ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PLP1

Gene summary

Gene information	Gene symbol	PLP1
	Gene ID	5354
	Gene name	proteolipid protein 1
	Synonyms	GPM6C\|HLD1\|MMPL\|PLP\|PLP/DM20\|PMD\|SPG2
	Cytomap	Xq22.2
	Type of gene	protein-coding
	Description	myelin proteolipid proteinlipophilinmajor myelin proteolipid protein
	Modification date	20200313
	UniProtAcc	A0A0S2Z4D4, A8K9L3, B1B1G1, B1B1G2, B1B1G3, B1B1G4, B1B1G6, P60201,
	Context	- 32255227(White Matter Alterations in Alzheimer's Disease Without Concomitant Pathologies)

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for PLP1

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.

ENSG00000123560

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
DLPFC	DOWN	ENST00000589298.2	APLP1-206:lncRNA:APLP1	5.136103e+00	-3.247793e+00	1.037787e-03	3.453471e-02
PCC	UP	ENST00000587274.1	APLP1-204:protein_coding:APLP1	1.945442e+01	9.844194e-01	6.444350e-04	1.937805e-02
STG	UP	ENST00000586861.5	APLP1-203:protein_coding:APLP1	1.059364e+02	3.289493e+00	1.768694e-07	1.318240e-04
STG	UP	ENST00000260379.11	RPLP1-201:protein_coding:RPLP1	3.420124e+02	1.039886e+00	7.146911e-06	2.194530e-03
STG	UP	ENST00000357790.5	RPLP1-202:protein_coding:RPLP1	3.351875e+02	9.289204e-01	1.086641e-05	2.855393e-03
STG	UP	ENST00000590561.5	APLP1-208:nonsense_mediated_decay:APLP1	2.955542e+02	1.123875e+00	2.735072e-04	1.975638e-02
STG	UP	ENST00000592316.1	APLP1-211:protein_coding:APLP1	8.675222e+00	9.618252e-01	1.064225e-03	3.987683e-02
PG	UP	ENST00000619236.1	PLP1-221:protein_coding:PLP1	6.910311e+03	1.175273e+00	1.137294e-07	1.680414e-05
CB	DOWN	ENST00000587274.1	APLP1-204:protein_coding:APLP1	2.164552e+02	-2.975298e+00	3.045696e-18	5.964041e-15
CB	DOWN	ENST00000591165.1	APLP1-210:lncRNA:APLP1	6.998201e+02	-1.372177e+00	1.983775e-16	1.612418e-13
CB	DOWN	ENST00000590561.5	APLP1-208:nonsense_mediated_decay:APLP1	5.644057e+02	-1.076465e+00	5.173509e-07	8.561152e-06
TC	DOWN	ENST00000587274.1	APLP1-204:protein_coding:APLP1	7.142629e+02	-1.973391e+00	7.706242e-15	5.464123e-12
TC	DOWN	ENST00000590926.1	APLP1-209:retained_intron:APLP1	8.574468e+01	-8.337220e-01	5.466772e-09	5.459194e-07
TC	DOWN	ENST00000619236.1	PLP1-221:protein_coding:PLP1	3.583398e+04	-8.300784e-01	3.284547e-07	1.631080e-05

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 PLP1

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_115021	chrX	103786465:103786726:103787798:103787966:103788437:103788460	103787798:103787966
exon_skip_12334	chrX	103776918:103776999:103779849:103779990:103785582:103785593	103779849:103779990
exon_skip_1985	chrX	103786465:103786621:103787798:103787966:103788437:103788460	103787798:103787966
exon_skip_222915	chrX	103788437:103788510:103789333:103789398:103790527:103790582	103789333:103789398
exon_skip_242530	chrX	103776918:103776999:103785582:103785768:103786465:103786509	103785582:103785768
exon_skip_274759	chrX	103786543:103786726:103787798:103787966:103788437:103788460	103787798:103787966
exon_skip_54175	chrX	103786543:103786621:103787798:103787966:103788437:103788460	103787798:103787966
exon_skip_55906	chrX	103786595:103786726:103787798:103787966:103788437:103788460	103787798:103787966
exon_skip_8458	chrX	103788439:103788510:103789333:103789398:103790527:103790582	103789333:103789398

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 PLP1

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
ENST00000612423	103787798	103787966	Frame-shift
ENST00000621218	103787798	103787966	Frame-shift
ENST00000612423	103789333	103789398	In-frame
ENST00000621218	103789333	103789398	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
ENST00000612423	103787798	103787966	Frame-shift
ENST00000621218	103787798	103787966	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
ENST00000612423	103785582	103785768	Frame-shift
ENST00000621218	103785582	103785768	Frame-shift
ENST00000612423	103787798	103787966	Frame-shift
ENST00000621218	103787798	103787966	Frame-shift
ENST00000612423	103789333	103789398	In-frame
ENST00000621218	103789333	103789398	In-frame

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Infer the effects of exon skipping event on protein functional features for PLP1

p-ENSG00000123560_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
ENST00000612423	3149	277	103789333	103789398	978	1042	232	254
ENST00000621218	3018	277	103789333	103789398	844	908	232	254

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
ENST00000612423	3149	277	103789333	103789398	978	1042	232	254
ENST00000621218	3018	277	103789333	103789398	844	908	232	254

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
P60201	232	254	2	277	Chain	ID=PRO_0000159005;Note=Myelin proteolipid protein
P60201	232	254	2	277	Chain	ID=PRO_0000159005;Note=Myelin proteolipid protein
P60201	232	254	234	234	Natural variant	ID=VAR_015048;Note=In HLD1. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	234	234	Natural variant	ID=VAR_015048;Note=In HLD1. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	237	237	Natural variant	ID=VAR_004563;Note=In SPG2. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8956049;Dbxref=dbSNP:rs132630291,PMID:8956049
P60201	232	254	237	237	Natural variant	ID=VAR_004563;Note=In SPG2. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8956049;Dbxref=dbSNP:rs132630291,PMID:8956049
P60201	232	254	239	239	Natural variant	ID=VAR_046916;Note=In HLD1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=PMID:15712223
P60201	232	254	239	239	Natural variant	ID=VAR_046916;Note=In HLD1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=PMID:15712223
P60201	232	254	242	242	Natural variant	ID=VAR_015049;Note=In HLD1. A->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:9143933,ECO:0000269\|PubMed:9894878;Dbxref=PMID:9143933,PMID:9894878
P60201	232	254	242	242	Natural variant	ID=VAR_015049;Note=In HLD1. A->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:9143933,ECO:0000269\|PubMed:9894878;Dbxref=PMID:9143933,PMID:9894878
P60201	232	254	243	243	Natural variant	ID=VAR_046917;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11786921;Dbxref=PMID:11786921
P60201	232	254	243	243	Natural variant	ID=VAR_046917;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11786921;Dbxref=PMID:11786921
P60201	232	254	243	243	Natural variant	ID=VAR_046918;Note=In HLD1. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9482656;Dbxref=PMID:9482656
P60201	232	254	243	243	Natural variant	ID=VAR_046918;Note=In HLD1. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9482656;Dbxref=PMID:9482656
P60201	232	254	246	246	Natural variant	ID=VAR_046919;Note=In HLD1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=dbSNP:rs398123467,PMID:15712223
P60201	232	254	246	246	Natural variant	ID=VAR_046919;Note=In HLD1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=dbSNP:rs398123467,PMID:15712223
P60201	232	254	246	246	Natural variant	ID=VAR_015050;Note=In HLD1. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	246	246	Natural variant	ID=VAR_015050;Note=In HLD1. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	247	247	Natural variant	ID=VAR_046920;Note=In HLD1. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10425042;Dbxref=dbSNP:rs886043504,PMID:10425042
P60201	232	254	247	247	Natural variant	ID=VAR_046920;Note=In HLD1. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10425042;Dbxref=dbSNP:rs886043504,PMID:10425042
P60201	232	254	248	248	Natural variant	ID=VAR_015051;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	248	248	Natural variant	ID=VAR_015051;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	249	249	Natural variant	ID=VAR_004565;Note=In HLD1. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:7541731;Dbxref=PMID:7541731
P60201	232	254	249	249	Natural variant	ID=VAR_004565;Note=In HLD1. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:7541731;Dbxref=PMID:7541731
P60201	232	254	253	253	Natural variant	ID=VAR_015052;Note=In HLD1. S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9788732;Dbxref=PMID:9788732
P60201	232	254	253	253	Natural variant	ID=VAR_015052;Note=In HLD1. S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9788732;Dbxref=PMID:9788732
P60201	232	254	178	233	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:1711121;Dbxref=PMID:1711121
P60201	232	254	178	233	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:1711121;Dbxref=PMID:1711121
P60201	232	254	234	260	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000305;evidence=ECO:0000305
P60201	232	254	234	260	Transmembrane	Note=Helical%3B Name%3D4;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

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
P60201	232	254	2	277	Chain	ID=PRO_0000159005;Note=Myelin proteolipid protein
P60201	232	254	2	277	Chain	ID=PRO_0000159005;Note=Myelin proteolipid protein
P60201	232	254	234	234	Natural variant	ID=VAR_015048;Note=In HLD1. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	234	234	Natural variant	ID=VAR_015048;Note=In HLD1. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	237	237	Natural variant	ID=VAR_004563;Note=In SPG2. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8956049;Dbxref=dbSNP:rs132630291,PMID:8956049
P60201	232	254	237	237	Natural variant	ID=VAR_004563;Note=In SPG2. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:8956049;Dbxref=dbSNP:rs132630291,PMID:8956049
P60201	232	254	239	239	Natural variant	ID=VAR_046916;Note=In HLD1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=PMID:15712223
P60201	232	254	239	239	Natural variant	ID=VAR_046916;Note=In HLD1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=PMID:15712223
P60201	232	254	242	242	Natural variant	ID=VAR_015049;Note=In HLD1. A->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:9143933,ECO:0000269\|PubMed:9894878;Dbxref=PMID:9143933,PMID:9894878
P60201	232	254	242	242	Natural variant	ID=VAR_015049;Note=In HLD1. A->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:9143933,ECO:0000269\|PubMed:9894878;Dbxref=PMID:9143933,PMID:9894878
P60201	232	254	243	243	Natural variant	ID=VAR_046917;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11786921;Dbxref=PMID:11786921
P60201	232	254	243	243	Natural variant	ID=VAR_046917;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11786921;Dbxref=PMID:11786921
P60201	232	254	243	243	Natural variant	ID=VAR_046918;Note=In HLD1. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9482656;Dbxref=PMID:9482656
P60201	232	254	243	243	Natural variant	ID=VAR_046918;Note=In HLD1. A->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9482656;Dbxref=PMID:9482656
P60201	232	254	246	246	Natural variant	ID=VAR_046919;Note=In HLD1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=dbSNP:rs398123467,PMID:15712223
P60201	232	254	246	246	Natural variant	ID=VAR_046919;Note=In HLD1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15712223;Dbxref=dbSNP:rs398123467,PMID:15712223
P60201	232	254	246	246	Natural variant	ID=VAR_015050;Note=In HLD1. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	246	246	Natural variant	ID=VAR_015050;Note=In HLD1. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	247	247	Natural variant	ID=VAR_046920;Note=In HLD1. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10425042;Dbxref=dbSNP:rs886043504,PMID:10425042
P60201	232	254	247	247	Natural variant	ID=VAR_046920;Note=In HLD1. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10425042;Dbxref=dbSNP:rs886043504,PMID:10425042
P60201	232	254	248	248	Natural variant	ID=VAR_015051;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	248	248	Natural variant	ID=VAR_015051;Note=In HLD1. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10417279;Dbxref=PMID:10417279
P60201	232	254	249	249	Natural variant	ID=VAR_004565;Note=In HLD1. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:7541731;Dbxref=PMID:7541731
P60201	232	254	249	249	Natural variant	ID=VAR_004565;Note=In HLD1. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:7541731;Dbxref=PMID:7541731
P60201	232	254	253	253	Natural variant	ID=VAR_015052;Note=In HLD1. S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9788732;Dbxref=PMID:9788732
P60201	232	254	253	253	Natural variant	ID=VAR_015052;Note=In HLD1. S->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9788732;Dbxref=PMID:9788732
P60201	232	254	178	233	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:1711121;Dbxref=PMID:1711121
P60201	232	254	178	233	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:1711121;Dbxref=PMID:1711121
P60201	232	254	234	260	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000305;evidence=ECO:0000305
P60201	232	254	234	260	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in PLP1

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 PLP1

- 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 PLP1

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 PLP1

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 PLP1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for PLP1

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 PLP1

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 PLP1

Gene structures and expression levels for PLP1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PLP1

Open reading frame (ORF) annotation in the exon skipping event for PLP1

Infer the effects of exon skipping event on protein functional features for PLP1

3'-UTR located exon skipping events that lost miRNA binding sites in PLP1

SNVs in the skipped exons for PLP1

AD stage-associated exon skippint events for PLP1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLP1

Correlation with RNA binding proteins (RBPs) for PLP1

RelatedDrugs for PLP1

RelatedDiseases for PLP1