ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for GFAP

Gene summary

Gene information	Gene symbol	GFAP
	Gene ID	2670
	Gene name	glial fibrillary acidic protein
	Synonyms	ALXDRD
	Cytomap	17q21.31
	Type of gene	protein-coding
	Description	glial fibrillary acidic protein
	Modification date	20200327
	UniProtAcc	A0A0G2JLI8, A0A1W2PP21, A0A1W2PPA3, A0A1W2PPF0, A0A1W2PPL2, A0A1W2PQ25, A0A1W2PQS4, A0A1W2PQU7, A0A1W2PR46, A0A1W2PRT3, A0A1W2PS58, A0A1X7SBR3, A0A1X7SCE1, A0A224AME3, B4DIR1, K7EJK1, K7EJU1, K7EKD1, K7EKH9, K7ELP4, K7EPI4, K7EPT8, P14136,
	Context	- 32514860(Synaptic Loss, ER Stress and Neuro-Inflammation Emerge Late in the Lateral Temporal Cortex and Associate with Progressive Tau Pathology in Alzheimer's Disease)

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

Gene	GO ID	GO term	PubMed ID
GFAP	GO:0045109	intermediate filament organization	15732097

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Gene structures and expression levels for GFAP

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.

ENSG00000131095

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

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
STG	UP	8.465721e+04	8.385520e-01	4.817248e-06	1.237087e-03
PG	UP	8.175671e+04	1.120557e+00	1.775072e-13	1.148188e-10

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
PCC	UP	ENST00000586125.2	GFAP-207:protein_coding:GFAP	1.131038e+02	1.523887e+00	1.548098e-07	6.941557e-05
STG	UP	ENST00000253408.10	GFAP-201:protein_coding:GFAP	6.213792e+04	8.455266e-01	1.012882e-05	2.722069e-03
STG	UP	ENST00000585543.6	GFAP-205:retained_intron:GFAP	5.219400e+03	8.217411e-01	1.736011e-05	3.878116e-03
STG	UP	ENST00000587997.6	GFAP-210:lncRNA:GFAP	9.876364e+02	8.546657e-01	3.450734e-04	2.231169e-02
STG	UP	ENST00000638618.1	GFAP-229:protein_coding:GFAP	3.034643e+03	1.036215e+00	4.516288e-04	2.603853e-02
STG	UP	ENST00000588037.1	GFAP-211:protein_coding:GFAP	4.521754e+02	9.926831e-01	7.380773e-04	3.273509e-02
PG	UP	ENST00000253408.10	GFAP-201:protein_coding:GFAP	6.260826e+04	1.235194e+00	6.676152e-15	2.907091e-11
PG	UP	ENST00000638921.1	GFAP-230:retained_intron:GFAP	4.713889e+03	1.127464e+00	1.906619e-13	4.704614e-10
PG	UP	ENST00000587997.6	GFAP-210:lncRNA:GFAP	7.065132e+02	1.195952e+00	1.410491e-12	2.320273e-09
PG	UP	ENST00000585543.6	GFAP-205:retained_intron:GFAP	4.177649e+03	1.086078e+00	1.808715e-12	2.774180e-09
PG	UP	ENST00000586125.2	GFAP-207:protein_coding:GFAP	5.991861e+01	1.692512e+00	3.171681e-11	2.746027e-08
PG	UP	ENST00000585728.5	GFAP-206:nonsense_mediated_decay:GFAP	9.946748e+02	9.765730e-01	2.568774e-10	1.398197e-07
PG	UP	ENST00000591719.5	GFAP-219:lncRNA:GFAP	9.929568e+01	1.050604e+00	6.403019e-10	2.934902e-07
PG	UP	ENST00000590922.1	GFAP-217:retained_intron:GFAP	3.898678e+01	8.934705e-01	1.356392e-08	3.223357e-06
PG	UP	ENST00000589701.2	GFAP-216:retained_intron:GFAP	2.009858e+02	1.017247e+00	1.464668e-08	3.398145e-06
PG	UP	ENST00000588640.5	GFAP-213:lncRNA:GFAP	4.398557e+01	9.857247e-01	4.406559e-08	7.813120e-06
PG	UP	ENST00000591327.2	GFAP-218:retained_intron:GFAP	5.061044e+02	9.320113e-01	6.973353e-08	1.130791e-05
PG	UP	ENST00000638618.1	GFAP-229:protein_coding:GFAP	3.841111e+03	1.061267e+00	6.215027e-07	6.126105e-05
PG	UP	ENST00000639921.1	GFAP-235:protein_coding:GFAP	4.643653e+01	9.331005e-01	1.605239e-05	7.147588e-04
PG	UP	ENST00000588037.1	GFAP-211:protein_coding:GFAP	3.851999e+02	8.869430e-01	1.626479e-05	7.213956e-04
PG	UP	ENST00000593179.1	GFAP-224:protein_coding:GFAP	8.685211e-01	1.495746e+00	3.024711e-04	6.165655e-03
PG	UP	ENST00000640552.1	GFAP-237:retained_intron:GFAP	2.371715e+02	9.475830e-01	5.993081e-04	1.004053e-02
PG	UP	ENST00000639369.1	GFAP-234:nonsense_mediated_decay:GFAP	4.395900e+00	9.735539e-01	3.606662e-03	3.638636e-02
CB	DOWN	ENST00000638921.1	GFAP-230:retained_intron:GFAP	1.282804e+04	-8.122740e-01	1.251603e-05	1.273313e-04
CB	UP	ENST00000638281.1	GFAP-225:protein_coding:GFAP	3.265844e+02	1.115136e+00	2.377257e-04	1.540952e-03
CB	UP	ENST00000376990.8	GFAP-202:nonsense_mediated_decay:GFAP	1.132609e+01	9.139405e-01	4.793044e-03	1.900601e-02
TC	UP	ENST00000586793.6	GFAP-209:protein_coding:GFAP	2.083894e+02	1.334863e+00	4.363039e-15	3.352861e-12
TC	UP	ENST00000592320.6	GFAP-222:protein_coding:GFAP	4.252757e+01	1.289396e+00	6.794483e-15	4.893309e-12
TC	UP	ENST00000588037.1	GFAP-211:protein_coding:GFAP	3.120949e+02	1.214535e+00	9.340578e-14	4.741153e-11
TC	UP	ENST00000585728.5	GFAP-206:nonsense_mediated_decay:GFAP	1.399240e+03	1.048164e+00	1.919478e-13	8.890093e-11
TC	UP	ENST00000638281.1	GFAP-225:protein_coding:GFAP	4.446290e+02	1.631152e+00	3.081190e-11	7.208099e-09
TC	UP	ENST00000638618.1	GFAP-229:protein_coding:GFAP	4.189550e+03	1.132773e+00	4.443415e-11	9.732778e-09
TC	UP	ENST00000588316.1	GFAP-212:protein_coding:GFAP	5.311722e+01	1.146805e+00	9.074195e-11	1.780613e-08
TC	UP	ENST00000587997.6	GFAP-210:lncRNA:GFAP	3.007215e+02	9.391938e-01	9.248811e-11	1.809715e-08
TC	UP	ENST00000588640.5	GFAP-213:lncRNA:GFAP	4.413470e+01	9.388995e-01	6.254526e-10	8.934035e-08
TC	UP	ENST00000589701.2	GFAP-216:retained_intron:GFAP	1.248595e+03	8.771504e-01	1.960610e-07	1.065983e-05
TC	UP	ENST00000586125.2	GFAP-207:protein_coding:GFAP	4.254912e+02	8.309577e-01	1.280781e-06	4.891147e-05
TC	UP	ENST00000435360.7	GFAP-203:protein_coding:GFAP	2.580552e+02	9.654189e-01	1.647662e-06	6.032626e-05
TC	UP	ENST00000591880.2	GFAP-220:protein_coding:GFAP	3.652463e+00	1.243752e+00	6.578209e-05	1.161433e-03
TC	UP	ENST00000593179.1	GFAP-224:protein_coding:GFAP	9.140108e-01	1.426098e+00	1.862068e-04	2.641149e-03
TC	UP	ENST00000639042.1	GFAP-231:nonsense_mediated_decay:GFAP	3.424939e+00	1.112298e+00	3.790931e-04	4.628665e-03
TC	UP	ENST00000376990.8	GFAP-202:nonsense_mediated_decay:GFAP	1.427418e+01	8.619259e-01	5.269017e-03	3.487896e-02

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 GFAP

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_101991	chr17	44910653:44910658:44911236:44911456:44911672:44911797	44911236:44911456
exon_skip_103035	chr17	44903314:44903559:44903959:44904233:44904442:44904554	44903959:44904233
exon_skip_11393	chr17	44913799:44913823:44914028:44914088:44915026:44915135	44914028:44914088
exon_skip_141299	chr17	44910653:44910658:44911236:44911456:44911672:44911796	44911236:44911456
exon_skip_164302	chr17	44913313:44913430:44913728:44913823:44914028:44914088	44913728:44913823
exon_skip_224029	chr17	44913799:44913823:44914028:44914088:44915026:44915057	44914028:44914088
exon_skip_233626	chr17	44913799:44913823:44914028:44914109:44915026:44915503	44914028:44914109
exon_skip_234773	chr17	44910653:44910658:44911236:44911321:44911672:44911796	44911236:44911321
exon_skip_241715	chr17	44908135:44908149:44910092:44910658:44911236:44911281	44910092:44910658
exon_skip_249856	chr17	44903241:44903559:44903959:44904233:44904442:44904554	44903959:44904233
exon_skip_252373	chr17	44908137:44908149:44910141:44910260:44910615:44910620	44910141:44910260
exon_skip_258390	chr17	44913324:44913430:44913728:44913823:44914028:44914047	44913728:44913823
exon_skip_258469	chr17	44913799:44913823:44914028:44914109:44915026:44915057	44914028:44914109
exon_skip_261495	chr17	44908135:44908149:44910141:44910260:44910615:44910620	44910141:44910260
exon_skip_280349	chr17	44908137:44908149:44910226:44910260:44910615:44910620	44910226:44910260
exon_skip_286583	chr17	44908135:44908149:44910092:44910260:44910615:44910620	44910092:44910260
exon_skip_45932	chr17	44913799:44913823:44914028:44914109:44915026:44915135	44914028:44914109
exon_skip_46702	chr17	44908135:44908149:44910226:44910260:44910615:44910620	44910226:44910260
exon_skip_58766	chr17	44908135:44908149:44910615:44910658:44911236:44911281	44910615:44910658
exon_skip_63352	chr17	44907205:44907388:44908064:44908149:44910615:44910620	44908064:44908149
exon_skip_7072	chr17	44910653:44910658:44911236:44911321:44911672:44911797	44911236:44911321
exon_skip_76625	chr17	44904442:44904554:44904766:44905149:44908064:44908076	44904766:44905149
exon_skip_95436	chr17	44913269:44913430:44913728:44913823:44914028:44914088	44913728:44913823

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

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

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
ENST00000588735	44910615	44910658	Frame-shift
ENST00000588735	44911236	44911456	Frame-shift
ENST00000588735	44913728	44913823	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
ENST00000588735	44910615	44910658	Frame-shift
ENST00000588735	44911236	44911456	Frame-shift
ENST00000588735	44913728	44913823	In-frame

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
ENST00000588735	44908064	44908149	Frame-shift
ENST00000588735	44910615	44910658	Frame-shift
ENST00000588735	44911236	44911456	Frame-shift
ENST00000588735	44913728	44913823	In-frame

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

p-ENSG00000131095_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
ENST00000588735	6555	432	44913728	44913823	1576	1670	174	205

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
ENST00000588735	6555	432	44913728	44913823	1576	1670	174	205

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
ENST00000588735	6555	432	44913728	44913823	1576	1670	174	205

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
P14136	174	205	1	432	Chain	ID=PRO_0000063805;Note=Glial fibrillary acidic protein
P14136	174	205	69	377	Domain	Note=IF rod;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01188
P14136	174	205	116	214	Region	Note=Coil 1B
P14136	174	205	174	174	Sequence conflict	Note=Q->QQ;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
P14136	174	205	1	432	Chain	ID=PRO_0000063805;Note=Glial fibrillary acidic protein
P14136	174	205	69	377	Domain	Note=IF rod;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01188
P14136	174	205	116	214	Region	Note=Coil 1B
P14136	174	205	174	174	Sequence conflict	Note=Q->QQ;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
P14136	174	205	1	432	Chain	ID=PRO_0000063805;Note=Glial fibrillary acidic protein
P14136	174	205	69	377	Domain	Note=IF rod;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01188
P14136	174	205	116	214	Region	Note=Coil 1B
P14136	174	205	174	174	Sequence conflict	Note=Q->QQ;Ontology_term=ECO:0000305;evidence=ECO:0000305

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

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 GFAP

- 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 GFAP

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 GFAP

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for GFAP

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for GFAP

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 GFAP

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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Gene summary for GFAP

Gene structures and expression levels for GFAP

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

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

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

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

SNVs in the skipped exons for GFAP

AD stage-associated exon skippint events for GFAP

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

Correlation with RNA binding proteins (RBPs) for GFAP

RelatedDrugs for GFAP

RelatedDiseases for GFAP