mutation | G | T | p.L317I |
| RCM1_LARGE_INTESTINE | 113617740 | 113617810 | 113617750 | 113617750 | Missense_Mutation | A | T | p.I122N |
| A388_SKIN | 113617740 | 113617810 | 113617753 | 113617753 | Missense_Mutation | G | T | p.P121H |
| SNUC4_LARGE_INTESTINE | 113601872 | 113602090 | 113602063 | 113602063 | Nonsense_Mutation | G | A | p.R583* |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 113616782 | 113616831 | 113616782 | 113616782 | Splice_Site | C | T | p.R205K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DDX54 |
| 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 DDX54 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for DDX54 |
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RelatedDrugs for DDX54 |
| 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 DDX54 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| DDX54 | C0023903 | Liver neoplasms | 1 | CTD_human |
| DDX54 | C0032460 | Polycystic Ovary Syndrome | 1 | CTD_human |
| DDX54 | C0032927 | Precancerous Conditions | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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