ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SEMA4D

Gene summary

Gene information	Gene symbol	SEMA4D
	Gene ID	10507
	Gene name	semaphorin 4D
	Synonyms	A8\|BB18\|C9orf164\|CD100\|COLL4\|GR3\|M-sema-G\|SEMAJ\|coll-4
	Cytomap	9q22.2
	Type of gene	protein-coding
	Description	semaphorin-4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4D
	Modification date	20200313
	UniProtAcc	A0A0C4DG45, C9JD54, C9JFP1, C9JYS7, E9PFD9, F5H044, Q92854,
	Context

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

Gene	GO ID	GO term	PubMed ID
SEMA4D	GO:0001934	positive regulation of protein phosphorylation	16055703
SEMA4D	GO:0007162	negative regulation of cell adhesion	15218527
SEMA4D	GO:0030335	positive regulation of cell migration	16055703
SEMA4D	GO:0071526	semaphorin-plexin signaling pathway	15218527

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Gene structures and expression levels for SEMA4D

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.

ENSG00000187764

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	ENST00000420101.6	SEMA4D-204:protein_coding:SEMA4D	1.622153e+02	-1.030000e+00	3.602340e-10	1.882085e-08
TC	DOWN	ENST00000420101.6	SEMA4D-204:protein_coding:SEMA4D	4.661945e+02	-1.026618e+00	5.555583e-13	2.202316e-10
TC	DOWN	ENST00000482128.1	SEMA4D-218:lncRNA:SEMA4D	6.185283e+00	-8.068954e-01	3.410640e-04	4.253822e-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 SEMA4D

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_108258	chr9	89392423:89392536:89393562:89393655:89396737:89396835	89393562:89393655
exon_skip_118117	chr9	89393631:89393655:89396737:89396835:89399276:89399338	89396737:89396835
exon_skip_122861	chr9	89418056:89418118:89455888:89455953:89479572:89479890	89455888:89455953
exon_skip_12287	chr9	89418363:89418437:89455888:89455953:89479572:89479890	89455888:89455953
exon_skip_126885	chr9	89405602:89405699:89418056:89418118:89436322:89436463	89418056:89418118
exon_skip_131283	chr9	89387396:89387608:89388636:89388792:89388872:89389047	89388636:89388792
exon_skip_135221	chr9	89418056:89418118:89418363:89418437:89455888:89455953	89418363:89418437
exon_skip_139713	chr9	89376833:89377051:89381055:89381098:89381174:89381346	89381055:89381098
exon_skip_143524	chr9	89405602:89405699:89455888:89455953:89479572:89479825	89455888:89455953
exon_skip_148344	chr9	89387386:89387608:89388636:89388792:89388872:89389047	89388636:89388792
exon_skip_160349	chr9	89418056:89418118:89418363:89418437:89436322:89436578	89418363:89418437
exon_skip_17442	chr9	89363741:89363950:89376833:89377051:89381055:89381082	89376833:89377051
exon_skip_177229	chr9	89399276:89399338:89402871:89403016:89405351:89405699	89402871:89403016
exon_skip_209802	chr9	89405602:89405699:89418056:89418118:89418363:89418437	89418056:89418118
exon_skip_22805	chr9	89405602:89405699:89455888:89455953:89479572:89479890	89455888:89455953
exon_skip_257699	chr9	89392423:89392536:89393562:89393655:89396737:89396831	89393562:89393655
exon_skip_266220	chr9	89379587:89379629:89381055:89381098:89381174:89381346	89381055:89381098
exon_skip_289750	chr9	89418056:89418118:89418363:89418437:89436322:89436463	89418363:89418437
exon_skip_49360	chr9	89405602:89405699:89455888:89455953:89497919:89498038	89455888:89455953
exon_skip_53570	chr9	89363741:89363950:89386367:89386482:89387386:89387608	89386367:89386482
exon_skip_58713	chr9	89391264:89391415:89392423:89392536:89393562:89393655	89392423:89392536
exon_skip_62585	chr9	89405602:89405699:89418056:89418118:89455888:89455953	89418056:89418118
exon_skip_79850	chr9	89381056:89381098:89381174:89381346:89386367:89386482	89381174:89381346
exon_skip_91854	chr9	89363741:89363950:89376833:89377051:89381055:89381098	89376833:89377051

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_289719	Mayo_CB	5.484146e-01	4.015789e-01	1.468357e-01	3.475051e-06

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Open reading frame (ORF) annotation in the exon skipping event for SEMA4D

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
ENST00000356444	89418363	89418437	3UTR-3UTR
ENST00000438547	89418363	89418437	3UTR-3UTR
ENST00000356444	89381174	89381346	Frame-shift
ENST00000422704	89381174	89381346	Frame-shift
ENST00000438547	89381174	89381346	Frame-shift
ENST00000450295	89381174	89381346	Frame-shift
ENST00000356444	89388636	89388792	Frame-shift
ENST00000422704	89388636	89388792	Frame-shift
ENST00000438547	89388636	89388792	Frame-shift
ENST00000450295	89388636	89388792	Frame-shift
ENST00000356444	89393562	89393655	Frame-shift
ENST00000422704	89393562	89393655	Frame-shift
ENST00000438547	89393562	89393655	Frame-shift
ENST00000450295	89393562	89393655	Frame-shift
ENST00000356444	89402871	89403016	Frame-shift
ENST00000422704	89402871	89403016	Frame-shift
ENST00000438547	89402871	89403016	Frame-shift
ENST00000450295	89402871	89403016	Frame-shift

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
ENST00000356444	89418363	89418437	3UTR-3UTR
ENST00000438547	89418363	89418437	3UTR-3UTR
ENST00000356444	89381174	89381346	Frame-shift
ENST00000422704	89381174	89381346	Frame-shift
ENST00000438547	89381174	89381346	Frame-shift
ENST00000450295	89381174	89381346	Frame-shift
ENST00000356444	89388636	89388792	Frame-shift
ENST00000422704	89388636	89388792	Frame-shift
ENST00000438547	89388636	89388792	Frame-shift
ENST00000450295	89388636	89388792	Frame-shift
ENST00000356444	89402871	89403016	Frame-shift
ENST00000422704	89402871	89403016	Frame-shift
ENST00000438547	89402871	89403016	Frame-shift
ENST00000450295	89402871	89403016	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
ENST00000356444	89418056	89418118	3UTR-3UTR
ENST00000438547	89418056	89418118	3UTR-3UTR
ENST00000450295	89418056	89418118	3UTR-3UTR
ENST00000356444	89418363	89418437	3UTR-3UTR
ENST00000438547	89418363	89418437	3UTR-3UTR
ENST00000422704	89455888	89455953	3UTR-3UTR
ENST00000438547	89455888	89455953	3UTR-3UTR
ENST00000356444	89381055	89381098	Frame-shift
ENST00000422704	89381055	89381098	Frame-shift
ENST00000438547	89381055	89381098	Frame-shift
ENST00000450295	89381055	89381098	Frame-shift
ENST00000356444	89381174	89381346	Frame-shift
ENST00000422704	89381174	89381346	Frame-shift
ENST00000438547	89381174	89381346	Frame-shift
ENST00000450295	89381174	89381346	Frame-shift
ENST00000356444	89388636	89388792	Frame-shift
ENST00000422704	89388636	89388792	Frame-shift
ENST00000438547	89388636	89388792	Frame-shift
ENST00000450295	89388636	89388792	Frame-shift
ENST00000356444	89393562	89393655	Frame-shift
ENST00000422704	89393562	89393655	Frame-shift
ENST00000438547	89393562	89393655	Frame-shift
ENST00000450295	89393562	89393655	Frame-shift
ENST00000356444	89402871	89403016	Frame-shift
ENST00000422704	89402871	89403016	Frame-shift
ENST00000438547	89402871	89403016	Frame-shift
ENST00000450295	89402871	89403016	Frame-shift
ENST00000356444	89392423	89392536	In-frame
ENST00000422704	89392423	89392536	In-frame
ENST00000438547	89392423	89392536	In-frame
ENST00000450295	89392423	89392536	In-frame
ENST00000356444	89396737	89396835	In-frame
ENST00000422704	89396737	89396835	In-frame
ENST00000438547	89396737	89396835	In-frame
ENST00000450295	89396737	89396835	In-frame

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Infer the effects of exon skipping event on protein functional features for SEMA4D

p-ENSG00000187764_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

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
ENST00000356444	4520	862	89396737	89396835	763	860	105	137
ENST00000422704	4399	862	89396737	89396835	796	893	105	137
ENST00000438547	4841	862	89396737	89396835	1082	1179	105	137
ENST00000450295	5701	862	89396737	89396835	1093	1190	105	137
ENST00000356444	4520	862	89392423	89392536	956	1068	169	207
ENST00000422704	4399	862	89392423	89392536	989	1101	169	207
ENST00000438547	4841	862	89392423	89392536	1275	1387	169	207
ENST00000450295	5701	862	89392423	89392536	1286	1398	169	207

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

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
Q92854	105	137	111	117	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	111	117	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	111	117	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	111	117	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	119	127	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	119	127	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	119	127	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	119	127	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	134	139	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	105	137	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	105	137	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	105	137	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	105	137	97	108	Disulfide bond	.
Q92854	105	137	97	108	Disulfide bond	.
Q92854	105	137	97	108	Disulfide bond	.
Q92854	105	137	97	108	Disulfide bond	.
Q92854	105	137	126	135	Disulfide bond	.
Q92854	105	137	126	135	Disulfide bond	.
Q92854	105	137	126	135	Disulfide bond	.
Q92854	105	137	126	135	Disulfide bond	.
Q92854	105	137	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	105	137	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	105	137	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	105	137	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	105	137	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	105	137	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	105	137	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	105	137	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	105	137	104	107	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	104	107	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	104	107	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	104	107	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	129	131	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	129	131	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	129	131	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	105	137	129	131	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	164	169	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	164	169	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	164	169	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	164	169	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	172	180	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	172	180	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	172	180	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	172	180	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	185	191	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	185	191	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	185	191	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	185	191	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	193	195	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OL2
Q92854	169	207	193	195	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OL2
Q92854	169	207	193	195	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OL2
Q92854	169	207	193	195	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OL2
Q92854	169	207	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	169	207	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	169	207	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	169	207	22	862	Chain	ID=PRO_0000032327;Note=Semaphorin-4D
Q92854	169	207	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	169	207	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	169	207	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	169	207	22	500	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q92854	169	207	191	191	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	191	191	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	191	191	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	191	191	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	181	182	Mutagenesis	Note=Abolishes PLXNB1 binding. FL->ER;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	181	182	Mutagenesis	Note=Abolishes PLXNB1 binding. FL->ER;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	181	182	Mutagenesis	Note=Abolishes PLXNB1 binding. FL->ER;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	181	182	Mutagenesis	Note=Abolishes PLXNB1 binding. FL->ER;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20877282;Dbxref=PMID:20877282
Q92854	169	207	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	169	207	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	169	207	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	169	207	22	734	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q92854	169	207	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ
Q92854	169	207	203	205	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1OLZ

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3'-UTR located exon skipping events that lost miRNA binding sites in SEMA4D

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
Mayo	ENST00000450295	89418056	89418118	hsa-miR-8067	chr9:89418089-89418096	8mer-1a	chr9:89418076-89418096	154.00	-14.02
Mayo	ENST00000438547	89455888	89455953	hsa-miR-21-3p	chr9:89455939-89455946	8mer-1a	chr9:89455930-89455950	149.00	-29.09
Mayo	ENST00000438547	89455888	89455953	hsa-miR-122b-3p	chr9:89455939-89455946	8mer-1a	chr9:89455930-89455950	149.00	-29.09
Mayo	ENST00000450295	89418056	89418118	hsa-miR-6508-5p	chr9:89418089-89418096	8mer-1a	chr9:89418076-89418096	154.00	-14.02
Mayo	ENST00000450295	89418056	89418118	hsa-miR-5680	chr9:89418087-89418094	8mer-1a	chr9:89418072-89418094	156.00	-15.27
Mayo	ENST00000438547	89418363	89418437	hsa-miR-6852-5p	chr9:89418380-89418387	8mer-1a	chr9:89418368-89418388	161.00	-26.86
MSBB	ENST00000438547	89418363	89418437	hsa-miR-6852-5p	chr9:89418380-89418387	8mer-1a	chr9:89418368-89418388	161.00	-26.86
ROSMAP	ENST00000438547	89418363	89418437	hsa-miR-6852-5p	chr9:89418380-89418387	8mer-1a	chr9:89418368-89418388	161.00	-26.86

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SNVs in the skipped exons for SEMA4D

- 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 SEMA4D

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 SEMA4D

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_135221	rs9410319	chr9:89401607	2.312712e-04	1.828139e-02
HCC	exon_skip_135221	rs9410475	chr9:89406341	4.095464e-04	2.895709e-02
HCC	exon_skip_135221	rs7041088	chr9:89437979	6.159270e-04	3.994735e-02
PCC	exon_skip_135221	rs10908931	chr9:89490362	7.229252e-05	1.329766e-02
PCC	exon_skip_135221	rs7044558	chr9:89502024	1.310251e-04	2.134410e-02

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Correlation with RNA binding proteins (RBPs) for SEMA4D

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	DAZAP1	exon_skip_289719	4.687950e-01	5.222183e-10
CB	HNRNPAB	exon_skip_289719	5.100280e-01	7.652036e-12
CB	SAMD4A	exon_skip_79850	-4.184416e-01	8.963996e-08
CB	TRA2A	exon_skip_79850	-4.307253e-01	3.380727e-08
CB	RBM4	exon_skip_79850	-5.341884e-01	1.620411e-12
CB	RBM4B	exon_skip_79850	-4.565056e-01	3.833928e-09
CB	DAZAP1	exon_skip_62585	-4.052460e-01	2.449068e-07
CB	TRA2A	exon_skip_62585	-4.530138e-01	5.203934e-09
CB	PTBP1	exon_skip_62585	-4.394653e-01	1.649228e-08
DLPFC	DAZAP1	exon_skip_20564	5.001997e-01	1.001119e-16
DLPFC	UNK	exon_skip_20564	4.083553e-01	3.842210e-11
DLPFC	KHDRBS2	exon_skip_20564	6.215099e-01	2.965019e-27
DLPFC	HNRNPA0	exon_skip_20564	5.746358e-01	1.151721e-22
DLPFC	HNRNPAB	exon_skip_20564	5.935158e-01	2.007753e-24
DLPFC	NUP42	exon_skip_20564	5.136745e-01	1.073914e-17
DLPFC	PABPC1	exon_skip_20564	4.705436e-01	9.764713e-15
DLPFC	RBM41	exon_skip_20564	4.487718e-01	2.149207e-13
DLPFC	NOVA1	exon_skip_20564	5.939881e-01	1.808157e-24
IFG	RBM3	exon_skip_289719	-5.113271e-01	1.500658e-02
IFG	KHDRBS2	exon_skip_289719	7.089496e-01	2.210574e-04
IFG	RBM41	exon_skip_289719	5.834060e-01	4.370438e-03
IFG	NOVA1	exon_skip_289719	6.013614e-01	3.072803e-03
IFG	FUBP1	exon_skip_135221	5.239659e-01	8.587986e-03
IFG	PABPC5	exon_skip_135221	4.215476e-01	4.020377e-02
PCC	ZNF326	exon_skip_289719	-4.327543e-01	3.173610e-11
TC	KHDRBS2	exon_skip_289719	5.834015e-01	5.704762e-16
TC	HNRNPA0	exon_skip_289719	4.205130e-01	3.089805e-08
TC	NUP42	exon_skip_289719	4.456580e-01	3.517246e-09
TC	PTBP1	exon_skip_62585	-4.321154e-01	1.158824e-08

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RelatedDrugs for SEMA4D

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 SEMA4D

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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