ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for NCALD

Gene summary

Gene information	Gene symbol	NCALD
	Gene ID	83988
	Gene name	neurocalcin delta
	Synonyms	-
	Cytomap	8q22.3
	Type of gene	protein-coding
	Description	neurocalcin-delta
	Modification date	20200313
	UniProtAcc	A0A1B0GXG3, B2RB70, E5RFL9, E5RGA9, E5RGZ0, E5RHC8, E5RHE8, E5RI78, E5RI95, E5RIA5, E5RIG4, E5RIX3, E5RIZ1, E5RJA1, E5RJF1, E5RJJ6, E5RJT1, E5RK89, P61601,
	Context

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

Gene

GO ID

GO term

PubMed ID

Top

Gene structures and expression levels for NCALD

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.

ENSG00000104490

Differentially expressed gene analysis across multiple brain tissues between AD and control.

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
PG	DOWN	1.133038e+03	-8.503657e-01	5.334064e-11	9.299825e-09

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
PCC	DOWN	ENST00000522951.5	NCALD-225:protein_coding:NCALD	3.440584e+01	-8.051370e-01	6.853255e-04	2.012096e-02
PG	DOWN	ENST00000521957.1	NCALD-218:lncRNA:NCALD	1.890256e+00	-1.089935e+00	3.269357e-06	2.189197e-04
PG	DOWN	ENST00000517639.5	NCALD-205:retained_intron:NCALD	2.369205e+00	-8.972639e-01	3.861884e-05	1.355835e-03
PG	DOWN	ENST00000520346.1	NCALD-213:protein_coding:NCALD	8.686151e-01	-1.088775e+00	2.278742e-04	5.017104e-03
PG	DOWN	ENST00000518952.5	NCALD-210:lncRNA:NCALD	1.166810e+00	-9.090498e-01	7.140834e-04	1.139629e-02
PG	DOWN	ENST00000518166.5	NCALD-207:protein_coding:NCALD	2.514215e+01	-1.017950e+00	2.255465e-03	2.604982e-02
PG	DOWN	ENST00000522206.5	NCALD-221:protein_coding:NCALD	1.257092e+00	-1.017040e+00	2.308276e-03	2.647730e-02
TC	DOWN	ENST00000521599.5	NCALD-217:protein_coding:NCALD	1.505440e+01	-1.346192e+00	5.442527e-04	6.145561e-03
TC	DOWN	ENST00000522951.5	NCALD-225:protein_coding:NCALD	5.798220e+00	-1.161556e+00	3.089356e-03	2.333532e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

Top

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

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_100801	chr8	101915809:101915858:102020237:102020289:102029010:102029096	102020237:102020289
exon_skip_106987	chr8	101719583:101719648:101745831:101745993:101750043:101750162	101745831:101745993
exon_skip_115592	chr8	101915809:101915858:102020237:102020289:102123759:102123950	102020237:102020289
exon_skip_145741	chr8	101719541:101719648:101852572:101852670:101915809:101915858	101852572:101852670
exon_skip_161103	chr8	102020237:102020289:102029010:102029096:102124237:102124320	102029010:102029096
exon_skip_171319	chr8	101719621:101719648:101745831:101745993:101750043:101750162	101745831:101745993
exon_skip_201435	chr8	101915809:101915858:102020237:102020289:102124570:102124857	102020237:102020289
exon_skip_206786	chr8	101750598:101750687:101779924:101779979:101790862:101790977	101779924:101779979
exon_skip_225481	chr8	102020237:102020289:102029010:102029096:102124237:102124261	102029010:102029096
exon_skip_228507	chr8	102020237:102020289:102069989:102070106:102124627:102124814	102069989:102070106
exon_skip_245796	chr8	101719473:101719648:101750598:101750687:101915809:101915858	101750598:101750687
exon_skip_25281	chr8	101719621:101719648:101750598:101750687:101779924:101779979	101750598:101750687
exon_skip_287948	chr8	101719541:101719648:101887141:101887227:101915809:101915858	101887141:101887227
exon_skip_291765	chr8	101915809:101915858:102020237:102020289:102069989:102070106	102020237:102020289
exon_skip_292525	chr8	101779924:101779979:101785855:101786052:101790862:101790977	101785855:101786052
exon_skip_32425	chr8	101719373:101719648:101750598:101750687:101779924:101779979	101750598:101750687
exon_skip_5142	chr8	101719621:101719648:101750043:101750162:101750598:101750687	101750043:101750162
exon_skip_52578	chr8	101915809:101915858:102020237:102020289:102124237:102124261	102020237:102020289
exon_skip_53523	chr8	101719621:101719648:101750598:101750687:101790862:101790934	101750598:101750687
exon_skip_60259	chr8	101750598:101750687:101779924:101779979:101790862:101790934	101779924:101779979
exon_skip_8431	chr8	101719252:101719648:101887141:101887227:101915809:101915858	101887141:101887227

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

Top

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

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
ENST00000311028	101887141	101887227	3UTR-3UTR
ENST00000311028	102020237	102020289	3UTR-3UTR
ENST00000395923	102020237	102020289	3UTR-3UTR
ENST00000521599	102020237	102020289	3UTR-3UTR
ENST00000521599	102029010	102029096	3UTR-3UTR

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
ENST00000311028	101887141	101887227	3UTR-3UTR
ENST00000311028	102020237	102020289	3UTR-3UTR
ENST00000521599	102029010	102029096	3UTR-3UTR

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
ENST00000311028	101887141	101887227	3UTR-3UTR
ENST00000311028	102020237	102020289	3UTR-3UTR
ENST00000521599	102029010	102029096	3UTR-3UTR

Top

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

p-ENSG00000104490_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

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

Top

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

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	ENST00000311028	101887141	101887227	hsa-miR-4694-5p	chr8:101887200-101887207	8mer-1a	chr8:101887190-101887209	146.00	-16.51
Mayo	ENST00000311028	101887141	101887227	hsa-miR-4708-3p	chr8:101887219-101887226	8mer-1a	chr8:101887204-101887226	161.00	-24.00
Mayo	ENST00000521599	102029010	102029096	hsa-miR-3667-3p	chr8:102029048-102029055	8mer-1a	chr8:102029045-102029068	158.00	-26.73
Mayo	ENST00000521599	102029010	102029096	hsa-miR-5193	chr8:102029066-102029073	8mer-1a	chr8:102029053-102029075	144.00	-21.34
Mayo	ENST00000521599	102029010	102029096	hsa-miR-145-3p	chr8:102029041-102029048	8mer-1a	chr8:102029023-102029048	155.00	-18.83
Mayo	ENST00000311028	102020237	102020289	hsa-miR-6499-3p	chr8:102020259-102020266	8mer-1a	chr8:102020247-102020268	145.00	-16.66
Mayo	ENST00000311028	102020237	102020289	hsa-miR-4659a-3p	chr8:102020277-102020284	8mer-1a	chr8:102020265-102020284	150.00	-15.01
Mayo	ENST00000311028	102020237	102020289	hsa-miR-4659b-3p	chr8:102020277-102020284	8mer-1a	chr8:102020265-102020284	150.00	-15.01
Mayo	ENST00000521599	102029010	102029096	hsa-miR-3927-5p	chr8:102029086-102029093	8mer-1a	chr8:102029074-102029093	145.00	-10.20
MSBB	ENST00000311028	101887141	101887227	hsa-miR-4694-5p	chr8:101887200-101887207	8mer-1a	chr8:101887190-101887209	146.00	-16.51
MSBB	ENST00000311028	101887141	101887227	hsa-miR-4708-3p	chr8:101887219-101887226	8mer-1a	chr8:101887204-101887226	161.00	-24.00
MSBB	ENST00000521599	102029010	102029096	hsa-miR-3667-3p	chr8:102029048-102029055	8mer-1a	chr8:102029045-102029068	158.00	-26.73
MSBB	ENST00000521599	102029010	102029096	hsa-miR-5193	chr8:102029066-102029073	8mer-1a	chr8:102029053-102029075	144.00	-21.34
MSBB	ENST00000521599	102029010	102029096	hsa-miR-145-3p	chr8:102029041-102029048	8mer-1a	chr8:102029023-102029048	155.00	-18.83
MSBB	ENST00000311028	102020237	102020289	hsa-miR-6499-3p	chr8:102020259-102020266	8mer-1a	chr8:102020247-102020268	145.00	-16.66
MSBB	ENST00000311028	102020237	102020289	hsa-miR-4659a-3p	chr8:102020277-102020284	8mer-1a	chr8:102020265-102020284	150.00	-15.01
MSBB	ENST00000311028	102020237	102020289	hsa-miR-4659b-3p	chr8:102020277-102020284	8mer-1a	chr8:102020265-102020284	150.00	-15.01
MSBB	ENST00000521599	102029010	102029096	hsa-miR-3927-5p	chr8:102029086-102029093	8mer-1a	chr8:102029074-102029093	145.00	-10.20
ROSMAP	ENST00000311028	101887141	101887227	hsa-miR-4694-5p	chr8:101887200-101887207	8mer-1a	chr8:101887190-101887209	146.00	-16.51
ROSMAP	ENST00000311028	101887141	101887227	hsa-miR-4708-3p	chr8:101887219-101887226	8mer-1a	chr8:101887204-101887226	161.00	-24.00
ROSMAP	ENST00000521599	102029010	102029096	hsa-miR-3667-3p	chr8:102029048-102029055	8mer-1a	chr8:102029045-102029068	158.00	-26.73
ROSMAP	ENST00000521599	102029010	102029096	hsa-miR-5193	chr8:102029066-102029073	8mer-1a	chr8:102029053-102029075	144.00	-21.34
ROSMAP	ENST00000521599	102029010	102029096	hsa-miR-145-3p	chr8:102029041-102029048	8mer-1a	chr8:102029023-102029048	155.00	-18.83
ROSMAP	ENST00000521599	102020237	102020289	hsa-miR-6499-3p	chr8:102020259-102020266	8mer-1a	chr8:102020247-102020268	145.00	-16.66
ROSMAP	ENST00000521599	102020237	102020289	hsa-miR-4659a-3p	chr8:102020277-102020284	8mer-1a	chr8:102020265-102020284	150.00	-15.01
ROSMAP	ENST00000521599	102020237	102020289	hsa-miR-4659b-3p	chr8:102020277-102020284	8mer-1a	chr8:102020265-102020284	150.00	-15.01
ROSMAP	ENST00000521599	102029010	102029096	hsa-miR-3927-5p	chr8:102029086-102029093	8mer-1a	chr8:102029074-102029093	145.00	-10.20

Top

SNVs in the skipped exons for NCALD

- 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

Top

AD stage-associated exon skippint events for NCALD

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

Top

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

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
TC	exon_skip_287948	rs554945	chr8:101882179	4.320239e-37	2.872872e-32
TC	exon_skip_287948	rs550281	chr8:101902092	4.320239e-37	2.872872e-32
TC	exon_skip_287948	rs478917	chr8:101876899	5.100669e-34	2.035106e-29
TC	exon_skip_287948	rs1264866	chr8:101847079	8.060794e-32	2.010100e-27
TC	exon_skip_287948	rs566501	chr8:101854142	8.060794e-32	2.010100e-27
TC	exon_skip_287948	rs472963	chr8:101850891	2.451954e-30	4.446819e-26
TC	exon_skip_287948	rs7829693	chr8:101830644	5.828093e-18	2.193716e-14
TC	exon_skip_287948	rs6468801	chr8:101828445	2.467085e-11	2.719164e-08
TC	exon_skip_287948	rs6468799	chr8:101798774	2.948789e-08	1.489280e-05
PCC	exon_skip_8431	rs490032	chr8:101883913	9.343591e-31	2.900251e-26
PCC	exon_skip_8431	rs512202	chr8:101890637	8.331571e-30	2.370610e-25
PCC	exon_skip_8431	rs1264865	chr8:101845605	6.524171e-29	1.713548e-24
PCC	exon_skip_8431	rs490125	chr8:101860647	1.310150e-27	3.195270e-23
PCC	exon_skip_8431	rs478092	chr8:101854259	5.391553e-26	1.082877e-21
PCC	exon_skip_8431	rs479742	chr8:101876917	1.505817e-25	2.856367e-21
PCC	exon_skip_8431	rs554945	chr8:101882179	2.378011e-24	3.690673e-20
PCC	exon_skip_8431	rs1264931	chr8:101841925	3.618462e-23	4.412456e-19
PCC	exon_skip_8431	rs578603	chr8:101872828	8.410830e-23	6.985319e-19
PCC	exon_skip_8431	rs564718	chr8:101853951	3.418115e-22	2.537133e-18
PCC	exon_skip_8431	rs1264866	chr8:101847079	7.065780e-22	4.923551e-18
PCC	exon_skip_8431	rs482023	chr8:101897779	6.403769e-20	3.363851e-16
PCC	exon_skip_8431	rs472638	chr8:101866801	5.970833e-19	2.613694e-15
PCC	exon_skip_8431	rs529684	chr8:101869499	5.970833e-19	2.613694e-15
PCC	exon_skip_8431	rs478917	chr8:101876899	5.970833e-19	2.613694e-15
PCC	exon_skip_8431	rs550281	chr8:101902092	7.583356e-19	3.277545e-15
PCC	exon_skip_8431	rs1148499	chr8:101846549	4.934814e-17	1.668260e-13
PCC	exon_skip_8431	rs520880	chr8:101848599	4.934814e-17	1.668260e-13
PCC	exon_skip_8431	rs472963	chr8:101850891	4.934814e-17	1.668260e-13
PCC	exon_skip_8431	rs479041	chr8:101860937	4.934814e-17	1.668260e-13
PCC	exon_skip_8431	rs566392	chr8:101862073	4.934814e-17	1.668260e-13
PCC	exon_skip_8431	rs566501	chr8:101854142	5.232432e-17	1.734526e-13
PCC	exon_skip_8431	rs1264930	chr8:101842182	7.203681e-17	2.365024e-13
PCC	exon_skip_8431	rs7829693	chr8:101830644	1.403298e-16	4.436500e-13
PCC	exon_skip_8431	rs489973	chr8:101864945	4.292388e-16	1.221327e-12
PCC	exon_skip_8431	rs549281	chr8:101882788	3.302960e-14	7.831686e-11
PCC	exon_skip_8431	rs7813132	chr8:101825792	1.221633e-11	1.495033e-08
PCC	exon_skip_8431	rs1264933	chr8:101840061	2.776920e-11	3.160505e-08
PCC	exon_skip_8431	rs16868698	chr8:101908285	1.361470e-09	9.604551e-07
PCC	exon_skip_8431	rs7830291	chr8:101787266	1.104641e-08	6.514139e-06
PCC	exon_skip_8431	rs13251735	chr8:101817847	1.625910e-08	9.145811e-06
PCC	exon_skip_8431	rs7011941	chr8:101806767	2.952238e-07	1.204069e-04
PCC	exon_skip_8431	rs6468799	chr8:101798774	1.325721e-05	3.244834e-03
PCC	exon_skip_8431	rs1893366	chr8:101822295	2.574331e-05	5.703955e-03
PCC	exon_skip_8431	rs11992131	chr8:101876150	2.419224e-04	3.482377e-02

Top

Correlation with RNA binding proteins (RBPs) for NCALD

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	RBM24	exon_skip_8431	4.241617e-01	3.080497e-02
IFG	TARDBP	exon_skip_225481	-5.831278e-01	1.768671e-03
IFG	ELAVL1	exon_skip_225481	-4.793745e-01	1.321432e-02
IFG	RBM6	exon_skip_225481	-5.446194e-01	4.018687e-03
IFG	TIA1	exon_skip_225481	-5.594039e-01	2.966534e-03
IFG	PCBP2	exon_skip_225481	-7.007161e-01	6.704973e-05
IFG	RC3H1	exon_skip_225481	-5.432441e-01	4.130932e-03
IFG	HNRNPD	exon_skip_225481	-5.266586e-01	5.707999e-03

Top

RelatedDrugs for NCALD

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

RelatedDiseases for NCALD

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

Home

Download

Statistics

Landscape

Help

Contact

Gene summary for NCALD

Gene structures and expression levels for NCALD

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

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

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

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

SNVs in the skipped exons for NCALD

AD stage-associated exon skippint events for NCALD

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

Correlation with RNA binding proteins (RBPs) for NCALD

RelatedDrugs for NCALD

RelatedDiseases for NCALD