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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 RECQL4 |
Gene summary |
Gene information | Gene symbol | RECQL4 | Gene ID | 9401 |
Gene name | RecQ like helicase 4 | |
Synonyms | RECQ4 | |
Cytomap | 8q24.3 | |
Type of gene | protein-coding | |
Description | ATP-dependent DNA helicase Q4DNA helicase, RecQ-like, type 4RecQ helicase-like 4RecQ protein-like 4 | |
Modification date | 20200313 | |
UniProtAcc | A0A087WTJ0, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
RECQL4 | GO:0000733 | DNA strand renaturation | 19177149 |
RECQL4 | GO:0006260 | DNA replication | 19177149 |
RECQL4 | GO:0032508 | DNA duplex unwinding | 19177149 |
RECQL4 | GO:0061820 | telomeric D-loop disassembly | 22039056 |
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Gene structures and expression levels for RECQL4 |
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 | ENST00000621189.4 | RECQL4-210:protein_coding:RECQL4 | 4.310378e+02 | 8.538543e-01 | 1.299830e-09 | 5.407214e-08 |
CB | UP | ENST00000534538.1 | RECQL4-207:nonsense_mediated_decay:RECQL4 | 1.278791e+01 | 8.809685e-01 | 8.686278e-07 | 1.329825e-05 |
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 RECQL4 |
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_112368 | chr8 | 144515326:144515457:144515764:144515890:144515988:144516003 | 144515764:144515890 |
exon_skip_152955 | chr8 | 144512144:144512324:144512392:144512561:144512642:144512713 | 144512392:144512561 |
exon_skip_156595 | chr8 | 144514936:144515072:144515150:144515242:144515326:144515453 | 144515150:144515242 |
exon_skip_168027 | chr8 | 144513416:144513480:144513571:144513712:144513928:144513940 | 144513571:144513712 |
exon_skip_187464 | chr8 | 144511681:144511789:144511911:144512067:144512144:144512324 | 144511911:144512067 |
exon_skip_247135 | chr8 | 144511681:144511789:144511902:144512067:144512144:144512324 | 144511902:144512067 |
exon_skip_55519 | chr8 | 144514936:144515042:144515150:144515242:144515326:144515453 | 144515150:144515242 |
exon_skip_79732 | chr8 | 144513416:144513480:144513571:144513712:144513928:144514107 | 144513571:144513712 |
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 RECQL4 |
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 |
ENST00000617875 | 144511911 | 144512067 | Frame-shift |
ENST00000617875 | 144512392 | 144512561 | Frame-shift |
ENST00000617875 | 144513571 | 144513712 | Frame-shift |
ENST00000617875 | 144515764 | 144515890 | Frame-shift |
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 |
ENST00000617875 | 144513571 | 144513712 | Frame-shift |
ENST00000617875 | 144515764 | 144515890 | Frame-shift |
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 |
ENST00000617875 | 144511911 | 144512067 | Frame-shift |
ENST00000617875 | 144512392 | 144512561 | Frame-shift |
ENST00000617875 | 144513571 | 144513712 | Frame-shift |
ENST00000617875 | 144515764 | 144515890 | Frame-shift |
ENST00000617875 | 144515150 | 144515242 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RECQL4 |
p-ENSG00000160957_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 |
ENST00000617875 | 3826 | 1208 | 144515150 | 144515242 | 1433 | 1524 | 463 | 494 |
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 |
O94761 | 463 | 494 | 1 | 1208 | Chain | ID=PRO_0000205053;Note=ATP-dependent DNA helicase Q4 |
O94761 | 463 | 494 | 489 | 662 | Domain | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
O94761 | 463 | 494 | 467 | 476 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LST |
O94761 | 463 | 494 | 485 | 492 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LST |
O94761 | 463 | 494 | 493 | 495 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5LST |
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3'-UTR located exon skipping events that lost miRNA binding sites in RECQL4 |
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 |
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SNVs in the skipped exons for RECQL4 |
- 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 RECQL4 |
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 RECQL4 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
CB | exon_skip_112368 | rs4925811 | chr8:144577063 | 6.602565e-05 | 1.241578e-02 |
CB | exon_skip_112368 | rs10108150 | chr8:144462092 | 2.449505e-04 | 3.487134e-02 |
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Correlation with RNA binding proteins (RBPs) for RECQL4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | CNOT4 | exon_skip_168027 | 5.189277e-01 | 3.343365e-12 |
CB | FUBP1 | exon_skip_168027 | 4.494177e-01 | 3.542639e-09 |
CB | EIF4G2 | exon_skip_168027 | 4.193448e-01 | 4.590500e-08 |
CB | RBM4 | exon_skip_168027 | 6.172251e-01 | 7.397352e-18 |
CB | RBM4B | exon_skip_168027 | 4.879702e-01 | 9.029644e-11 |
CB | TRA2A | exon_skip_112368 | 4.198864e-01 | 4.855272e-08 |
CB | RBM4B | exon_skip_112368 | 4.047862e-01 | 1.595312e-07 |
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RelatedDrugs for RECQL4 |
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 RECQL4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |