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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 PHACTR2 |
Gene summary |
Gene information | Gene symbol | PHACTR2 | Gene ID | 9749 |
Gene name | phosphatase and actin regulator 2 | |
Synonyms | C6orf56 | |
Cytomap | 6q24.2 | |
Type of gene | protein-coding | |
Description | phosphatase and actin regulator 2 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for PHACTR2 |
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 |
TC | UP | ENST00000420771.2 | PHACTR2-206:retained_intron:PHACTR2 | 5.122077e+00 | 8.189057e-01 | 2.817355e-03 | 2.173756e-02 |
TC | UP | ENST00000367582.7 | PHACTR2-202:protein_coding:PHACTR2 | 4.558662e+00 | 2.134661e+00 | 4.112249e-03 | 2.890911e-02 |
TC | UP | ENST00000451827.6 | PHACTR2-209:protein_coding:PHACTR2 | 2.467274e+00 | 9.373336e-01 | 6.762775e-03 | 4.193951e-02 |
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 PHACTR2 |
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_202862 | chr6 | 143748985:143749065:143753754:143753912:143765261:143765474 | 143753754:143753912 |
exon_skip_212822 | chr6 | 143712016:143712183:143748985:143749065:143765261:143765474 | 143748985:143749065 |
exon_skip_220188 | chr6 | 143678048:143678209:143712016:143712183:143748985:143749065 | 143712016:143712183 |
exon_skip_239946 | chr6 | 143678173:143678209:143712016:143712183:143748985:143749065 | 143712016:143712183 |
exon_skip_255397 | chr6 | 143748985:143749065:143753754:143753912:143765261:143765500 | 143753754:143753912 |
exon_skip_270877 | chr6 | 143753754:143753912:143760401:143760640:143765261:143765474 | 143760401:143760640 |
exon_skip_60539 | chr6 | 143712016:143712183:143748985:143749065:143765261:143765500 | 143748985:143749065 |
exon_skip_64742 | chr6 | 143765261:143765798:143772258:143772457:143774059:143774215 | 143772258:143772457 |
exon_skip_77081 | chr6 | 143712016:143712183:143748985:143749065:143753754:143753912 | 143748985:143749065 |
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 PHACTR2 |
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 |
ENST00000427704 | 143772258 | 143772457 | Frame-shift |
ENST00000427704 | 143748985 | 143749065 | In-frame |
ENST00000427704 | 143760401 | 143760640 | In-frame |
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 |
ENST00000427704 | 143760401 | 143760640 | In-frame |
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 |
ENST00000427704 | 143772258 | 143772457 | Frame-shift |
ENST00000427704 | 143760401 | 143760640 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PHACTR2 |
p-ENSG00000112419_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 |
ENST00000427704 | 9548 | 634 | 143748985 | 143749065 | 313 | 392 | 61 | 87 |
ENST00000427704 | 9548 | 634 | 143760401 | 143760640 | 553 | 791 | 141 | 220 |
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 |
ENST00000427704 | 9548 | 634 | 143760401 | 143760640 | 553 | 791 | 141 | 220 |
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 |
ENST00000427704 | 9548 | 634 | 143760401 | 143760640 | 553 | 791 | 141 | 220 |
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 |
O75167 | 61 | 87 | 1 | 634 | Chain | ID=PRO_0000126636;Note=Phosphatase and actin regulator 2 |
O75167 | 61 | 87 | 60 | 85 | Repeat | Note=RPEL 1 |
O75167 | 141 | 220 | 141 | 220 | Alternative sequence | ID=VSP_012273;Note=In isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:17974005;Dbxref=PMID:14702039,PMID:17974005 |
O75167 | 141 | 220 | 1 | 634 | Chain | ID=PRO_0000126636;Note=Phosphatase and actin regulator 2 |
O75167 | 141 | 220 | 165 | 165 | Natural variant | ID=VAR_045628;Note=P->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9734811;Dbxref=dbSNP:rs2073214,PMID:15489334,PMID:9734811 |
O75167 | 141 | 220 | 197 | 197 | Sequence conflict | Note=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
O75167 | 141 | 220 | 141 | 220 | Alternative sequence | ID=VSP_012273;Note=In isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:17974005;Dbxref=PMID:14702039,PMID:17974005 |
O75167 | 141 | 220 | 1 | 634 | Chain | ID=PRO_0000126636;Note=Phosphatase and actin regulator 2 |
O75167 | 141 | 220 | 165 | 165 | Natural variant | ID=VAR_045628;Note=P->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9734811;Dbxref=dbSNP:rs2073214,PMID:15489334,PMID:9734811 |
O75167 | 141 | 220 | 197 | 197 | Sequence conflict | Note=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
O75167 | 141 | 220 | 141 | 220 | Alternative sequence | ID=VSP_012273;Note=In isoform 2 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:17974005;Dbxref=PMID:14702039,PMID:17974005 |
O75167 | 141 | 220 | 1 | 634 | Chain | ID=PRO_0000126636;Note=Phosphatase and actin regulator 2 |
O75167 | 141 | 220 | 165 | 165 | Natural variant | ID=VAR_045628;Note=P->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9734811;Dbxref=dbSNP:rs2073214,PMID:15489334,PMID:9734811 |
O75167 | 141 | 220 | 197 | 197 | Sequence conflict | Note=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PHACTR2 |
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 PHACTR2 |
- 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 PHACTR2 |
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 PHACTR2 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
HCC | exon_skip_270877 | rs12663714 | chr6:143835332 | 4.228133e-04 | 2.960800e-02 |
HCC | exon_skip_270877 | rs1072385 | chr6:143829472 | 5.697390e-04 | 3.757559e-02 |
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Correlation with RNA binding proteins (RBPs) for PHACTR2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PHACTR2 |
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 PHACTR2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |