ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CHL1

Gene summary

Gene information	Gene symbol	CHL1
	Gene ID	10752
	Gene name	cell adhesion molecule L1 like
	Synonyms	CALL\|L1CAM2
	Cytomap	3p26.3
	Type of gene	protein-coding
	Description	neural cell adhesion molecule L1-like proteinL1 cell adhesion molecule 2cell adhesion molecule with homology to L1CAM (close homolog of L1)cell adhesion molecule with homology to L1CAM (close homologue of L1)close homolog of L1
	Modification date	20200313
	UniProtAcc	A0A087X0M8, C9J905, C9JEY3, C9JH37, C9JW79, F8WEP4, H7C0J0, O00533,
	Context	- 29391027(BACE1 Elevation Engendered by GGA3 Deletion Increases β-amyloid Pathology in Association With APP Elevation and Decreased CHL1 Processing in 5XFAD Mice)

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 CHL1

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.

ENSG00000134121

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
STG	DOWN	ENST00000381760.8	UCHL1-202:retained_intron:UCHL1	1.025107e+03	-8.219713e-01	6.153067e-04	3.009335e-02
PG	DOWN	ENST00000514924.5	UCHL1-212:protein_coding:UCHL1	1.621151e+00	-9.755010e-01	4.641173e-05	1.550734e-03
PG	DOWN	ENST00000284440.9	UCHL1-201:protein_coding:UCHL1	1.294056e+03	-8.675879e-01	4.456442e-03	4.217891e-02
CB	UP	ENST00000510566.1	UCHL1-208:retained_intron:UCHL1	3.330333e+01	9.268402e-01	1.398176e-11	1.280984e-09
CB	DOWN	ENST00000657108.1	CHL1-AS2-204:lncRNA:CHL1	3.147001e+01	-1.068385e+00	1.200369e-06	1.748918e-05
CB	UP	ENST00000427688.5	CHL1-204:protein_coding:CHL1	4.491203e+00	9.896959e-01	1.271583e-04	9.079630e-04
CB	UP	ENST00000503431.5	UCHL1-204:protein_coding:UCHL1	8.554966e+01	8.405842e-01	3.229588e-04	1.993654e-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 CHL1

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_105017	chr3	340794:340916:341912:342082:342984:343031	341912:342082
exon_skip_10725	chr3	197005:197063:244613:244692:319683:319867	244613:244692
exon_skip_11928	chr3	196783:197063:244613:244692:319683:319867	244613:244692
exon_skip_148688	chr3	382186:382280:382474:382671:383816:383886	382474:382671
exon_skip_207319	chr3	340794:340916:341912:342082:344589:344709	341912:342082
exon_skip_222254	chr3	394693:394872:398227:398385:399017:399148	398227:398385
exon_skip_252643	chr3	341918:342082:342984:343031:344589:344709	342984:343031
exon_skip_256624	chr3	197290:197368:244613:244692:319683:319867	244613:244692
exon_skip_42302	chr3	390701:390816:390955:391159:391675:391797	390955:391159
exon_skip_48410	chr3	198024:198092:244613:244692:319683:319867	244613:244692
exon_skip_60357	chr3	198014:198092:244613:244692:319683:319867	244613:244692
exon_skip_64839	chr3	341912:342082:342984:343031:344589:344709	342984:343031
exon_skip_67755	chr3	361699:361810:363217:363383:365950:366115	363217:363383
exon_skip_85955	chr3	383816:383886:389252:389474:390701:390816	389252:389474

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_222254	MSBB_STG	7.718182e-01	8.783333e-01	-1.065152e-01	3.809247e-02
exon_skip_252643	MSBB_PG	4.020690e-01	2.708772e-01	1.311918e-01	3.565941e-06
exon_skip_222254	MSBB_PG	6.846377e-01	8.101818e-01	-1.255441e-01	2.008855e-04
exon_skip_222254	Mayo_TC	5.736585e-01	6.934848e-01	-1.198263e-01	8.350979e-06

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Open reading frame (ORF) annotation in the exon skipping event for CHL1

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
ENST00000397491	244613	244692	5UTR-5UTR
ENST00000397491	389252	389474	Frame-shift
ENST00000397491	390955	391159	Frame-shift
ENST00000397491	341912	342082	In-frame
ENST00000397491	382474	382671	In-frame
ENST00000397491	398227	398385	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
ENST00000397491	244613	244692	5UTR-5UTR
ENST00000397491	389252	389474	Frame-shift
ENST00000397491	390955	391159	Frame-shift
ENST00000397491	341912	342082	In-frame
ENST00000397491	398227	398385	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
ENST00000397491	244613	244692	5UTR-5UTR
ENST00000397491	363217	363383	Frame-shift
ENST00000397491	389252	389474	Frame-shift
ENST00000397491	390955	391159	Frame-shift
ENST00000397491	341912	342082	In-frame
ENST00000397491	398227	398385	In-frame

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Infer the effects of exon skipping event on protein functional features for CHL1

p-ENSG00000134121_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
ENST00000397491	5252	1208	341912	342082	977	1146	170	226
ENST00000397491	5252	1208	382474	382671	2399	2595	644	709
ENST00000397491	5252	1208	398227	398385	3515	3672	1016	1068

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
ENST00000397491	5252	1208	341912	342082	977	1146	170	226
ENST00000397491	5252	1208	398227	398385	3515	3672	1016	1068

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
ENST00000397491	5252	1208	341912	342082	977	1146	170	226
ENST00000397491	5252	1208	398227	398385	3515	3672	1016	1068

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
O00533	170	226	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	170	226	153	204	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
O00533	170	226	128	223	Domain	Note=Ig-like C2-type 2
O00533	170	226	25	1082	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O00533	644	709	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	644	709	614	709	Domain	Note=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00316
O00533	644	709	25	1082	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O00533	1016	1068	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	1016	1068	1026	1026	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16335952;Dbxref=PMID:16335952
O00533	1016	1068	1034	1034	Natural variant	ID=VAR_027169;Note=I->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:9799093,ECO:0000269\|Ref.2;Dbxref=dbSNP:rs6442827,PMID:15489334,PMID:9799093
O00533	1016	1068	1039	1040	Site	Note=Cleavage%3B by ADAM8;Ontology_term=ECO:0000250;evidence=ECO:0000250
O00533	1016	1068	25	1082	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
O00533	170	226	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	170	226	153	204	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
O00533	170	226	128	223	Domain	Note=Ig-like C2-type 2
O00533	170	226	25	1082	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O00533	1016	1068	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	1016	1068	1026	1026	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16335952;Dbxref=PMID:16335952
O00533	1016	1068	1034	1034	Natural variant	ID=VAR_027169;Note=I->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:9799093,ECO:0000269\|Ref.2;Dbxref=dbSNP:rs6442827,PMID:15489334,PMID:9799093
O00533	1016	1068	1039	1040	Site	Note=Cleavage%3B by ADAM8;Ontology_term=ECO:0000250;evidence=ECO:0000250
O00533	1016	1068	25	1082	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
O00533	170	226	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	170	226	153	204	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
O00533	170	226	128	223	Domain	Note=Ig-like C2-type 2
O00533	170	226	25	1082	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
O00533	1016	1068	25	1208	Chain	ID=PRO_0000247896;Note=Neural cell adhesion molecule L1-like protein
O00533	1016	1068	1026	1026	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16335952;Dbxref=PMID:16335952
O00533	1016	1068	1034	1034	Natural variant	ID=VAR_027169;Note=I->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:9799093,ECO:0000269\|Ref.2;Dbxref=dbSNP:rs6442827,PMID:15489334,PMID:9799093
O00533	1016	1068	1039	1040	Site	Note=Cleavage%3B by ADAM8;Ontology_term=ECO:0000250;evidence=ECO:0000250
O00533	1016	1068	25	1082	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 CHL1

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 CHL1

- 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 CHL1

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

ADstage

MSBB

IFG

exon_skip_64839

4.410036e-01

1.882229e-02

chr3

341912

342082

342984

343031

344589

344709

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CHL1

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_11928	rs332479	chr3:298757	4.484782e-04	3.117624e-02
HCC	exon_skip_11928	rs13093895	chr3:301339	5.609743e-04	3.714247e-02

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Correlation with RNA binding proteins (RBPs) for CHL1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
DLPFC	HNRNPF	exon_skip_222254	-4.547538e-01	3.908690e-15
FL	RBFOX2	exon_skip_252643	-5.930038e-01	3.430415e-20
FL	MSI1	exon_skip_222254	-5.310391e-01	1.392622e-15
FL	RBM3	exon_skip_222254	4.067265e-01	3.631083e-09
FL	MATR3	exon_skip_222254	6.135624e-01	1.484607e-21
FL	HNRNPA0	exon_skip_222254	5.587826e-01	2.086244e-17
FL	HNRNPC	exon_skip_222254	5.152800e-01	1.282431e-14
FL	RALYL	exon_skip_222254	5.938521e-01	5.690951e-20
FL	HNRNPL	exon_skip_222254	4.780811e-01	1.572004e-12
FL	SRSF9	exon_skip_222254	4.173081e-01	1.286212e-09
FL	HNRNPH2	exon_skip_222254	6.450221e-01	2.517398e-24
FL	EIF4B	exon_skip_222254	5.408050e-01	3.316672e-16
FL	ESRP1	exon_skip_222254	4.574387e-01	1.782342e-11
FL	NOVA1	exon_skip_222254	4.012252e-01	6.140880e-09
HCC	RBFOX2	exon_skip_64839	-4.845534e-01	5.224297e-17
HCC	SFPQ	exon_skip_64839	6.572340e-01	3.740059e-34
HCC	CNOT4	exon_skip_64839	4.967809e-01	6.380943e-18
HCC	RBM4	exon_skip_64839	5.289800e-01	1.650061e-20
HCC	RBMS3	exon_skip_222254	-5.030736e-01	9.993075e-19
HCC	MSI1	exon_skip_222254	-7.495353e-01	6.238825e-50
HCC	PABPN1	exon_skip_222254	-6.063378e-01	1.701194e-28
HCC	SFPQ	exon_skip_222254	-6.670659e-01	3.971809e-36
HCC	U2AF2	exon_skip_222254	-5.977260e-01	1.525368e-27
HCC	TIA1	exon_skip_222254	-5.838925e-01	4.517132e-26
HCC	RBM5	exon_skip_222254	-6.739967e-01	4.090429e-37
HCC	IGF2BP2	exon_skip_222254	-4.533683e-01	4.309740e-15
HCC	TRNAU1AP	exon_skip_222254	-5.424850e-01	4.626231e-22
HCC	CPEB2	exon_skip_222254	-4.198528e-01	5.913908e-13
HCC	EWSR1	exon_skip_222254	-4.247904e-01	2.962121e-13
HCC	HNRNPF	exon_skip_222254	-6.939982e-01	4.034125e-40
IFG	RBFOX2	exon_skip_64839	-5.680583e-01	1.614013e-03
IFG	TIA1	exon_skip_222254	-5.102834e-01	5.531722e-03
IFG	IGF2BP2	exon_skip_222254	-5.755746e-01	1.352200e-03
IFG	MATR3	exon_skip_222254	4.710003e-01	1.141282e-02
IFG	RALYL	exon_skip_222254	4.200721e-01	2.604263e-02
IFG	HNRNPH2	exon_skip_222254	4.979444e-01	7.007621e-03
PCC	RBFOX2	exon_skip_252643	-6.385238e-01	4.519893e-24
PCC	RBMS3	exon_skip_222254	-4.186611e-01	4.184129e-10
PCC	MSI1	exon_skip_222254	-5.774742e-01	1.256783e-19
PCC	RALYL	exon_skip_222254	4.838218e-01	1.998501e-13
PCC	HNRNPF	exon_skip_222254	-5.546032e-01	6.255241e-18
PG	RBFOX2	exon_skip_252643	-7.228331e-01	6.142699e-34
PG	RBM4	exon_skip_252643	-4.006097e-01	3.469300e-09
PG	MSI1	exon_skip_222254	-4.950301e-01	2.514610e-13
PG	IGF2BP2	exon_skip_222254	-4.444404e-01	9.493451e-11
PG	MATR3	exon_skip_222254	6.032335e-01	1.636095e-20
PG	HNRNPA0	exon_skip_222254	5.156763e-01	1.662848e-14
PG	HNRNPC	exon_skip_222254	5.003901e-01	1.264193e-13
PG	RALYL	exon_skip_222254	7.018554e-01	5.932010e-30
PG	HNRNPL	exon_skip_222254	4.942021e-01	2.793460e-13
PG	HNRNPH2	exon_skip_222254	6.553268e-01	4.648047e-25
PG	EIF4B	exon_skip_222254	4.067850e-01	4.348096e-09
PG	NOVA1	exon_skip_222254	5.132928e-01	2.296824e-14
STG	RBFOX2	exon_skip_252643	-7.005762e-01	2.137646e-14
STG	MBNL1	exon_skip_252643	-4.118986e-01	6.059915e-05
STG	MSI1	exon_skip_222254	-5.055183e-01	3.736244e-07
STG	RBM3	exon_skip_222254	4.636194e-01	4.186103e-06
STG	IGF2BP2	exon_skip_222254	-5.046855e-01	3.932591e-07
STG	MATR3	exon_skip_222254	6.675956e-01	6.659904e-13
STG	HNRNPA0	exon_skip_222254	6.611205e-01	1.323775e-12
STG	HNRNPC	exon_skip_222254	5.120840e-01	2.483000e-07
STG	NUP42	exon_skip_222254	4.786349e-01	1.826493e-06
STG	RALYL	exon_skip_222254	6.697054e-01	5.304592e-13
STG	HNRNPL	exon_skip_222254	5.321514e-01	6.743224e-08
STG	CPEB2	exon_skip_222254	4.218233e-01	3.460924e-05
STG	SRSF9	exon_skip_222254	4.966791e-01	6.390746e-07
STG	HNRNPH2	exon_skip_222254	6.779878e-01	2.132211e-13
STG	EIF4B	exon_skip_222254	4.631043e-01	4.303935e-06
STG	NOVA1	exon_skip_222254	5.105676e-01	2.730815e-07
TC	RBFOX2	exon_skip_252643	-8.420001e-01	2.858479e-38
TC	MBNL1	exon_skip_252643	-4.129765e-01	4.808775e-07
TC	MSI1	exon_skip_222254	-5.959585e-01	1.343704e-15
TC	RBM3	exon_skip_222254	4.362483e-01	2.983688e-08
TC	MATR3	exon_skip_222254	8.240059e-01	7.550786e-38
TC	HNRNPA0	exon_skip_222254	7.599567e-01	4.158060e-29
TC	HNRNPD	exon_skip_222254	6.593180e-01	8.175992e-20
TC	NUP42	exon_skip_222254	7.221997e-01	3.839707e-25
TC	RALYL	exon_skip_222254	8.877102e-01	4.876188e-51
TC	PTBP3	exon_skip_222254	4.884569e-01	3.015985e-10
TC	HNRNPL	exon_skip_222254	4.719028e-01	1.408474e-09
TC	EWSR1	exon_skip_222254	4.140991e-01	1.678508e-07
TC	SRSF9	exon_skip_222254	4.263749e-01	6.543383e-08
TC	HNRNPH2	exon_skip_222254	7.882781e-01	1.346572e-32
TC	ESRP1	exon_skip_222254	6.591730e-01	8.382197e-20
TC	NOVA1	exon_skip_222254	7.797818e-01	1.699154e-31

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RelatedDrugs for CHL1

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 CHL1

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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