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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 TCGA

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Exon skipping events with PSIs in GTEx

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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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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for CUBN

check button Gene summary
Gene informationGene symbol

CUBN

Gene ID

8029

Gene namecubilin
SynonymsIFCR|MGA1|gp280
Cytomap

10p13

Type of geneprotein-coding
Descriptioncubilin460 kDa receptorcubilin (intrinsic factor-cobalamin receptor)cubilin precursor variant 1cubilin precursor variant 2cubilin precursor variant 3intestinal intrinsic factor receptorintrinsic factor-vitamin B12 receptor
Modification date20180519
UniProtAcc

O60494

ContextPubMed: CUBN [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

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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Exon skipping events across known transcript of Ensembl for CUBN from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx 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

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Gene isoform structures and expression levels for CUBN

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for CUBN

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_480731016873250:16873416:16877012:16877194:16878233:1687838116877012:16877194ENSG00000107611.10ENST00000377833.4
exon_skip_480751016882883:16883046:16893233:16893442:16911634:1691185216893233:16893442ENSG00000107611.10ENST00000377833.4
exon_skip_480771016930415:16930565:16932369:16932526:16940994:1694118216932369:16932526ENSG00000107611.10ENST00000377833.4
exon_skip_480781016948201:16948408:16949506:16949678:16955809:1695599116949506:16949678ENSG00000107611.10ENST00000377833.4
exon_skip_480791016949506:16949678:16955809:16955991:16957030:1695717116955809:16955991ENSG00000107611.10ENST00000377833.4
exon_skip_480801016990476:16990605:16991999:16992110:16994274:1699438816991999:16992110ENSG00000107611.10ENST00000377833.4
exon_skip_480821017032332:17032514:17061831:17061982:17083031:1708321917061831:17061982ENSG00000107611.10ENST00000377833.4
exon_skip_480881017061831:17061982:17083031:17083219:17085825:1708598217083031:17083219ENSG00000107611.10ENST00000377833.4
exon_skip_480901017146417:17146604:17147455:17147574:17151638:1715173417147455:17147574ENSG00000107611.10ENST00000377833.4
exon_skip_480911017151638:17151734:17152917:17153049:17156025:1715618817152917:17153049ENSG00000107611.10ENST00000377833.4

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for CUBN

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_480731016873250:16873416:16877012:16877194:16878233:1687838116877012:16877194ENSG00000107611.10ENST00000377833.4
exon_skip_480751016882883:16883046:16893233:16893442:16911634:1691185216893233:16893442ENSG00000107611.10ENST00000377833.4
exon_skip_480771016930415:16930565:16932369:16932526:16940994:1694118216932369:16932526ENSG00000107611.10ENST00000377833.4
exon_skip_480781016948201:16948408:16949506:16949678:16955809:1695599116949506:16949678ENSG00000107611.10ENST00000377833.4
exon_skip_480791016949506:16949678:16955809:16955991:16957030:1695717116955809:16955991ENSG00000107611.10ENST00000377833.4
exon_skip_480801016990476:16990605:16991999:16992110:16994274:1699438816991999:16992110ENSG00000107611.10ENST00000377833.4
exon_skip_480821017032332:17032514:17061831:17061982:17083031:1708321917061831:17061982ENSG00000107611.10ENST00000377833.4
exon_skip_480881017061831:17061982:17083031:17083219:17085825:1708598217083031:17083219ENSG00000107611.10ENST00000377833.4
exon_skip_480901017146417:17146604:17147455:17147574:17151638:1715173417147455:17147574ENSG00000107611.10ENST00000377833.4
exon_skip_480911017151638:17151734:17152917:17153049:17156025:1715618817152917:17153049ENSG00000107611.10ENST00000377833.4

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003778331687701216877194Frame-shift
ENST000003778331689323316893442Frame-shift
ENST000003778331693236916932526Frame-shift
ENST000003778331694950616949678Frame-shift
ENST000003778331695580916955991Frame-shift
ENST000003778331706183117061982Frame-shift
ENST000003778331708303117083219Frame-shift
ENST000003778331714745517147574Frame-shift
ENST000003778331699199916992110In-frame
ENST000003778331715291717153049In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003778331687701216877194Frame-shift
ENST000003778331689323316893442Frame-shift
ENST000003778331693236916932526Frame-shift
ENST000003778331694950616949678Frame-shift
ENST000003778331695580916955991Frame-shift
ENST000003778331706183117061982Frame-shift
ENST000003778331708303117083219Frame-shift
ENST000003778331714745517147574Frame-shift
ENST000003778331699199916992110In-frame
ENST000003778331715291717153049In-frame

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

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000037783311966362317152917171530499501081294338
ENST0000037783311966362316991999169921105036514616561693

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000037783311966362317152917171530499501081294338
ENST0000037783311966362316991999169921105036514616561693

check button Lost protein functional features of individual exon skipping events in TCGA.
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
O60494294338363623ChainID=PRO_0000046073;Note=Cubilin
O60494294338292303Disulfide bondOntology_term=ECO:0000250;evidence=ECO:0000250
O60494294338263304DomainNote=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00076
O60494294338305348DomainNote=EGF-like 4%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00076
O60494294338335335Natural variantID=VAR_061154;Note=A->T;Dbxref=dbSNP:rs57335729
O6049416561693363623ChainID=PRO_0000046073;Note=Cubilin
O604941656169316751697Disulfide bondOntology_term=ECO:0000250;evidence=ECO:0000250
O604941656169316201734DomainNote=CUB 11;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059


check button Lost protein functional features of individual exon skipping events in GTEx.
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
O60494294338363623ChainID=PRO_0000046073;Note=Cubilin
O60494294338292303Disulfide bondOntology_term=ECO:0000250;evidence=ECO:0000250
O60494294338263304DomainNote=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00076
O60494294338305348DomainNote=EGF-like 4%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00076
O60494294338335335Natural variantID=VAR_061154;Note=A->T;Dbxref=dbSNP:rs57335729
O6049416561693363623ChainID=PRO_0000046073;Note=Cubilin
O604941656169316751697Disulfide bondOntology_term=ECO:0000250;evidence=ECO:0000250
O604941656169316201734DomainNote=CUB 11;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00059


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SNVs in the skipped exons for CUBN

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

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

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
UCECTCGA-A5-A0G5-01exon_skip_48073
16877013168771941687709616877096Frame_Shift_DelC-p.A3427fs
LUADTCGA-49-6743-01exon_skip_48075
16893234168934421689330616893306Frame_Shift_DelA-p.I3197fs
BRCATCGA-BH-A0AZ-01exon_skip_48075
16893234168934421689331916893322Frame_Shift_DelACAG-p.P3192fs
HNSCTCGA-UF-A7J9-01exon_skip_48075
16893234168934421689333616893336Frame_Shift_DelC-p.W3187fs
LIHCTCGA-DD-A39Y-01exon_skip_48075
16893234168934421689337016893370Frame_Shift_DelT-p.N3176fs
STADTCGA-BR-4201-01exon_skip_48078
16949507169496781694956916949569Frame_Shift_DelA-p.F2548fs
STADTCGA-MX-A5UJ-01exon_skip_48078
16949507169496781694956916949569Frame_Shift_DelA-p.F2548fs
PRADTCGA-EJ-7321-01exon_skip_48079
16955810169559911695587616955876Frame_Shift_DelC-p.R2489fs
OVTCGA-09-2049-01exon_skip_48079
16955810169559911695594816955948Frame_Shift_DelA-p.S2465fs
LIHCTCGA-G3-A3CJ-01exon_skip_48082
17061832170619821706187717061877Frame_Shift_DelC-p.V1375fs
LIHCTCGA-DD-A3A0-01exon_skip_48082
17061832170619821706195717061957Frame_Shift_DelC-p.G1348fs
LUADTCGA-44-2656-01exon_skip_48073
16877013168771941687708916877090Frame_Shift_Ins-Gp.Q3429fs
UCECTCGA-BG-A0M0-01exon_skip_48073
16877013168771941687708916877090Frame_Shift_Ins-Gp.Q3429fs
UCECTCGA-BG-A0M3-01exon_skip_48073
16877013168771941687708916877090Frame_Shift_Ins-Gp.Q3429fs
UCECTCGA-BG-A0M9-01exon_skip_48073
16877013168771941687708916877090Frame_Shift_Ins-Gp.Q3429fs
UCECTCGA-BK-A0CC-01exon_skip_48073
16877013168771941687708916877090Frame_Shift_Ins-Gp.Q3429fs
LIHCTCGA-CC-A5UD-01exon_skip_48073
16877013168771941687718616877186Nonsense_MutationTAp.R3397*
LIHCTCGA-CC-A5UD-01exon_skip_48073
16877013168771941687718616877186Nonsense_MutationTAp.R3397X
LUADTCGA-86-8073-01exon_skip_48075
16893234168934421689327816893278Nonsense_MutationCAp.E3207*
SKCMTCGA-W3-A824-06exon_skip_48075
16893234168934421689333616893336Nonsense_MutationCTp.W3187*
STADTCGA-CG-5723-0116992000169921101699200316992003Nonsense_MutationGAp.R1693*
STADTCGA-CG-5723-0116992000169921101699200316992003Nonsense_MutationGAp.R1693X
SKCMTCGA-GN-A266-06exon_skip_48082
17061832170619821706185317061853Nonsense_MutationGAp.Q1383*
UCECTCGA-A5-A0G9-01exon_skip_48073
16877013168771941687701116877011Splice_SiteAGe64+2
UCECTCGA-A5-A0G9-01exon_skip_48073
16877013168771941687701116877011Splice_SiteAGp.E3454_splice
STADTCGA-BR-4257-01exon_skip_48077
16932370169325261693236916932369Splice_SiteCTp.R2919_splice
STADTCGA-BR-7901-01exon_skip_48077
16932370169325261693236916932369Splice_SiteCT.
STADTCGA-BR-4292-01exon_skip_48090
17147456171475741714745517147455Splice_SiteCT.
STADTCGA-BR-4292-01exon_skip_48090
17147456171475741714745517147455Splice_SiteCTp.I410_splice
LUADTCGA-38-4631-01exon_skip_48091
17152918171530491715291717152917Splice_SiteCAp.G339_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SISO_CERVIX16949507169496781694956916949569Frame_Shift_DelA-p.F2548fs
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16949507169496781694956916949569Frame_Shift_DelA-p.F2548fs
MM426_SKIN17061832170619821706186817061868Frame_Shift_DelG-p.R1378fs
EN_ENDOMETRIUM16949507169496781694956816949569Frame_Shift_Ins-Ap.F2548fs
ES2_OVARY16877013168771941687703916877039Missense_MutationCGp.V3446L
SW684_SOFT_TISSUE16877013168771941687707416877074Missense_MutationGAp.S3434F
NCIH1573_LUNG16877013168771941687707716877077Missense_MutationAGp.I3433T
JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16877013168771941687713716877137Missense_MutationTCp.D3413G
JHU028_LUNG16877013168771941687716116877161Missense_MutationTCp.N3405S
NCIH526_LUNG16893234168934421689327516893275Missense_MutationCAp.A3208S
NCIH2291_LUNG16893234168934421689343616893436Missense_MutationTAp.Q3154L
SNU1040_LARGE_INTESTINE16932370169325261693242016932420Missense_MutationAGp.F2902S
NH6_AUTONOMIC_GANGLIA16932370169325261693252316932523Missense_MutationACp.W2868G
HOS_BONE16949507169496781694954516949545Missense_MutationCTp.G2556D
HTK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16949507169496781694954516949545Missense_MutationCTp.G2556D
NCIH2172_LUNG16949507169496781694960916949609Missense_MutationCGp.E2535Q
OC316_OVARY16955810169559911695587716955877Missense_MutationCTp.R2489Q
OC314_OVARY16955810169559911695587716955877Missense_MutationCTp.R2489Q
HCC1438_LUNG16955810169559911695589216955892Missense_MutationGAp.A2484V
BICR18_UPPER_AERODIGESTIVE_TRACT16955810169559911695591416955914Missense_MutationTCp.I2477V
BICR18_UPPER_AERODIGESTIVE_TRACT17061832170619821706185817061858Missense_MutationCAp.G1381V
HEC1A_ENDOMETRIUM17061832170619821706188517061885Missense_MutationGAp.T1372I
CORL47_LUNG17061832170619821706191517061915Missense_MutationGTp.T1362K
EVSAT_BREAST17061832170619821706192217061922Missense_MutationTCp.S1360G
NCIH630_LARGE_INTESTINE17061832170619821706193017061930Missense_MutationGTp.P1357H
NCIH1355_LUNG17061832170619821706195917061959Missense_MutationCAp.M1347I
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE17083032170832191708311517083115Missense_MutationCTp.A1312T
SNU1040_LARGE_INTESTINE17083032170832191708311517083115Missense_MutationCTp.A1312T
SNU1040_LARGE_INTESTINE17083032170832191708311717083117Missense_MutationCTp.R1311Q
CP50MELB_SKIN17083032170832191708312317083123Missense_MutationGAp.T1309I
LB771HNC_UPPER_AERODIGESTIVE_TRACT17083032170832191708320117083201Missense_MutationAGp.I1283T
LB771PBL_MATCHED_NORMAL_TISSUE17083032170832191708320117083201Missense_MutationAGp.I1283T
NCIH69_LUNG17147456171475741714752317147523Missense_MutationCAp.G388V
P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE17147456171475741714752417147524Missense_MutationCGp.G388R
KM12_LARGE_INTESTINE17147456171475741714754817147548Missense_MutationGAp.P380S
SW156_KIDNEY17152918171530491715296417152964Missense_MutationCGp.E323D
SW948_LARGE_INTESTINE17152918171530491715301417153014Missense_MutationTCp.N307D
HEC251_ENDOMETRIUM17061832170619821706185917061859Nonsense_MutationCAp.G1381*
NCIH128_LUNG17147456171475741714757417147574Splice_SiteCAp.G371V

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

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CUBN


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CUBN


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RelatedDrugs for CUBN

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
O60494DB00200HydroxocobalaminCubilinsmall moleculeapproved

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RelatedDiseases for CUBN

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
CUBNC0025202melanoma1CTD_human
CUBNC0236733Amphetamine-Related Disorders1CTD_human
CUBNC1306856Megaloblastic anemia due to inborn errors of metabolism1CTD_human;ORPHANET;UNIPROT