ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for COL23A1

Gene summary

Gene information	Gene symbol	COL23A1
	Gene ID	91522
	Gene name	collagen type XXIII alpha 1 chain
	Synonyms	-
	Cytomap	5q35.3
	Type of gene	protein-coding
	Description	collagen alpha-1(XXIII) chaincollagen, type XXIII, alpha 1procollagen, type XXIII, alpha 1
	Modification date	20200313
	UniProtAcc	A0A0A0MSD3, A0A2R8Y887, L8EAS4, Q86Y22,
	Context

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 COL23A1

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.

ENSG00000050767

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

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 COL23A1

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_118197	chr5	178256353:178256397:178256866:178256928:178257523:178257567	178256866:178256928
exon_skip_153062	chr5	178247775:178247831:178248192:178248254:178249117:178249206	178248192:178248254
exon_skip_201556	chr5	178261722:178261748:178262217:178262252:178263208:178263324	178262217:178262252
exon_skip_209382	chr5	178248192:178248254:178249117:178249206:178250061:178250105	178249117:178249206
exon_skip_236310	chr5	178263208:178263324:178267307:178267333:178268730:178268756	178267307:178267333
exon_skip_252963	chr5	178252544:178252597:178254949:178255026:178256353:178256397	178254949:178255026
exon_skip_254673	chr5	178250061:178250105:178252544:178252597:178254949:178255026	178252544:178252597
exon_skip_262165	chr5	178242042:178242128:178242341:178242394:178245942:178245963	178242341:178242394
exon_skip_62769	chr5	178257523:178257567:178259721:178259747:178261722:178261748	178259721:178259747
exon_skip_7146	chr5	178242042:178242128:178242341:178242394:178245942:178245968	178242341:178242394
exon_skip_8043	chr5	178247526:178247552:178247775:178247831:178248192:178248254	178247775:178247831
exon_skip_84363	chr5	178246254:178246307:178246391:178246453:178247526:178247552	178246391:178246453

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_236310	Mayo_CB	5.879221e-01	7.141791e-01	-1.262570e-01	1.280867e-06

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Open reading frame (ORF) annotation in the exon skipping event for COL23A1

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
ENST00000390654	178242341	178242394	In-frame
ENST00000390654	178246391	178246453	In-frame
ENST00000390654	178252544	178252597	In-frame
ENST00000390654	178254949	178255026	In-frame
ENST00000390654	178256866	178256928	In-frame
ENST00000390654	178259721	178259747	In-frame
ENST00000390654	178262217	178262252	In-frame
ENST00000390654	178267307	178267333	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
ENST00000390654	178252544	178252597	In-frame
ENST00000390654	178254949	178255026	In-frame
ENST00000390654	178256866	178256928	In-frame
ENST00000390654	178259721	178259747	In-frame
ENST00000390654	178262217	178262252	In-frame
ENST00000390654	178267307	178267333	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
ENST00000390654	178242341	178242394	In-frame
ENST00000390654	178246391	178246453	In-frame
ENST00000390654	178247775	178247831	In-frame
ENST00000390654	178248192	178248254	In-frame
ENST00000390654	178249117	178249206	In-frame
ENST00000390654	178252544	178252597	In-frame
ENST00000390654	178254949	178255026	In-frame
ENST00000390654	178256866	178256928	In-frame
ENST00000390654	178259721	178259747	In-frame
ENST00000390654	178262217	178262252	In-frame
ENST00000390654	178267307	178267333	In-frame

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Infer the effects of exon skipping event on protein functional features for COL23A1

p-ENSG00000050767_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
ENST00000390654	3078	540	178262217	178262252	998	1032	213	224
ENST00000390654	3078	540	178256866	178256928	1133	1194	258	278
ENST00000390654	3078	540	178254949	178255026	1241	1317	294	319
ENST00000390654	3078	540	178252544	178252597	1319	1371	320	337
ENST00000390654	3078	540	178246391	178246453	1655	1716	432	452
ENST00000390654	3078	540	178242341	178242394	1799	1851	480	497

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
ENST00000390654	3078	540	178262217	178262252	998	1032	213	224
ENST00000390654	3078	540	178256866	178256928	1133	1194	258	278
ENST00000390654	3078	540	178254949	178255026	1241	1317	294	319
ENST00000390654	3078	540	178252544	178252597	1319	1371	320	337

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
ENST00000390654	3078	540	178262217	178262252	998	1032	213	224
ENST00000390654	3078	540	178256866	178256928	1133	1194	258	278
ENST00000390654	3078	540	178254949	178255026	1241	1317	294	319
ENST00000390654	3078	540	178252544	178252597	1319	1371	320	337
ENST00000390654	3078	540	178249117	178249206	1418	1506	353	382
ENST00000390654	3078	540	178248192	178248254	1508	1569	383	403
ENST00000390654	3078	540	178246391	178246453	1655	1716	432	452
ENST00000390654	3078	540	178242341	178242394	1799	1851	480	497

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
Q86Y22	213	224	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	213	224	2	536	Compositional bias	Note=Gly-rich
Q86Y22	213	224	124	243	Domain	Note=Collagen-like 1
Q86Y22	213	224	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	258	278	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	258	278	2	536	Compositional bias	Note=Gly-rich
Q86Y22	258	278	251	305	Domain	Note=Collagen-like 2
Q86Y22	258	278	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	294	319	296	345	Alternative sequence	ID=VSP_019630;Note=In isoform 2. APGLKGEQGDTVVIDYDGRILDALKGPPGPQGPPGPPGIPGAKGELGLPG->DVRDPGLGSVSSCSQRLASSSKKNGSEPPPGCAGCPRPQGRAGRHSGDRL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	294	319	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	294	319	2	536	Compositional bias	Note=Gly-rich
Q86Y22	294	319	251	305	Domain	Note=Collagen-like 2
Q86Y22	294	319	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	320	337	296	345	Alternative sequence	ID=VSP_019630;Note=In isoform 2. APGLKGEQGDTVVIDYDGRILDALKGPPGPQGPPGPPGIPGAKGELGLPG->DVRDPGLGSVSSCSQRLASSSKKNGSEPPPGCAGCPRPQGRAGRHSGDRL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	320	337	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	320	337	2	536	Compositional bias	Note=Gly-rich
Q86Y22	320	337	321	380	Domain	Note=Collagen-like 3
Q86Y22	320	337	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	432	452	346	540	Alternative sequence	ID=VSP_019631;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	432	452	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	432	452	2	536	Compositional bias	Note=Gly-rich
Q86Y22	432	452	412	460	Domain	Note=Collagen-like 4
Q86Y22	432	452	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	480	497	346	540	Alternative sequence	ID=VSP_019631;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	480	497	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	480	497	2	536	Compositional bias	Note=Gly-rich
Q86Y22	480	497	463	522	Domain	Note=Collagen-like 5
Q86Y22	480	497	57	540	Topological domain	Note=Extracellular;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
Q86Y22	213	224	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	213	224	2	536	Compositional bias	Note=Gly-rich
Q86Y22	213	224	124	243	Domain	Note=Collagen-like 1
Q86Y22	213	224	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	258	278	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	258	278	2	536	Compositional bias	Note=Gly-rich
Q86Y22	258	278	251	305	Domain	Note=Collagen-like 2
Q86Y22	258	278	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	294	319	296	345	Alternative sequence	ID=VSP_019630;Note=In isoform 2. APGLKGEQGDTVVIDYDGRILDALKGPPGPQGPPGPPGIPGAKGELGLPG->DVRDPGLGSVSSCSQRLASSSKKNGSEPPPGCAGCPRPQGRAGRHSGDRL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	294	319	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	294	319	2	536	Compositional bias	Note=Gly-rich
Q86Y22	294	319	251	305	Domain	Note=Collagen-like 2
Q86Y22	294	319	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	320	337	296	345	Alternative sequence	ID=VSP_019630;Note=In isoform 2. APGLKGEQGDTVVIDYDGRILDALKGPPGPQGPPGPPGIPGAKGELGLPG->DVRDPGLGSVSSCSQRLASSSKKNGSEPPPGCAGCPRPQGRAGRHSGDRL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	320	337	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	320	337	2	536	Compositional bias	Note=Gly-rich
Q86Y22	320	337	321	380	Domain	Note=Collagen-like 3
Q86Y22	320	337	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q86Y22	213	224	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	213	224	2	536	Compositional bias	Note=Gly-rich
Q86Y22	213	224	124	243	Domain	Note=Collagen-like 1
Q86Y22	213	224	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	258	278	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	258	278	2	536	Compositional bias	Note=Gly-rich
Q86Y22	258	278	251	305	Domain	Note=Collagen-like 2
Q86Y22	258	278	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	294	319	296	345	Alternative sequence	ID=VSP_019630;Note=In isoform 2. APGLKGEQGDTVVIDYDGRILDALKGPPGPQGPPGPPGIPGAKGELGLPG->DVRDPGLGSVSSCSQRLASSSKKNGSEPPPGCAGCPRPQGRAGRHSGDRL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	294	319	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	294	319	2	536	Compositional bias	Note=Gly-rich
Q86Y22	294	319	251	305	Domain	Note=Collagen-like 2
Q86Y22	294	319	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	320	337	296	345	Alternative sequence	ID=VSP_019630;Note=In isoform 2. APGLKGEQGDTVVIDYDGRILDALKGPPGPQGPPGPPGIPGAKGELGLPG->DVRDPGLGSVSSCSQRLASSSKKNGSEPPPGCAGCPRPQGRAGRHSGDRL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	320	337	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	320	337	2	536	Compositional bias	Note=Gly-rich
Q86Y22	320	337	321	380	Domain	Note=Collagen-like 3
Q86Y22	320	337	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	353	382	346	540	Alternative sequence	ID=VSP_019631;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	353	382	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	353	382	2	536	Compositional bias	Note=Gly-rich
Q86Y22	353	382	321	380	Domain	Note=Collagen-like 3
Q86Y22	353	382	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	383	403	346	540	Alternative sequence	ID=VSP_019631;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	383	403	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	383	403	2	536	Compositional bias	Note=Gly-rich
Q86Y22	383	403	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	432	452	346	540	Alternative sequence	ID=VSP_019631;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	432	452	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	432	452	2	536	Compositional bias	Note=Gly-rich
Q86Y22	432	452	412	460	Domain	Note=Collagen-like 4
Q86Y22	432	452	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q86Y22	480	497	346	540	Alternative sequence	ID=VSP_019631;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q86Y22	480	497	1	540	Chain	ID=PRO_0000245226;Note=Collagen alpha-1(XXIII) chain
Q86Y22	480	497	2	536	Compositional bias	Note=Gly-rich
Q86Y22	480	497	463	522	Domain	Note=Collagen-like 5
Q86Y22	480	497	57	540	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in COL23A1

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 COL23A1

- 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 COL23A1

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 COL23A1

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 COL23A1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	SAMD4A	exon_skip_201556	-4.334848e-01	4.618879e-08
CB	CNOT4	exon_skip_236310	-5.860650e-01	1.192536e-14
CB	HNRNPF	exon_skip_236310	-4.816521e-01	9.861050e-10
CB	RBM4B	exon_skip_236310	-5.391834e-01	3.121282e-12

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RelatedDrugs for COL23A1

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 COL23A1

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 COL23A1

Gene structures and expression levels for COL23A1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for COL23A1

Open reading frame (ORF) annotation in the exon skipping event for COL23A1

Infer the effects of exon skipping event on protein functional features for COL23A1

3'-UTR located exon skipping events that lost miRNA binding sites in COL23A1

SNVs in the skipped exons for COL23A1

AD stage-associated exon skippint events for COL23A1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL23A1

Correlation with RNA binding proteins (RBPs) for COL23A1

RelatedDrugs for COL23A1

RelatedDiseases for COL23A1