ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SEC23A

Gene summary

Gene information	Gene symbol	SEC23A
	Gene ID	10484
	Gene name	Sec23 homolog A, coat complex II component
	Synonyms	CLSD\|hSec23A
	Cytomap	14q21.1
	Type of gene	protein-coding
	Description	protein transport protein Sec23ASEC23-related protein ASec23 homolog A, COPII coat complex component
	Modification date	20180523
	UniProtAcc	Q15436
	Context	PubMed: SEC23A [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
SEC23A	GO:0090110	cargo loading into COPII-coated vesicle	17499046\|18843296

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Exon skipping events across known transcript of Ensembl for SEC23A from UCSC genome browser

Skipped 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.

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Gene isoform structures and expression levels for SEC23A

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for SEC23A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_112855	14	39509935:39510091:39511989:39512076:39514366:39514528	39511989:39512076	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112857	14	39511989:39512076:39514366:39514528:39517855:39517933	39514366:39514528	ENSG00000100934.10	ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112858	14	39514366:39514528:39516570:39516642:39517855:39517927	39516570:39516642	ENSG00000100934.10	ENST00000536508.1
exon_skip_112862	14	39514366:39514528:39517855:39517933:39524346:39524500	39517855:39517933	ENSG00000100934.10	ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112866	14	39517855:39517933:39524346:39524500:39530968:39531075	39524346:39524500	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112872	14	39530968:39531075:39532527:39532617:39534116:39534197	39532527:39532617	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112873	14	39532527:39532617:39534116:39534197:39536376:39536415	39534116:39534197	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112874	14	39534116:39534197:39536376:39536500:39543618:39543734	39536376:39536500	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112876	14	39536376:39536500:39543618:39543734:39545138:39545297	39543618:39543734	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112878	14	39543618:39543734:39545138:39545297:39554965:39555110	39545138:39545297	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112879	14	39545138:39545297:39554965:39555110:39556132:39556212	39554965:39555110	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000537403.1,ENST00000545328.2
exon_skip_112880	14	39556132:39556212:39560680:39560917:39562390:39562448	39560680:39560917	ENSG00000100934.10	ENST00000545328.2
exon_skip_112881	14	39560861:39560917:39561744:39561831:39562390:39562448	39561744:39561831	ENSG00000100934.10	ENST00000536508.1,ENST00000307712.6,ENST00000555017.1,ENST00000556092.1
exon_skip_112883	14	39562390:39562448:39565101:39565343:39572235:39572279	39565101:39565343	ENSG00000100934.10	ENST00000307712.6,ENST00000556092.1,ENST00000548032.2,ENST00000545328.2
exon_skip_112884	14	39565202:39565343:39572235:39572432:39572796:39573033	39572235:39572432	ENSG00000100934.10	ENST00000557437.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SEC23A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_112855	14	39509935:39510091:39511989:39512076:39514366:39514528	39511989:39512076	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112857	14	39511989:39512076:39514366:39514528:39517855:39517933	39514366:39514528	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000545328.2
exon_skip_112858	14	39514366:39514528:39516570:39516642:39517855:39517927	39516570:39516642	ENSG00000100934.10	ENST00000536508.1
exon_skip_112862	14	39514366:39514528:39517855:39517933:39524346:39524500	39517855:39517933	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000545328.2
exon_skip_112866	14	39517855:39517933:39524346:39524500:39530968:39531075	39524346:39524500	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112872	14	39530968:39531075:39532527:39532617:39534116:39534197	39532527:39532617	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112873	14	39532527:39532617:39534116:39534197:39536376:39536415	39534116:39534197	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112874	14	39534116:39534197:39536376:39536500:39543618:39543734	39536376:39536500	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112876	14	39536376:39536500:39543618:39543734:39545138:39545297	39543618:39543734	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112878	14	39543618:39543734:39545138:39545297:39554965:39555110	39545138:39545297	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112879	14	39545138:39545297:39554965:39555110:39556132:39556212	39554965:39555110	ENSG00000100934.10	ENST00000537403.1,ENST00000307712.6,ENST00000536508.1,ENST00000545328.2
exon_skip_112880	14	39556132:39556212:39560680:39560917:39562390:39562448	39560680:39560917	ENSG00000100934.10	ENST00000545328.2
exon_skip_112881	14	39560861:39560917:39561744:39561831:39562390:39562448	39561744:39561831	ENSG00000100934.10	ENST00000307712.6,ENST00000536508.1,ENST00000555017.1,ENST00000556092.1
exon_skip_112883	14	39562390:39562448:39565101:39565343:39572235:39572279	39565101:39565343	ENSG00000100934.10	ENST00000307712.6,ENST00000545328.2,ENST00000556092.1,ENST00000548032.2
exon_skip_112884	14	39565202:39565343:39572235:39572432:39572796:39573033	39572235:39572432	ENSG00000100934.10	ENST00000557437.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for SEC23A

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000307712	39565101	39565343	3UTR-3CDS
ENST00000307712	39524346	39524500	Frame-shift
ENST00000307712	39536376	39536500	Frame-shift
ENST00000307712	39543618	39543734	Frame-shift
ENST00000307712	39554965	39555110	Frame-shift
ENST00000307712	39511989	39512076	In-frame
ENST00000307712	39514366	39514528	In-frame
ENST00000307712	39517855	39517933	In-frame
ENST00000307712	39532527	39532617	In-frame
ENST00000307712	39534116	39534197	In-frame
ENST00000307712	39545138	39545297	In-frame
ENST00000307712	39561744	39561831	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000307712	39565101	39565343	3UTR-3CDS
ENST00000307712	39524346	39524500	Frame-shift
ENST00000307712	39536376	39536500	Frame-shift
ENST00000307712	39543618	39543734	Frame-shift
ENST00000307712	39554965	39555110	Frame-shift
ENST00000307712	39511989	39512076	In-frame
ENST00000307712	39514366	39514528	In-frame
ENST00000307712	39517855	39517933	In-frame
ENST00000307712	39532527	39532617	In-frame
ENST00000307712	39534116	39534197	In-frame
ENST00000307712	39545138	39545297	In-frame
ENST00000307712	39561744	39561831	In-frame

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Infer the effects of exon skipping event on protein functional features for SEC23A

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000307712	4152	765	39561744	39561831	798	884	93	122
ENST00000307712	4152	765	39545138	39545297	1347	1505	276	329
ENST00000307712	4152	765	39534116	39534197	1746	1826	409	436
ENST00000307712	4152	765	39532527	39532617	1827	1916	436	466
ENST00000307712	4152	765	39517855	39517933	2178	2255	553	579
ENST00000307712	4152	765	39514366	39514528	2256	2417	579	633
ENST00000307712	4152	765	39511989	39512076	2418	2504	633	662

Loci of skipped exons in GTEx 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
ENST00000307712	4152	765	39561744	39561831	798	884	93	122
ENST00000307712	4152	765	39545138	39545297	1347	1505	276	329
ENST00000307712	4152	765	39534116	39534197	1746	1826	409	436
ENST00000307712	4152	765	39532527	39532617	1827	1916	436	466
ENST00000307712	4152	765	39517855	39517933	2178	2255	553	579
ENST00000307712	4152	765	39514366	39514528	2256	2417	579	633
ENST00000307712	4152	765	39511989	39512076	2418	2504	633	662

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 feature	Description of feature
Q15436	93	122	1	202	Alternative sequence	ID=VSP_056230;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q15436	93	122	91	93	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	103	105	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNL
Q15436	93	122	115	121	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	93	122	96	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	108	110	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	112	114	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	285	292	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	296	299	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	276	329	264	278	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	313	317	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	324	341	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	308	308	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q15436	409	436	401	410	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	409	436	414	422	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	409	436	431	433	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3EG9
Q15436	409	436	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	436	466	439	442	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNL
Q15436	436	466	444	451	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	436	466	457	463	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	436	466	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	553	579	558	561	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3EGD
Q15436	553	579	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	553	579	542	557	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	553	579	565	567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	553	579	577	586	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	553	579	572	576	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	622	626	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	628	631	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	633	635	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNF
Q15436	579	633	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	579	633	577	586	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	592	594	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3EFO
Q15436	579	633	597	607	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	612	619	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	628	628	Mutagenesis	Note=Decreased interaction with MIA3%3B when associated with A-681. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27551091;Dbxref=PMID:27551091
Q15436	579	633	632	718	Repeat	Note=Gelsolin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q15436	579	633	623	623	Sequence conflict	Note=L->M;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15436	579	633	588	590	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	633	635	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNF
Q15436	633	662	647	651	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	653	660	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	633	662	639	641	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	662	670	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	632	718	Repeat	Note=Gelsolin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255

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 feature	Description of feature
Q15436	93	122	1	202	Alternative sequence	ID=VSP_056230;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q15436	93	122	91	93	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	103	105	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNL
Q15436	93	122	115	121	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	93	122	96	98	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	108	110	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	93	122	112	114	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	285	292	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	296	299	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	276	329	264	278	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	313	317	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	324	341	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	276	329	308	308	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q15436	409	436	401	410	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	409	436	414	422	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	409	436	431	433	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3EG9
Q15436	409	436	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	436	466	439	442	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNL
Q15436	436	466	444	451	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	436	466	457	463	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	436	466	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	553	579	558	561	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3EGD
Q15436	553	579	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	553	579	542	557	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	553	579	565	567	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	553	579	577	586	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	553	579	572	576	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	622	626	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	628	631	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	633	635	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNF
Q15436	579	633	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	579	633	577	586	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	592	594	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3EFO
Q15436	579	633	597	607	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	612	619	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	579	633	628	628	Mutagenesis	Note=Decreased interaction with MIA3%3B when associated with A-681. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27551091;Dbxref=PMID:27551091
Q15436	579	633	632	718	Repeat	Note=Gelsolin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q15436	579	633	623	623	Sequence conflict	Note=L->M;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q15436	579	633	588	590	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	633	635	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5VNF
Q15436	633	662	647	651	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	653	660	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	2	765	Chain	ID=PRO_0000205146;Note=Protein transport protein Sec23A
Q15436	633	662	639	641	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	662	670	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2NUT
Q15436	633	662	632	718	Repeat	Note=Gelsolin-like;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for SEC23A

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

SEC23A_ESCA_exon_skip_112879_psi_boxplot.png
boxplot

SEC23A_LIHC_exon_skip_112883_psi_boxplot.png
boxplot

SEC23A_LUSC_exon_skip_112857_psi_boxplot.png
boxplot

SEC23A_LUSC_exon_skip_112883_psi_boxplot.png
boxplot

SEC23A_SKCM_exon_skip_112883_psi_boxplot.png
boxplot

SEC23A_STAD_exon_skip_112857_psi_boxplot.png
boxplot

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

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
STAD	TCGA-BR-4370-01	exon_skip_112857	39514367	39514528	39514487	39514487	Frame_Shift_Del	A	-	p.N594fs
KIRP	TCGA-A4-7732-01	exon_skip_112857	39514367	39514528	39514526	39514526	Frame_Shift_Del	A	-	p.F378fs
KIRP	TCGA-A4-7732-01	exon_skip_112857	39514367	39514528	39514526	39514526	Frame_Shift_Del	A	-	p.F580fs
LIHC	TCGA-DD-A39Y-01	exon_skip_112866	39524347	39524500	39524400	39524400	Frame_Shift_Del	T	-	p.T334fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_112873	39534117	39534197	39534181	39534181	Frame_Shift_Del	T	-	p.K213fs
LIHC	TCGA-DD-A3A0-01	exon_skip_112878	39545139	39545297	39545235	39545235	Frame_Shift_Del	C	-	p.G95fs
LIHC	TCGA-DD-A3A0-01	exon_skip_112879	39554966	39555110	39554998	39554998	Frame_Shift_Del	C	-	p.V64fs
ESCA	TCGA-JY-A938-01	exon_skip_112879	39554966	39555110	39555002	39555008	Frame_Shift_Del	AGAGGAA	-	p.RSS60fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_112880	39560681	39560917	39560853	39560853	Frame_Shift_Del	A	-	p.L144fs
LIHC	TCGA-DD-A3A0-01	exon_skip_112881	39561745	39561831	39561768	39561768	Frame_Shift_Del	A	-	p.S116fs
LIHC	TCGA-DD-A3A0-01	exon_skip_112881	39561745	39561831	39561779	39561779	Frame_Shift_Del	A	-	p.L111fs
LIHC	TCGA-DD-A1EG-01	exon_skip_112883	39565102	39565343	39565266	39565266	Frame_Shift_Del	A	-	p.F19fs
LIHC	TCGA-DD-A3A0-01	exon_skip_112883	39565102	39565343	39565291	39565291	Frame_Shift_Del	T	-	p.N11fs
SARC	TCGA-IW-A3M4-01	exon_skip_112862	39517856	39517933	39517881	39517882	Frame_Shift_Ins	-	A	p.R369fs
LIHC	TCGA-BC-A112-01	exon_skip_112866	39524347	39524500	39524454	39524455	Frame_Shift_Ins	-	A	p.LP315fs
ESCA	TCGA-JY-A938-01	exon_skip_112879	39554966	39555110	39555000	39555001	Frame_Shift_Ins	-	T	p.G265fs
ESCA	TCGA-JY-A938-01	exon_skip_112879	39554966	39555110	39555000	39555001	Frame_Shift_Ins	-	T	p.G63fs
KIRC	TCGA-B0-5075-01	exon_skip_112855	39511990	39512076	39511999	39511999	Nonsense_Mutation	A	C	p.Y457*
KIRC	TCGA-B0-5075-01	exon_skip_112855	39511990	39512076	39511999	39511999	Nonsense_Mutation	A	C	p.Y659X
SKCM	TCGA-FR-A726-01	exon_skip_112866	39524347	39524500	39524352	39524352	Nonsense_Mutation	G	A	p.R350*
PRAD	TCGA-G9-6342-01	exon_skip_112876	39543619	39543734	39543647	39543647	Nonsense_Mutation	C	A	p.E157*
SKCM	TCGA-EE-A29B-06	exon_skip_112876	39543619	39543734	39543713	39543713	Nonsense_Mutation	G	A	p.R135*
SKCM	TCGA-EE-A29B-06	exon_skip_112876	39543619	39543734	39543713	39543713	Nonsense_Mutation	G	A	p.R337X
BLCA	TCGA-XF-AAMY-01	exon_skip_112879	39554966	39555110	39555049	39555049	Nonsense_Mutation	G	A	p.R47*
UCEC	TCGA-D1-A16X-01	exon_skip_112880	39560681	39560917	39560823	39560823	Nonsense_Mutation	G	T	p.S154*
LUSC	TCGA-66-2734-01	exon_skip_112883	39565102	39565343	39565184	39565184	Nonsense_Mutation	C	A	p.E47*
SKCM	TCGA-FR-A726-01	exon_skip_112883	39565102	39565343	39565260	39565260	Nonsense_Mutation	C	T	p.W21*
COAD	TCGA-CA-6717-01	exon_skip_112855	39511990	39512076	39512077	39512077	Splice_Site	C	A	.
LUSC	TCGA-66-2787-01	exon_skip_112857	39514367	39514528	39514366	39514366	Splice_Site	C	A	p.E633_splice
HNSC	TCGA-CN-5363-01	exon_skip_112862	39517856	39517933	39517935	39517935	Splice_Site	T	A	p.C554_splice

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-66-2734-01
	Cancer type: LUSC
	ESID: exon_skip_112883
	Skipped exon start: 39565102
	Skipped exon end: 39565343
	Mutation start: 39565184
	Mutation end: 39565184
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.E47*
exon_skip_112883_LUSC_TCGA-66-2734-01.png
	Sample: TCGA-JY-A938-01
	Cancer type: ESCA
	ESID: exon_skip_112879
	Skipped exon start: 39554966
	Skipped exon end: 39555110
	Mutation start: 39555002
	Mutation end: 39555008
	Mutation type: Frame_Shift_Del
	Reference seq: AGAGGAA
	Mutation seq: -
	AAchange: p.RSS60fs
	Sample: TCGA-JY-A938-01
	Cancer type: ESCA
	ESID: exon_skip_112879
	Skipped exon start: 39554966
	Skipped exon end: 39555110
	Mutation start: 39555000
	Mutation end: 39555001
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: T
	AAchange: p.G63fs
	Sample: TCGA-JY-A938-01
	Cancer type: ESCA
	ESID: exon_skip_112879
	Skipped exon start: 39554966
	Skipped exon end: 39555110
	Mutation start: 39555000
	Mutation end: 39555001
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: T
	AAchange: p.G265fs
exon_skip_112879_ESCA_TCGA-JY-A938-01.png
exon_skip_489575_ESCA_TCGA-JY-A938-01.png
exon_skip_494466_ESCA_TCGA-JY-A938-01.png
	Sample: TCGA-66-2787-01
	Cancer type: LUSC
	ESID: exon_skip_112857
	Skipped exon start: 39514367
	Skipped exon end: 39514528
	Mutation start: 39514366
	Mutation end: 39514366
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: p.E633_splice
exon_skip_112857_LUSC_TCGA-66-2787-01.png
exon_skip_124924_LUSC_TCGA-66-2787-01.png
exon_skip_506700_LUSC_TCGA-66-2787-01.png

- 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
SCC25_UPPER_AERODIGESTIVE_TRACT	39514367	39514528	39514410	39514410	Missense_Mutation	A	G	p.I619T
UACC893_BREAST	39514367	39514528	39514477	39514477	Missense_Mutation	G	C	p.P597A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39514367	39514528	39514504	39514504	Missense_Mutation	A	G	p.S588P
BICR18_UPPER_AERODIGESTIVE_TRACT	39514367	39514528	39514504	39514504	Missense_Mutation	A	G	p.S588P
JIYOYEP2003_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39517856	39517933	39517891	39517891	Missense_Mutation	A	C	p.F568V
NCIH2286_LUNG	39524347	39524500	39524367	39524367	Missense_Mutation	C	A	p.D547Y
JHUEM7_ENDOMETRIUM	39532528	39532617	39532547	39532547	Missense_Mutation	T	G	p.Y460S
HEC59_ENDOMETRIUM	39532528	39532617	39532612	39532612	Missense_Mutation	T	C	p.I438M
SKNAS_AUTONOMIC_GANGLIA	39534117	39534197	39534161	39534161	Missense_Mutation	G	A	p.P422S
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39543619	39543734	39543676	39543676	Missense_Mutation	G	A	p.A349V
SF172_CENTRAL_NERVOUS_SYSTEM	39543619	39543734	39543712	39543712	Missense_Mutation	C	A	p.R337L
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39545139	39545297	39545156	39545156	Missense_Mutation	C	T	p.V324I
IM95_STOMACH	39545139	39545297	39545165	39545165	Missense_Mutation	C	T	p.A321T
EVSAT_BREAST	39545139	39545297	39545273	39545273	Missense_Mutation	G	A	p.R285C
NCIH661_LUNG	39545139	39545297	39545278	39545278	Missense_Mutation	C	A	p.G283V
SW684_SOFT_TISSUE	39554966	39555110	39555006	39555006	Missense_Mutation	G	A	p.S263F
YD38_UPPER_AERODIGESTIVE_TRACT	39554966	39555110	39555009	39555009	Missense_Mutation	C	T	p.R262H
CAL27_UPPER_AERODIGESTIVE_TRACT	39560681	39560917	39560697	39560697	Missense_Mutation	G	C	p.S196C
NH12_AUTONOMIC_GANGLIA	39560681	39560917	39560802	39560802	Missense_Mutation	G	T	p.T161K
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39560681	39560917	39560817	39560817	Missense_Mutation	C	T	p.S156N
NCIH1651_LUNG	39560681	39560917	39560835	39560835	Missense_Mutation	G	A	p.S150F
HCT15_LARGE_INTESTINE	39560681	39560917	39560896	39560896	Missense_Mutation	T	A	p.I130L
NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39565102	39565343	39565193	39565193	Missense_Mutation	G	C	p.P44A
DMS114_LUNG	39565102	39565343	39565213	39565213	Missense_Mutation	G	A	p.P37L
SNUC5_LARGE_INTESTINE	39511990	39512076	39511999	39511999	Nonsense_Mutation	A	T	p.Y659*
HEC251_ENDOMETRIUM	39560681	39560917	39560755	39560755	Nonsense_Mutation	C	A	p.E177*
JHUEM7_ENDOMETRIUM	39560681	39560917	39560839	39560839	Nonsense_Mutation	C	A	p.E149*
HCT15_LARGE_INTESTINE	39565102	39565343	39565251	39565251	Nonsense_Mutation	C	T	p.W24*
LS180_LARGE_INTESTINE	39517856	39517933	39517932	39517932	Splice_Site	C	A	p.C554F

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SEC23A

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEC23A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEC23A

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RelatedDrugs for SEC23A

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for SEC23A

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SEC23A	C0029408	Degenerative polyarthritis	1	CTD_human
SEC23A	C1843042	Craniolenticulosutural Dysplasia	1	CTD_human;ORPHANET;UNIPROT

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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