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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 R3HDM2

check button Gene summary
Gene informationGene symbol

R3HDM2

Gene ID

22864

Gene nameR3H domain containing 2
SynonymsCAG6|PR01365
Cytomap

12q13.3

Type of geneprotein-coding
DescriptionR3H domain-containing protein 2
Modification date20200320
UniProtAcc

A0A024RB92,

A0A0U1RRA6,

B5MCG9,

B5MCU0,

C9J7N6,

H0YIX9,

H7C0E9,

Q9Y2K5,

Context

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

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Gene structures and expression levels for R3HDM2

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

ENSG00000179912
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
CBUPENST00000429355.6R3HDM2-206:protein_coding:R3HDM24.824586e+011.395274e+009.405126e-082.015282e-06

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 R3HDM2

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_103990chr1257303176:57303217:57310264:57310463:57395749:5739581857310264:57310463
exon_skip_107623chr1257283824:57284056:57288857:57288910:57289009:5728904057288857:57288910
exon_skip_119994chr1257310453:57310463:57395749:57395818:57430720:5743079057395749:57395818
exon_skip_121005chr1257269752:57269994:57272453:57272554:57280358:5728053057272453:57272554
exon_skip_150466chr1257310340:57310463:57395749:57395818:57430720:5743079057395749:57395818
exon_skip_18768chr1257297328:57297387:57298090:57298168:57299352:5729943657298090:57298168
exon_skip_195579chr1257283824:57284056:57292572:57292667:57295399:5729550757292572:57292667
exon_skip_227710chr1257300095:57300181:57303176:57303217:57310264:5731045157303176:57303217
exon_skip_236852chr1257283824:57284056:57289009:57289040:57295399:5729550757289009:57289040
exon_skip_258320chr1257289009:57289040:57292572:57292667:57295399:5729550757292572:57292667
exon_skip_65939chr1257303176:57303217:57305640:57305663:57310264:5731045157305640:57305663
exon_skip_85918chr1257303176:57303217:57305640:57305663:57310264:5731033257305640:57305663
exon_skip_94610chr1257283824:57284056:57289009:57289040:57292572:5729266757289009:57289040

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
psi tcga
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value
exon_skip_107623MSBB_STG4.812121e-015.813043e-01-1.000922e-013.499761e-02
exon_skip_107623MSBB_PG4.411719e-015.989091e-01-1.577372e-011.272144e-03
exon_skip_150474Mayo_TC2.111250e-013.733803e-01-1.622553e-016.893968e-07


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Open reading frame (ORF) annotation in the exon skipping event for R3HDM2

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
ENST0000034714057310264573104633UTR-3CDS
ENST0000034714057395749573958183UTR-3UTR
ENST000003471405728885757288910In-frame
ENST000003589075728885757288910In-frame
ENST000003471405730317657303217In-frame
ENST000003589075730317657303217In-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
ENST0000034714057310264573104633UTR-3CDS
ENST0000034714057395749573958183UTR-3UTR
ENST000003471405728885757288910In-frame
ENST000003589075728885757288910In-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
ENST0000034714057310264573104633UTR-3CDS
ENST0000034714057395749573958183UTR-3UTR
ENST000003471405729809057298168Frame-shift
ENST000003589075729809057298168Frame-shift
ENST000003471405728885757288910In-frame
ENST000003589075728885757288910In-frame
ENST000003471405730317657303217In-frame
ENST000003589075730317657303217In-frame

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Infer the effects of exon skipping event on protein functional features for R3HDM2

p-ENSG00000179912_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
ENST00000347140434897657303176573032175575975568
ENST00000358907399197657303176573032172012415568
ENST000003471404348976572888575728891012341286281298
ENST0000035890739919765728885757288910878930281298

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
ENST000003471404348976572888575728891012341286281298
ENST0000035890739919765728885757288910878930281298

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
ENST00000347140434897657303176573032175575975568
ENST00000358907399197657303176573032172012415568
ENST000003471404348976572888575728891012341286281298
ENST0000035890739919765728885757288910878930281298

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
Q9Y2K555681339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K555681976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K52812981339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5281298296298Alternative sequenceID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5281298296298Alternative sequenceID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K52812981976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5281298288369Compositional biasNote=Ser-rich
Q9Y2K5281298288369Compositional biasNote=Ser-rich
Q9Y2K5281298233310DomainNote=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01009
Q9Y2K5281298233310DomainNote=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01009

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
Q9Y2K52812981339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5281298296298Alternative sequenceID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5281298296298Alternative sequenceID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K52812981976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5281298288369Compositional biasNote=Ser-rich
Q9Y2K5281298288369Compositional biasNote=Ser-rich
Q9Y2K5281298233310DomainNote=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01009
Q9Y2K5281298233310DomainNote=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01009

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
Q9Y2K555681339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K555681976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K555681976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K52812981339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981339Alternative sequenceID=VSP_057391;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981295Alternative sequenceID=VSP_026087;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5281298296298Alternative sequenceID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K5281298296298Alternative sequenceID=VSP_026088;Note=In isoform 2. QIF->MIT;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2K52812981976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K52812981976ChainID=PRO_0000050787;Note=R3H domain-containing protein 2
Q9Y2K5281298288369Compositional biasNote=Ser-rich
Q9Y2K5281298288369Compositional biasNote=Ser-rich
Q9Y2K5281298233310DomainNote=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01009
Q9Y2K5281298233310DomainNote=SUZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01009


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3'-UTR located exon skipping events that lost miRNA binding sites in R3HDM2

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

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SNVs in the skipped exons for R3HDM2

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 R3HDM2

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 R3HDM2

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 R3HDM2

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBTRA2Aexon_skip_107623-5.920411e-012.055055e-16
CBHNRNPA2B1exon_skip_107623-4.578159e-011.300262e-09
CBNUP42exon_skip_1076235.326933e-014.922356e-13
CBCNOT4exon_skip_65939-4.686490e-014.663820e-10
DLPFCG3BP2exon_skip_258320-4.396036e-013.245375e-17
DLPFCPTBP3exon_skip_1076234.143240e-011.878366e-15
DLPFCCPEB1exon_skip_1076236.091739e-011.032976e-35
DLPFCELAVL4exon_skip_1210055.140300e-018.720501e-24
FLRBM24exon_skip_1076234.508590e-015.294884e-11
FLHNRNPH2exon_skip_1076234.386246e-011.972192e-10
FLRALYLexon_skip_258320-4.075234e-013.362303e-09
FLSRSF9exon_skip_258320-4.372952e-011.637296e-10
FLNOVA1exon_skip_258320-4.042056e-014.625074e-09
HCCRBM6exon_skip_121005-5.654172e-011.822089e-24
HCCSRSF4exon_skip_121005-4.977448e-011.699924e-18
HCCRBM25exon_skip_107623-4.239022e-012.480890e-13
HCCTIA1exon_skip_107623-5.214585e-011.945464e-20
HCCRBM5exon_skip_107623-6.188825e-012.972164e-30
HCCTRNAU1APexon_skip_107623-4.783090e-015.162173e-17
HCCTRA2Aexon_skip_107623-4.769213e-016.533036e-17
HCCHNRNPA2B1exon_skip_107623-5.892930e-016.434621e-27
HCCPTBP1exon_skip_107623-7.156608e-013.883051e-44
HCCSRSF1exon_skip_107623-4.536137e-012.920738e-15
HCCHNRNPFexon_skip_107623-6.298247e-011.405236e-31
HCCZNF326exon_skip_659394.420790e-011.725250e-14
HCCPTBP1exon_skip_659394.258685e-011.873623e-13
IFGELAVL4exon_skip_1210055.003429e-016.697249e-03
IFGTIA1exon_skip_107623-4.914443e-017.910448e-03
IFGRBM5exon_skip_107623-4.870637e-018.572560e-03
IFGTRA2Aexon_skip_107623-4.449008e-011.768000e-02
IFGHNRNPA2B1exon_skip_107623-4.342232e-012.095404e-02
IFGPTBP1exon_skip_107623-5.501095e-012.422776e-03
IFGIGF2BP2exon_skip_236852-4.443796e-011.782936e-02
IFGHNRNPDLexon_skip_2583204.409399e-011.884144e-02
IFGRALYLexon_skip_65939-5.000768e-016.731104e-03
PCCELAVL4exon_skip_1210055.198559e-016.182737e-16
PCCTRNAU1APexon_skip_107623-4.104620e-015.059905e-10
PCCTRA2Aexon_skip_107623-4.486297e-016.803353e-12
PCCHNRNPA2B1exon_skip_107623-4.051642e-018.827700e-10
PCCPTBP1exon_skip_107623-7.102589e-017.403989e-34
PCCCPEB1exon_skip_1076234.670279e-016.980862e-13
PCCHNRNPFexon_skip_107623-6.292438e-018.938168e-25
PCCZNF326exon_skip_2583204.860318e-015.734772e-14
PCCSFPQexon_skip_2583204.029389e-011.112037e-09
PCCTRA2Aexon_skip_2583204.046377e-019.324779e-10
PCCHNRNPFexon_skip_2583204.870260e-015.010303e-14
PCCZNF326exon_skip_659394.994177e-018.967915e-15
PCCPTBP1exon_skip_659395.465933e-016.511619e-18
PGRBM25exon_skip_1076235.904208e-011.413936e-18
PGTIA1exon_skip_1076235.025148e-014.219787e-13
PGRBM5exon_skip_1076234.233811e-012.352414e-09
PGTRNAU1APexon_skip_1076234.357830e-017.015333e-10
PGILF2exon_skip_1076235.596762e-011.780338e-16
PGRBM24exon_skip_1076236.560269e-016.816362e-24
PGNUP42exon_skip_1076235.586526e-012.073640e-16
PGRALYLexon_skip_1076236.697050e-013.574951e-25
PGCPEB1exon_skip_1076235.485020e-019.148295e-16
PGSRSF1exon_skip_1076235.151920e-018.522797e-14
PGSRSF9exon_skip_1076235.204436e-014.307846e-14
PGHNRNPH2exon_skip_1076235.998886e-012.869479e-19
STGRBM24exon_skip_1076234.623973e-015.068943e-06
STGRALYLexon_skip_1076234.768929e-012.304768e-06
STGHNRNPH2exon_skip_1076234.929023e-019.245716e-07
TCSRSF2exon_skip_1210054.568712e-011.258861e-09
TCELAVL4exon_skip_1210058.470385e-013.210325e-45
TCSRSF5exon_skip_1210054.176021e-013.929112e-08
TCRBM25exon_skip_1076234.864816e-016.934728e-11
TCILF2exon_skip_1076235.508278e-014.467040e-14
TCRBM24exon_skip_1076237.972510e-011.830665e-36
TCNUP42exon_skip_1076236.868049e-011.173836e-23
TCRALYLexon_skip_1076238.679596e-016.861448e-50
TCPTBP1exon_skip_107623-4.233632e-012.436608e-08
TCPTBP3exon_skip_1076235.536315e-013.126413e-14
TCCPEB1exon_skip_1076235.719766e-012.781662e-15
TCSRSF9exon_skip_1076234.038897e-011.182515e-07
TCHNRNPH2exon_skip_1076237.642871e-016.516386e-32
TCESRP1exon_skip_1076236.638725e-011.093361e-21
TCHNRNPH2exon_skip_2368524.379347e-017.795344e-09
TCNOVA1exon_skip_2368524.224421e-012.912143e-08
TCSRSF2exon_skip_258320-4.550220e-011.495148e-09
TCILF2exon_skip_258320-4.847982e-018.238936e-11
TCG3BP2exon_skip_258320-6.863525e-011.288862e-23
TCHNRNPDLexon_skip_258320-4.385608e-016.613040e-09
TCRALYLexon_skip_258320-7.938335e-015.924244e-36
TCHNRNPH2exon_skip_258320-6.738554e-011.596875e-22
TCESRP1exon_skip_258320-5.523936e-013.661416e-14
TCNOVA1exon_skip_258320-5.066142e-018.196277e-12
TCG3BP2exon_skip_65939-5.293501e-016.175216e-13
TCRALYLexon_skip_65939-5.672140e-015.288684e-15

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RelatedDrugs for R3HDM2

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 R3HDM2

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