ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CERS5

Gene summary

Gene information	Gene symbol	CERS5
	Gene ID	91012
	Gene name	ceramide synthase 5
	Synonyms	LASS5\|Trh4
	Cytomap	12q13.12
	Type of gene	protein-coding
	Description	ceramide synthase 5LAG1 homolog, ceramide synthase 5LAG1 longevity assurance homolog 5TRAM homolog 4sphingosine N-acyltransferase CERS5
	Modification date	20200313
	UniProtAcc	B4DQR7, F8VQZ6, F8VSK7, F8VXY1, F8VY42, F8W1K4, F8W1N7, F8W1Z3, H0YHG4, H0YHK2, H0YI10, H0YIG1, Q49AQ3, Q8N5B7,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
CERS5	GO:0046513	ceramide biosynthetic process	16951403\|29632068

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Gene structures and expression levels for CERS5

Skipped 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.

ENSG00000139624

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	DOWN	ENST00000550919.5	CERS5-223:protein_coding:CERS5	1.752715e+02	-4.768120e+00	2.281065e-05	2.115628e-04
CB	UP	ENST00000550258.5	CERS5-220:nonsense_mediated_decay:CERS5	2.083212e+00	9.935784e-01	3.057037e-05	2.708547e-04
CB	UP	ENST00000547787.5	CERS5-211:nonsense_mediated_decay:CERS5	9.853153e+01	9.302486e-01	1.215113e-03	6.086297e-03
TC	UP	ENST00000547787.5	CERS5-211:nonsense_mediated_decay:CERS5	6.730119e+01	9.262339e-01	4.766895e-07	2.213010e-05
TC	DOWN	ENST00000551757.1	CERS5-227:retained_intron:CERS5	6.240143e+01	-8.389779e-01	1.746286e-06	6.334708e-05
TC	DOWN	ENST00000550919.5	CERS5-223:protein_coding:CERS5	5.975331e+01	-2.911738e+00	4.075520e-04	4.905173e-03

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CERS5

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

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_108176	chr12	50144019:50144057:50148472:50148588:50167101:50167359	50148472:50148588
exon_skip_114833	chr12	50130549:50130694:50132962:50134068:50134546:50134702	50132962:50134068
exon_skip_116795	chr12	50135941:50136069:50137728:50137820:50138567:50138617	50137728:50137820
exon_skip_139472	chr12	50130413:50130694:50132962:50133064:50134546:50134702	50132962:50133064
exon_skip_161524	chr12	50130549:50130694:50134400:50134702:50135732:50135838	50134400:50134702
exon_skip_167847	chr12	50138567:50138617:50142053:50142110:50143074:50143204	50142053:50142110
exon_skip_168998	chr12	50130549:50130694:50132962:50133064:50134546:50134702	50132962:50133064
exon_skip_175020	chr12	50134620:50134702:50135433:50135652:50135732:50135792	50135433:50135652
exon_skip_189424	chr12	50130413:50130694:50132962:50134068:50134546:50134702	50132962:50134068
exon_skip_19694	chr12	50130549:50130694:50134546:50134702:50135732:50135838	50134546:50134702
exon_skip_211148	chr12	50135958:50136069:50138567:50138617:50142053:50142093	50138567:50138617
exon_skip_212597	chr12	50144019:50144057:50165822:50165943:50167101:50167326	50165822:50165943
exon_skip_215836	chr12	50143952:50144057:50153829:50153951:50167101:50167300	50153829:50153951
exon_skip_238734	chr12	50129798:50130694:50134546:50134702:50135732:50135838	50134546:50134702
exon_skip_256129	chr12	50129798:50130694:50134400:50134702:50135732:50135838	50134400:50134702
exon_skip_2589	chr12	50143952:50144057:50148472:50148588:50167101:50167359	50148472:50148588
exon_skip_259621	chr12	50143074:50143204:50143952:50144057:50167101:50167393	50143952:50144057
exon_skip_259904	chr12	50143165:50143204:50143952:50144057:50144769:50144791	50143952:50144057
exon_skip_291683	chr12	50135941:50136069:50138567:50138617:50142053:50142093	50138567:50138617
exon_skip_36343	chr12	50143952:50144057:50165822:50165943:50167101:50167326	50165822:50165943
exon_skip_48356	chr12	50143165:50143204:50143952:50144057:50165822:50165943	50143952:50144057
exon_skip_60196	chr12	50143165:50143204:50143952:50144057:50167101:50167300	50143952:50144057
exon_skip_60704	chr12	50137728:50137820:50138567:50138617:50143074:50143204	50138567:50138617
exon_skip_61599	chr12	50144019:50144057:50144769:50144969:50167101:50167300	50144769:50144969
exon_skip_84643	chr12	50144019:50144057:50144769:50144969:50167101:50167303	50144769:50144969
exon_skip_85065	chr12	50135958:50136069:50137728:50137820:50138567:50138617	50137728:50137820

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information	Tissue type	Avg(PSIs) in AD	Avg(PSIs) in control	Difference (PSI)	Adj. p-value
exon_skip_114833	Mayo_TC	4.828049e-01	5.864103e-01	-1.036054e-01	4.899030e-05

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Open reading frame (ORF) annotation in the exon skipping event for CERS5

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000317551	50134546	50134702	Frame-shift
ENST00000317551	50142053	50142110	Frame-shift
ENST00000317551	50137728	50137820	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000317551	50142053	50142110	Frame-shift

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000317551	50142053	50142110	Frame-shift
ENST00000317551	50137728	50137820	In-frame

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Infer the effects of exon skipping event on protein functional features for CERS5

p-ENSG00000139624_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000317551	2068	392	50137728	50137820	669	760	181	211

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST

Length of mRNA

Length of AA seq.

Genomic start

Genomic end

mRNA start

mRNA end

AA start

AA end

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000317551	2068	392	50137728	50137820	669	760	181	211

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 feature	Description of feature
Q8N5B7	181	211	1	392	Chain	ID=PRO_0000185514;Note=Ceramide synthase 5
Q8N5B7	181	211	139	340	Domain	Note=TLC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00205
Q8N5B7	181	211	169	182	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N5B7	181	211	204	213	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N5B7	181	211	183	203	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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 feature

Description of feature

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 feature	Description of feature
Q8N5B7	181	211	1	392	Chain	ID=PRO_0000185514;Note=Ceramide synthase 5
Q8N5B7	181	211	139	340	Domain	Note=TLC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00205
Q8N5B7	181	211	169	182	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N5B7	181	211	204	213	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N5B7	181	211	183	203	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in CERS5

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for CERS5

- Differential PSIs between mutated versus non-mutated samples.

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

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

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for CERS5

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CERS5

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
CB	exon_skip_60196	rs7302981	chr12:50144032	1.506182e-08	8.999053e-06
CB	exon_skip_175020	rs17124432	chr12:50116994	2.805673e-06	8.619831e-04
CB	exon_skip_175020	rs7307230	chr12:50118849	2.805673e-06	8.619831e-04
CB	exon_skip_175020	rs1554844	chr12:50120582	2.805673e-06	8.619831e-04
CB	exon_skip_114833	rs17124432	chr12:50116994	1.381420e-05	3.410940e-03
CB	exon_skip_114833	rs7307230	chr12:50118849	1.381420e-05	3.410940e-03
CB	exon_skip_114833	rs1554844	chr12:50120582	1.381420e-05	3.410940e-03
CB	exon_skip_175020	rs7302981	chr12:50144032	1.589194e-05	3.855606e-03
CB	exon_skip_60196	rs10783342	chr12:50234683	5.593638e-05	1.084999e-02
TC	exon_skip_175020	rs10783342	chr12:50234683	7.095528e-05	1.245158e-02
TC	exon_skip_114833	rs7302981	chr12:50144032	2.396505e-04	3.281321e-02
HCC	exon_skip_175020	rs7136570	chr12:50136153	6.169995e-05	6.064559e-03
HCC	exon_skip_139472	rs7972465	chr12:50152342	6.823292e-05	6.614093e-03
HCC	exon_skip_175020	rs7302981	chr12:50144032	7.060764e-05	6.815855e-03
HCC	exon_skip_139472	rs17124432	chr12:50116994	1.384682e-04	1.201024e-02
HCC	exon_skip_139472	rs7307230	chr12:50118849	1.384682e-04	1.201024e-02
HCC	exon_skip_139472	rs1554844	chr12:50120582	1.384682e-04	1.201024e-02
HCC	exon_skip_139472	rs11169282	chr12:50136188	1.384682e-04	1.201024e-02
HCC	exon_skip_175020	rs10783342	chr12:50234683	3.168518e-04	2.361080e-02
HCC	exon_skip_139472	rs11169270	chr12:50089249	3.647481e-04	2.640210e-02
HCC	exon_skip_175020	rs17124432	chr12:50116994	4.552854e-04	3.147878e-02
HCC	exon_skip_175020	rs7307230	chr12:50118849	4.552854e-04	3.147878e-02
HCC	exon_skip_175020	rs1554844	chr12:50120582	4.552854e-04	3.147878e-02
HCC	exon_skip_175020	rs11169282	chr12:50136188	4.552854e-04	3.147878e-02
HCC	exon_skip_139472	rs12425229	chr12:50231275	7.225131e-04	4.534131e-02
DLPFC	exon_skip_175020	rs17124432	chr12:50116994	3.688495e-08	7.653878e-06
DLPFC	exon_skip_175020	rs7307230	chr12:50118849	3.688495e-08	7.653878e-06
DLPFC	exon_skip_175020	rs1554844	chr12:50120582	3.688495e-08	7.653878e-06
DLPFC	exon_skip_175020	rs11169282	chr12:50136188	3.688495e-08	7.653878e-06
DLPFC	exon_skip_175020	rs7972465	chr12:50152342	2.482482e-07	4.197179e-05
DLPFC	exon_skip_175020	rs7136570	chr12:50136153	1.331381e-05	1.449790e-03
DLPFC	exon_skip_175020	rs7302981	chr12:50144032	1.482062e-05	1.586975e-03
DLPFC	exon_skip_114833	rs17124432	chr12:50116994	2.615065e-05	2.623593e-03
DLPFC	exon_skip_114833	rs7307230	chr12:50118849	2.615065e-05	2.623593e-03
DLPFC	exon_skip_114833	rs1554844	chr12:50120582	2.615065e-05	2.623593e-03
DLPFC	exon_skip_114833	rs11169282	chr12:50136188	2.615065e-05	2.623593e-03
DLPFC	exon_skip_114833	rs7972465	chr12:50152342	9.332154e-05	7.965616e-03
DLPFC	exon_skip_175020	rs11169270	chr12:50089249	1.034749e-04	8.716472e-03
DLPFC	exon_skip_175020	rs12425229	chr12:50231275	1.201794e-04	9.874635e-03
DLPFC	exon_skip_175020	rs836172	chr12:50096316	1.751957e-04	1.368812e-02
DLPFC	exon_skip_114833	rs7136570	chr12:50136153	2.426744e-04	1.809690e-02
DLPFC	exon_skip_114833	rs7302981	chr12:50144032	3.222494e-04	2.281879e-02
DLPFC	exon_skip_175020	rs12425705	chr12:50216538	4.974014e-04	3.213930e-02
DLPFC	exon_skip_114833	rs12425229	chr12:50231275	5.717809e-04	3.592027e-02

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Correlation with RNA binding proteins (RBPs) for CERS5

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RALYL	exon_skip_114833	4.800019e-01	1.531400e-10
CB	RALYL	exon_skip_287377	4.158565e-01	4.999652e-08
CB	SAMD4A	exon_skip_61599	4.455291e-01	7.039161e-09
CB	FXR2	exon_skip_61599	4.036404e-01	2.093741e-07
CB	PCBP4	exon_skip_61599	-4.937721e-01	7.661947e-11
CB	HNRNPC	exon_skip_61599	4.113915e-01	1.156592e-07
CB	RBM4B	exon_skip_61599	4.080993e-01	1.490908e-07
CB	PCBP4	exon_skip_227106	-4.390013e-01	3.787559e-07
CB	RBM6	exon_skip_145092	4.582646e-01	4.192753e-08
CB	PCBP4	exon_skip_145092	-4.018032e-01	2.155544e-06
DLPFC	RBFOX2	exon_skip_114833	5.108154e-01	1.279980e-17
DLPFC	ELAVL4	exon_skip_114833	4.774895e-01	2.671381e-15
DLPFC	KHDRBS2	exon_skip_114833	4.145121e-01	1.502882e-11
DLPFC	NOVA1	exon_skip_114833	5.327368e-01	2.736640e-19
HCC	RBFOX2	exon_skip_139472	4.017874e-01	8.082799e-12
HCC	SAMD4A	exon_skip_139472	-4.426647e-01	2.748533e-14
HCC	RALY	exon_skip_139472	-4.712318e-01	3.207957e-16
HCC	PTBP1	exon_skip_139472	-4.605042e-01	1.791926e-15
PCC	RBFOX2	exon_skip_139472	5.536546e-01	1.274851e-17
PCC	G3BP2	exon_skip_139472	5.558898e-01	8.875011e-18
PCC	PTBP1	exon_skip_139472	-4.653314e-01	3.004095e-12
PCC	RBFOX2	exon_skip_189424	4.969452e-01	2.653072e-12
PCC	CPEB1	exon_skip_189424	4.426474e-01	8.593753e-10
TC	RBFOX2	exon_skip_168998	5.511634e-01	5.146488e-14
TC	G3BP2	exon_skip_168998	5.170658e-01	2.996505e-12
TC	ENOX1	exon_skip_168998	4.685015e-01	4.730555e-10
TC	RALYL	exon_skip_168998	6.477280e-01	2.777464e-20
TC	PTBP1	exon_skip_168998	-4.050676e-01	1.182375e-07
TC	SRSF5	exon_skip_168998	4.104188e-01	7.744448e-08
TC	HNRNPH2	exon_skip_168998	4.850579e-01	9.202964e-11
TC	MSI1	exon_skip_114833	-4.910022e-01	4.345257e-11
TC	NOVA1	exon_skip_114833	5.446407e-01	9.703993e-14
TC	SRSF2	exon_skip_175020	4.176816e-01	4.309153e-08
TC	ELAVL4	exon_skip_175020	4.282105e-01	1.796598e-08
TC	RALYL	exon_skip_175020	4.856563e-01	8.659822e-11
TC	CELF1	exon_skip_175020	4.243502e-01	2.484619e-08

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RelatedDrugs for CERS5

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for CERS5

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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