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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 RAB5A

check button Gene summary
Gene informationGene symbol

RAB5A

Gene ID

5868

Gene nameRAB5A, member RAS oncogene family
SynonymsRAB5
Cytomap

3p24.3

Type of geneprotein-coding
Descriptionras-related protein Rab-5ARAS-associated protein RAB5A
Modification date20180527
UniProtAcc

P20339

ContextPubMed: RAB5A [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
RAB5A

GO:0006897

endocytosis

15378032

RAB5A

GO:0036465

synaptic vesicle recycling

16141272

RAB5A

GO:0051489

regulation of filopodium assembly

14978216


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Exon skipping events across known transcript of Ensembl for RAB5A 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 RAB5A

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 RAB5A

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_372109319992492:19992553:20012039:20012209:20017092:2001724420012039:20012209ENSG00000144566.6ENST00000446547.1
exon_skip_372112319992492:19992553:20017078:20017244:20017538:2001759520017078:20017244ENSG00000144566.6ENST00000412966.1
exon_skip_372113319992492:19992553:20017092:20017244:20017538:2001759520017092:20017244ENSG00000144566.6ENST00000469122.1,ENST00000273047.4
exon_skip_372114319992492:19992553:20017134:20017244:20017538:2001759520017134:20017244ENSG00000144566.6ENST00000422242.1
exon_skip_372115320017134:20017244:20017538:20017661:20019801:2001989520017538:20017661ENSG00000144566.6ENST00000446547.1,ENST00000469122.1,ENST00000273047.4,ENST00000473608.1,ENST00000422242.1
exon_skip_372116320017538:20017661:20019801:20019895:20025199:2002561320019801:20019895ENSG00000144566.6ENST00000446547.1,ENST00000273047.4,ENST00000473608.1,ENST00000422242.1

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

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Exon skipping events with PSIs in GTEx for RAB5A

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_372109319992492:19992553:20012039:20012209:20017092:2001724420012039:20012209ENSG00000144566.6ENST00000446547.1
exon_skip_372112319992492:19992553:20017078:20017244:20017538:2001759520017078:20017244ENSG00000144566.6ENST00000412966.1
exon_skip_372113319992492:19992553:20017092:20017244:20017538:2001759520017092:20017244ENSG00000144566.6ENST00000273047.4,ENST00000469122.1
exon_skip_372114319992492:19992553:20017134:20017244:20017538:2001759520017134:20017244ENSG00000144566.6ENST00000422242.1
exon_skip_372115320017134:20017244:20017538:20017661:20019801:2001989520017538:20017661ENSG00000144566.6ENST00000273047.4,ENST00000446547.1,ENST00000422242.1,ENST00000469122.1,ENST00000473608.1
exon_skip_372116320017538:20017661:20019801:20019895:20025199:2002561320019801:20019895ENSG00000144566.6ENST00000273047.4,ENST00000446547.1,ENST00000422242.1,ENST00000473608.1

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 RAB5A

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
ENST000002730472001709220017244Frame-shift
ENST000002730472001980120019895Frame-shift
ENST000002730472001753820017661In-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
ENST000002730472001709220017244Frame-shift
ENST000002730472001980120019895Frame-shift
ENST000002730472001753820017661In-frame

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Infer the effects of exon skipping event on protein functional features for RAB5A

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
ENST0000027304725532152001753820017661852974105146

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
ENST0000027304725532152001753820017661852974105146

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
P20339105146127133Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P203391051461215ChainID=PRO_0000121104;Note=Ras-related protein Rab-5A
P20339105146105121HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P20339105146135140HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P20339105146145154HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P20339105146116116MutagenesisNote=No effect on RABEP1 binding affinity. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15378032;Dbxref=PMID:15378032
P20339105146120120MutagenesisNote=No effect on RABEP1 binding affinity. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15378032;Dbxref=PMID:15378032
P20339105146133136Nucleotide bindingNote=GTP;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:1N6H,ECO:0000244|PDB:1N6L,ECO:0000244|PDB:1N6N,ECO:


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
P20339105146127133Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P203391051461215ChainID=PRO_0000121104;Note=Ras-related protein Rab-5A
P20339105146105121HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P20339105146135140HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P20339105146145154HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1R2Q
P20339105146116116MutagenesisNote=No effect on RABEP1 binding affinity. K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15378032;Dbxref=PMID:15378032
P20339105146120120MutagenesisNote=No effect on RABEP1 binding affinity. R->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15378032;Dbxref=PMID:15378032
P20339105146133136Nucleotide bindingNote=GTP;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:1N6H,ECO:0000244|PDB:1N6L,ECO:0000244|PDB:1N6N,ECO:


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SNVs in the skipped exons for RAB5A

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.
RAB5A_CESC_exon_skip_372115_psi_boxplot.png
boxplot
RAB5A_HNSC_exon_skip_372115_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-G3-A3CJ-01exon_skip_372115
20017539200176612001755620017556Frame_Shift_DelA-p.A111fs
LIHCTCGA-G3-A3CJ-01exon_skip_372115
20017539200176612001764120017641Frame_Shift_DelA-p.K140fs
HNSCTCGA-UF-A71A-01exon_skip_372115
20017539200176612001755120017551Nonsense_MutationATp.R110*
HNSCTCGA-UF-A71A-06exon_skip_372115
20017539200176612001755120017551Nonsense_MutationATp.R110*
CESCTCGA-Q1-A73R-01exon_skip_372115
20017539200176612001766220017662Splice_SiteGAe3+1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
RAB5A_20017134_20017244_20017538_20017661_20019801_20019895_TCGA-Q1-A73R-01Sample: TCGA-Q1-A73R-01
Cancer type: CESC
ESID: exon_skip_372115
Skipped exon start: 20017539
Skipped exon end: 20017661
Mutation start: 20017662
Mutation end: 20017662
Mutation type: Splice_Site
Reference seq: G
Mutation seq: A
AAchange: e3+1
exon_skip_372115_CESC_TCGA-Q1-A73R-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
MFE319_ENDOMETRIUM20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
ACHN_KIDNEY20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
HS611T_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
JHUEM2_ENDOMETRIUM20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
NCIH2073_LUNG20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
SNU398_LIVER20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
T84_LARGE_INTESTINE20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
TGBC11TKB_STOMACH20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
UMUC1_URINARY_TRACT20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
YH13_CENTRAL_NERVOUS_SYSTEM20017539200176612001755520017556Frame_Shift_Ins-Ap.AK111fs
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017093200172442001712820017128Missense_MutationAGp.T67A
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017079200172442001712820017128Missense_MutationAGp.T67A
GP5D_LARGE_INTESTINE20017093200172442001714120017141Missense_MutationTCp.F71S
GP5D_LARGE_INTESTINE20017079200172442001714120017141Missense_MutationTCp.F71S
GP5D_LARGE_INTESTINE20017135200172442001714120017141Missense_MutationTCp.F71S
SNU81_LARGE_INTESTINE20019802200198952001983320019833Missense_MutationTCp.L157S
HT115_LARGE_INTESTINE20019802200198952001985320019853Missense_MutationGAp.A164T
SNU1040_LARGE_INTESTINE20019802200198952001985320019853Missense_MutationGAp.A164T
GP2D_LARGE_INTESTINE20019802200198952001986520019865Missense_MutationAGp.M168V
GP5D_LARGE_INTESTINE20019802200198952001986520019865Missense_MutationAGp.M168V
KMOE2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017093200172442001719920017199Nonsense_MutationCAp.Y90*
KMOE2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017079200172442001719920017199Nonsense_MutationCAp.Y90*
KMOE2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20017135200172442001719920017199Nonsense_MutationCAp.Y90*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB5A

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 RAB5A


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB5A


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RelatedDrugs for RAB5A

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

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RelatedDiseases for RAB5A

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
RAB5AC0151744Myocardial Ischemia1CTD_human