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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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3'-UTR located exon skipping events lost miRNA binding sites

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for PSPH

check button Gene summary
Gene informationGene symbol

PSPH

Gene ID

5723

Gene namephosphoserine phosphatase
SynonymsPSP|PSPHD
Cytomap

7p11.2

Type of geneprotein-coding
Descriptionphosphoserine phosphataseL-3-phosphoserine phosphataseO-phosphoserine phosphohydrolasePSPase
Modification date20200313
UniProtAcc

A0A024RDL3,

A0A024RDL9,

A0A1D5RMN5,

C9JBI3,

C9JEJ7,

F8WD74,

P78330,

Context- 21303680(Monocyte-mediated regulation of genes by the amyloid and prion peptides in SH-SY5Y neuroblastoma cells)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
PSPH

GO:0006563

L-serine metabolic process

15291819


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Gene structures and expression levels for PSPH

check buttonSkipped 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.
all structure

ENSG00000146733
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
PGUPENST00000416592.1PSPH-204:protein_coding:PSPH6.106811e+009.614806e-014.721916e-034.390406e-02

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PSPH

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_106451chr756031929:56032054:56033961:56034154:56051138:5605128856033961:56034154
exon_skip_129971chr756031929:56032054:56033961:56034154:56051314:5605146756033961:56034154
exon_skip_133661chr756031929:56032054:56033961:56034106:56051138:5605128856033961:56034106
exon_skip_147379chr756015031:56015171:56017234:56017379:56019600:5601973456017234:56017379
exon_skip_1622chr756031929:56032054:56033961:56034154:56043148:5604326156033961:56034154
exon_skip_189309chr756021206:56021231:56031929:56031977:56033961:5603410356031929:56031977
exon_skip_218505chr756021206:56021231:56031929:56032054:56033961:5603410356031929:56032054
exon_skip_24931chr756017277:56017379:56019600:56019734:56021073:5602123156019600:56019734
exon_skip_259748chr756033961:56034154:56043148:56043261:56051314:5605146756043148:56043261
exon_skip_290298chr756031929:56032054:56033381:56033494:56033961:5603410356033381:56033494
exon_skip_37837chr756033961:56034154:56043148:56043261:56051314:5605139256043148:56043261
exon_skip_62245chr756011544:56011869:56015023:56015171:56017234:5601737956015023:56015171
exon_skip_78778chr756031929:56031977:56033961:56034106:56051138:5605128856033961:56034106

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value


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Open reading frame (ORF) annotation in the exon skipping event for PSPH

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000027560556031929560320543UTR-3UTR
ENST0000039547156031929560320543UTR-3UTR
ENST0000027560556033961560341063UTR-3UTR
ENST0000039547156033961560341543UTR-3UTR
ENST000002756055601502356015171Frame-shift
ENST000003954715601502356015171Frame-shift
ENST000002756055601723456017379Frame-shift
ENST000003954715601723456017379Frame-shift
ENST000002756055601960056019734In-frame
ENST000003954715601960056019734In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002756055601960056019734In-frame
ENST000003954715601960056019734In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000027560556033961560341063UTR-3UTR
ENST0000039547156033961560341543UTR-3UTR
ENST000002756055601502356015171Frame-shift
ENST000003954715601502356015171Frame-shift
ENST000002756055601723456017379Frame-shift
ENST000003954715601723456017379Frame-shift
ENST000002756055601960056019734In-frame
ENST000003954715601960056019734In-frame

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Infer the effects of exon skipping event on protein functional features for PSPH

p-ENSG00000146733_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002756052148225560196005601973489910324791
ENST000003954712195225560196005601973494710804791

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002756052148225560196005601973489910324791
ENST000003954712195225560196005601973494710804791

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002756052148225560196005601973489910324791
ENST000003954712195225560196005601973494710804791

check button 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 featureDescription of feature
P7833047916565Binding siteNote=Substrate
P7833047916565Binding siteNote=Substrate
P7833047911225ChainID=PRO_0000156879;Note=Phosphoserine phosphatase
P7833047911225ChainID=PRO_0000156879;Note=Phosphoserine phosphatase
P7833047915869HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047915869HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047917382HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047917382HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P78330479191100HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P78330479191100HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047916565MutagenesisNote=Loss of activity. R->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12213811;Dbxref=PMID:12213811
P7833047916565MutagenesisNote=Loss of activity. R->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12213811;Dbxref=PMID:12213811
P7833047915252Natural variantID=VAR_022379;Note=In PSPHD. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14673469;Dbxref=dbSNP:rs104894036,PMID:14673469
P7833047915252Natural variantID=VAR_022379;Note=In PSPHD. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14673469;Dbxref=dbSNP:rs104894036,PMID:14673469
P7833047914547TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914547TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914952TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914952TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L

check button 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 featureDescription of feature
P7833047916565Binding siteNote=Substrate
P7833047916565Binding siteNote=Substrate
P7833047911225ChainID=PRO_0000156879;Note=Phosphoserine phosphatase
P7833047911225ChainID=PRO_0000156879;Note=Phosphoserine phosphatase
P7833047915869HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047915869HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047917382HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047917382HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P78330479191100HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P78330479191100HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047916565MutagenesisNote=Loss of activity. R->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12213811;Dbxref=PMID:12213811
P7833047916565MutagenesisNote=Loss of activity. R->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12213811;Dbxref=PMID:12213811
P7833047915252Natural variantID=VAR_022379;Note=In PSPHD. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14673469;Dbxref=dbSNP:rs104894036,PMID:14673469
P7833047915252Natural variantID=VAR_022379;Note=In PSPHD. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14673469;Dbxref=dbSNP:rs104894036,PMID:14673469
P7833047914547TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914547TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914952TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914952TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L

check button 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 featureDescription of feature
P7833047916565Binding siteNote=Substrate
P7833047916565Binding siteNote=Substrate
P7833047911225ChainID=PRO_0000156879;Note=Phosphoserine phosphatase
P7833047911225ChainID=PRO_0000156879;Note=Phosphoserine phosphatase
P7833047915869HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047915869HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047917382HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047917382HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P78330479191100HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P78330479191100HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1NNL
P7833047916565MutagenesisNote=Loss of activity. R->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12213811;Dbxref=PMID:12213811
P7833047916565MutagenesisNote=Loss of activity. R->A%2CK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12213811;Dbxref=PMID:12213811
P7833047915252Natural variantID=VAR_022379;Note=In PSPHD. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14673469;Dbxref=dbSNP:rs104894036,PMID:14673469
P7833047915252Natural variantID=VAR_022379;Note=In PSPHD. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:14673469;Dbxref=dbSNP:rs104894036,PMID:14673469
P7833047914547TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914547TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914952TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L
P7833047914952TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1L8L


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3'-UTR located exon skipping events that lost miRNA binding sites in PSPH

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda
MayoENST000002756055603396156034106hsa-miR-8059chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
MayoENST000003954715603396156034154hsa-miR-8059chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
MayoENST000002756055603396156034106hsa-miR-6791-5pchr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
MayoENST000003954715603396156034154hsa-miR-6791-5pchr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
MayoENST000003954715603396156034154hsa-miR-3617-3pchr7:56034105-560341128mer-1achr7:56034104-56034127150.00-19.49
MayoENST000002756055603396156034106hsa-miR-1306-5pchr7:56034054-560340618mer-1achr7:56034049-56034074158.00-25.98
MayoENST000003954715603396156034154hsa-miR-1306-5pchr7:56034054-560340618mer-1achr7:56034049-56034074158.00-25.98
MayoENST000003954715603396156034154hsa-miR-922chr7:56034103-560341108mer-1achr7:56034088-56034110149.00-20.19
MayoENST000002756055603396156034106hsa-miR-4471chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
MayoENST000003954715603396156034154hsa-miR-4471chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
MayoENST000002756055603396156034106hsa-miR-4292chr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
MayoENST000003954715603396156034154hsa-miR-4292chr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000002756055603396156034106hsa-miR-8059chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
ROSMAPENST000003954715603396156034154hsa-miR-8059chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
ROSMAPENST000002756055603396156034106hsa-miR-6791-5pchr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000003954715603396156034154hsa-miR-6791-5pchr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000003954715603192956032054hsa-miR-526b-5pchr7:56032018-560320258mer-1achr7:56032003-56032025158.00-19.20
ROSMAPENST000003954715603192956032054hsa-miR-9500chr7:56031973-560319808mer-1achr7:56031955-56031981145.00-27.77
ROSMAPENST000003954715603396156034154hsa-miR-3617-3pchr7:56034105-560341128mer-1achr7:56034104-56034127150.00-19.49
ROSMAPENST000002756055603396156034106hsa-miR-1306-5pchr7:56034054-560340618mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000003954715603396156034154hsa-miR-1306-5pchr7:56034054-560340618mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000003954715603396156034154hsa-miR-922chr7:56034103-560341108mer-1achr7:56034088-56034110149.00-20.19
ROSMAPENST000002756055603396156034106hsa-miR-4471chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
ROSMAPENST000003954715603396156034154hsa-miR-4471chr7:56034045-560340528mer-1achr7:56034041-56034061155.00-20.06
ROSMAPENST000002756055603396156034106hsa-miR-4292chr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000003954715603396156034154hsa-miR-4292chr7:56034049-560340568mer-1achr7:56034049-56034074158.00-25.98
ROSMAPENST000003954715603192956032054hsa-miR-3915chr7:56032015-560320228mer-1achr7:56032003-56032025158.00-19.20

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SNVs in the skipped exons for PSPH

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for PSPH

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PSPH

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for PSPH

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value

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RelatedDrugs for PSPH

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P78330approved|investigationalDB01593Zincsmall moleculeP78330
P78330approved|investigationalDB14487Zinc acetatesmall moleculeP78330
P78330approved|investigationalDB14533Zinc chloridesmall moleculeP78330

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RelatedDiseases for PSPH

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource