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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 RNPS1

check button Gene summary
Gene informationGene symbol

RNPS1

Gene ID

10921

Gene nameRNA binding protein with serine rich domain 1
SynonymsE5.1
Cytomap

16p13.3

Type of geneprotein-coding
DescriptionRNA-binding protein with serine-rich domain 1RNA binding protein with serine-rich domainRNA-binding protein S1, serine-rich domainSR proteinSR-related protein LDC2
Modification date20200313
UniProtAcc

D3DU92,

H3BMM9,

H3BMS0,

H3BNI3,

H3BNU7,

H3BP82,

H3BPG5,

H3BRK4,

H3BTC0,

H3BTR6,

H3BTV0,

H3BTY0,

H3BUG0,

H3BUL0,

H3BV80,

Q15287,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
RNPS1

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

11546874

RNPS1

GO:0043065

positive regulation of apoptotic process

12665594

RNPS1

GO:0048025

negative regulation of mRNA splicing, via spliceosome

12665594


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Gene structures and expression levels for RNPS1

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

ENSG00000205937
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
PCCUPENST00000565589.5RNPS1-215:protein_coding:RNPS14.410470e+001.322146e+002.335505e-082.040837e-05
HCCUPENST00000565589.5RNPS1-215:protein_coding:RNPS13.368035e+001.110111e+001.056186e-051.473501e-03
HCCUPENST00000566180.5RNPS1-218:protein_coding:RNPS12.628916e+008.769322e-019.011881e-043.160179e-02
STGUPENST00000566397.5RNPS1-219:protein_coding:RNPS13.644377e+012.444433e+011.642488e-243.284374e-21
PGUPENST00000562205.1RNPS1-206:retained_intron:RNPS13.531676e+001.860838e+002.175143e-032.538084e-02
CBUPENST00000565589.5RNPS1-215:protein_coding:RNPS15.492600e+011.596410e+001.291991e-161.122763e-13
CBDOWNENST00000562205.1RNPS1-206:retained_intron:RNPS11.451801e+02-8.356520e-011.169773e-048.455850e-04
CBUPENST00000566180.5RNPS1-218:protein_coding:RNPS14.610452e+001.026102e+004.936574e-031.947002e-02
CBDOWNENST00000566397.5RNPS1-219:protein_coding:RNPS19.434423e+02-1.393960e+006.508655e-032.444474e-02
TCUPENST00000565589.5RNPS1-215:protein_coding:RNPS11.354590e+018.917723e-016.792689e-061.899876e-04

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 RNPS1

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_149407chr162264627:2264760:2267175:2267218:2268055:22680712267175:2267218
exon_skip_172505chr162264573:2264760:2267175:2267237:2268055:22680712267175:2267237
exon_skip_178307chr162264315:2264331:2264573:2264760:2266110:22662162264573:2264760
exon_skip_183080chr162255641:2255726:2262278:2262431:2262740:22628422262278:2262431
exon_skip_190240chr162263260:2263287:2264176:2264331:2268055:22680712264176:2264331
exon_skip_22238chr162264573:2264760:2267189:2267237:2268055:22680712267189:2267237
exon_skip_239833chr162264315:2264331:2264573:2264760:2268055:22680712264573:2264760
exon_skip_292273chr162264627:2264760:2267175:2267237:2268055:22680712267175:2267237
exon_skip_296667chr162264315:2264331:2264573:2264760:2267933:22680542264573:2264760
exon_skip_41930chr162254029:2254063:2255585:2255726:2262278:22624312255585:2255726
exon_skip_44287chr162264573:2264760:2267175:2267218:2268055:22680712267175:2267218
exon_skip_7205chr162264627:2264760:2267189:2267237:2268055:22680712267189:2267237
exon_skip_92467chr162264315:2264331:2264573:2264760:2267575:22678522264573:2264760

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 RNPS1

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
ENST00000320225226457322647603UTR-3CDS
ENST00000301730226717522672373UTR-3UTR
ENST0000030173022555852255726Frame-shift
ENST0000032022522555852255726Frame-shift
ENST0000039708622555852255726Frame-shift
ENST0000056567822555852255726Frame-shift
ENST0000056863122555852255726Frame-shift
ENST0000030173022622782262431Frame-shift
ENST0000032022522622782262431Frame-shift
ENST0000039708622622782262431Frame-shift
ENST0000056567822622782262431Frame-shift
ENST0000056863122622782262431Frame-shift

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
ENST00000320225226457322647603UTR-3CDS
ENST00000301730226717522672373UTR-3UTR
ENST0000030173022555852255726Frame-shift
ENST0000032022522555852255726Frame-shift
ENST0000039708622555852255726Frame-shift
ENST0000056567822555852255726Frame-shift
ENST0000056863122555852255726Frame-shift

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
ENST00000320225226457322647603UTR-3CDS
ENST00000301730226717522672373UTR-3UTR
ENST0000030173022555852255726Frame-shift
ENST0000032022522555852255726Frame-shift
ENST0000039708622555852255726Frame-shift
ENST0000056567822555852255726Frame-shift
ENST0000056863122555852255726Frame-shift

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Infer the effects of exon skipping event on protein functional features for RNPS1

p-ENSG00000205937_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

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

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

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

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

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


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3'-UTR located exon skipping events that lost miRNA binding sites in RNPS1

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
MayoENST0000030173022671752267237hsa-miR-5698chr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MayoENST0000030173022671752267237hsa-miR-4723-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MayoENST0000030173022671752267237hsa-miR-6870-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MayoENST0000030173022671752267237hsa-miR-7111-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MSBBENST0000030173022671752267237hsa-miR-5698chr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MSBBENST0000030173022671752267237hsa-miR-4723-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MSBBENST0000030173022671752267237hsa-miR-6870-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
MSBBENST0000030173022671752267237hsa-miR-7111-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
ROSMAPENST0000030173022671752267237hsa-miR-5698chr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
ROSMAPENST0000030173022671752267237hsa-miR-4723-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
ROSMAPENST0000030173022671752267237hsa-miR-6870-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82
ROSMAPENST0000030173022671752267237hsa-miR-7111-5pchr16:2267209-22672168mer-1achr16:2267199-2267223161.00-26.82

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SNVs in the skipped exons for RNPS1

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 RNPS1

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 RNPS1

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 RNPS1

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBSRSF2exon_skip_2398334.956753e-013.073003e-11
CBRBM25exon_skip_2398334.660620e-015.977174e-10
CBSRSF11exon_skip_2398335.931465e-011.750656e-16
CBRBM5exon_skip_2398334.968996e-012.701317e-11
CBSF1exon_skip_2398334.343562e-011.063182e-08
CBHNRNPA1exon_skip_2398335.359140e-013.353129e-13
CBHNRNPA0exon_skip_2398336.246338e-011.388486e-18
CBHNRNPA1L2exon_skip_2398334.063960e-011.065212e-07
CBHNRNPDLexon_skip_2398335.213323e-011.846789e-12
CBPUF60exon_skip_2398334.105487e-017.664623e-08
CBHNRNPDexon_skip_2398335.613155e-011.400600e-14
CBNUP42exon_skip_2398334.550647e-011.677505e-09
CBRALYLexon_skip_2398335.599006e-011.683608e-14
CBPABPC1exon_skip_2398335.250396e-011.206083e-12
CBEWSR1exon_skip_2398334.821261e-011.237686e-10
CBSRSF9exon_skip_2398335.937216e-011.610177e-16
CBHNRNPH2exon_skip_2398334.866380e-017.835442e-11
CBSART3exon_skip_2398335.272887e-019.289984e-13
DLPFCKHDRBS2exon_skip_2398335.829017e-012.024589e-32
DLPFCKHDRBS3exon_skip_2398335.064932e-011.279255e-23
DLPFCHNRNPA0exon_skip_2398334.326594e-015.467323e-17
DLPFCHNRNPDLexon_skip_2398334.216845e-013.916660e-16
DLPFCHNRNPDexon_skip_2398334.103662e-012.771634e-15
DLPFCNUP42exon_skip_2398334.074823e-014.510133e-15
DLPFCRALYLexon_skip_2398335.434884e-011.338888e-27
DLPFCHNRNPH2exon_skip_2398334.404126e-011.302150e-17
DLPFCESRP1exon_skip_2398334.155722e-011.137185e-15
DLPFCRBM25exon_skip_442875.382543e-018.805915e-27
DLPFCTRA2Aexon_skip_442874.151479e-011.632002e-15
DLPFCEWSR1exon_skip_442875.697363e-011.763843e-30
DLPFCSRSF1exon_skip_442874.356952e-014.312297e-17
DLPFCSRSF9exon_skip_442875.372504e-011.138661e-26
DLPFCHNRNPH2exon_skip_442874.373552e-013.180358e-17
DLPFCESRP1exon_skip_442874.491515e-013.480413e-18
FLSRSF2exon_skip_2398335.238752e-011.190115e-13
FLMSI1exon_skip_239833-5.073882e-018.996021e-13
FLMBNL1exon_skip_2398334.142879e-011.324406e-08
FLILF2exon_skip_2398335.081436e-018.219119e-13
FLKHDRBS3exon_skip_2398335.570609e-011.432613e-15
FLHNRNPA0exon_skip_2398334.724356e-014.652892e-11
FLNUP42exon_skip_2398334.009058e-014.207917e-08
FLRALYLexon_skip_2398335.616210e-017.506245e-16
FLEIF4G2exon_skip_2398334.263650e-014.463472e-09
FLSRSF9exon_skip_2398334.860824e-011.051078e-11
FLHNRNPH2exon_skip_2398334.326845e-012.483158e-09
FLESRP1exon_skip_2398334.205968e-017.543892e-09
FLSART3exon_skip_2398334.060765e-012.708252e-08
HCCMSI1exon_skip_239833-4.822648e-012.622464e-17
HCCRBM47exon_skip_239833-4.930352e-013.965901e-18
HCCKHDRBS2exon_skip_2398335.774451e-011.123024e-25
HCCRALYLexon_skip_2398335.363299e-019.811856e-22
HCCHNRNPFexon_skip_239833-4.220549e-013.224274e-13
HCCHNRNPFexon_skip_44287-4.322652e-019.160518e-14
IFGDAZAP1exon_skip_239833-4.020586e-013.392776e-02
IFGRBM25exon_skip_239833-4.166792e-012.740108e-02
IFGPABPN1Lexon_skip_239833-5.167176e-014.873004e-03
IFGZNF326exon_skip_239833-4.937588e-017.578366e-03
IFGRBM6exon_skip_239833-5.724882e-011.454875e-03
IFGIGF2BP3exon_skip_239833-4.870139e-018.580343e-03
IFGA1CFexon_skip_239833-5.833143e-011.121897e-03
IFGRBM47exon_skip_239833-5.637018e-011.784985e-03
IFGSNRNP70exon_skip_239833-4.229884e-012.491920e-02
IFGPABPC5exon_skip_239833-4.249966e-012.416880e-02
IFGPABPC4exon_skip_239833-4.328636e-012.140442e-02
IFGTRA2Aexon_skip_44287-4.079882e-013.463776e-02
PCCMSI1exon_skip_239833-4.132780e-012.811746e-10
PCCRBM47exon_skip_239833-4.749000e-011.709805e-13
PCCRALYLexon_skip_2398336.593963e-013.347730e-28
PCCHNRNPFexon_skip_239833-4.517388e-013.296820e-12
PGTARDBPexon_skip_2398334.231582e-019.307619e-08
PGSRSF2exon_skip_2398335.542656e-013.265611e-13
PGRBM25exon_skip_2398334.743019e-011.290355e-09
PGSRSF11exon_skip_2398334.155022e-011.665478e-07
PGMBNL1exon_skip_2398334.975433e-011.444672e-10
PGILF2exon_skip_2398336.283769e-011.594212e-17
PGKHDRBS2exon_skip_2398335.089939e-014.616997e-11
PGKHDRBS3exon_skip_2398336.456407e-011.060336e-18
PGHNRNPA0exon_skip_2398336.085713e-012.921125e-16
PGHNRNPDLexon_skip_2398335.161667e-012.210666e-11
PGHNRNPDexon_skip_2398334.390023e-012.664220e-08
PGNUP42exon_skip_2398335.196015e-011.544206e-11
PGRALYLexon_skip_2398336.748016e-017.177369e-21
PGEIF4G2exon_skip_2398335.380186e-012.102438e-12
PGSRSF9exon_skip_2398334.563096e-016.302921e-09
PGHNRNPH2exon_skip_2398336.962141e-011.253655e-22
PGESRP1exon_skip_2398334.439005e-011.786153e-08
PGSART3exon_skip_2398335.186536e-011.705619e-11
PGRBM4exon_skip_2398334.052664e-013.545876e-07
STGSRSF2exon_skip_2398334.183959e-011.527056e-04
STGPABPN1exon_skip_2398334.032905e-012.761317e-04
STGMBNL1exon_skip_2398334.429007e-015.492965e-05
STGKHDRBS2exon_skip_2398334.396544e-016.318317e-05
STGKHDRBS3exon_skip_2398334.857844e-017.518299e-06
STGPUF60exon_skip_2398334.001824e-013.108532e-04
STGNUP42exon_skip_2398334.275224e-011.053004e-04
STGRALYLexon_skip_2398335.339190e-015.717560e-07
STGEIF4G2exon_skip_2398334.081159e-012.292204e-04
STGRBM4exon_skip_2398334.236901e-011.232467e-04
TCSRSF2exon_skip_2398334.736852e-012.511199e-10
TCILF2exon_skip_2398335.014977e-011.429140e-11
TCKHDRBS2exon_skip_2398337.590020e-012.984032e-31
TCKHDRBS3exon_skip_2398336.822785e-012.968358e-23
TCHNRNPA0exon_skip_2398336.542614e-016.507636e-21
TCHNRNPA1L2exon_skip_2398334.223958e-012.641806e-08
TCHNRNPDLexon_skip_2398334.061891e-019.863988e-08
TCHNRNPDexon_skip_2398335.415015e-011.429807e-13
TCNUP42exon_skip_2398336.626962e-011.364926e-21
TCRALYLexon_skip_2398338.150259e-012.772620e-39
TCHNRNPH2exon_skip_2398336.519201e-019.951874e-21
TCESRP1exon_skip_2398335.844889e-014.890337e-16
TCMBNL1exon_skip_1494074.058281e-011.014978e-07
TCILF2exon_skip_1494074.481716e-012.802687e-09
TCG3BP2exon_skip_1494076.330204e-012.688953e-19
TCHNRNPH2exon_skip_1494076.187315e-012.806750e-18
TCESRP1exon_skip_1494075.495453e-015.253284e-14
TCESRP1exon_skip_2922734.238500e-012.339230e-08

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RelatedDrugs for RNPS1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RNPS1

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