ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NID1

Gene summary

Gene information	Gene symbol	NID1
	Gene ID	4811
	Gene name	nidogen 1
	Synonyms	NID
	Cytomap	1q42.3
	Type of gene	protein-coding
	Description	nidogen-1NID-1enactinentactin
	Modification date	20180522
	UniProtAcc	P14543
	Context	PubMed: NID1 [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

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Exon skipping events across known transcript of Ensembl for NID1 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 NID1

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 NID1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_38358	1	236148678:236148805:236154185:236154358:236156944:236157172	236154185:236154358	ENSG00000116962.10	ENST00000264187.6,ENST00000366595.3
exon_skip_38359	1	236154185:236154358:236156944:236157172:236175220:236175343	236156944:236157172	ENSG00000116962.10	ENST00000264187.6
exon_skip_38361	1	236156944:236157172:236175220:236175343:236176710:236176860	236175220:236175343	ENSG00000116962.10	ENST00000264187.6
exon_skip_38370	1	236175220:236175343:236176710:236176860:236180447:236180573	236176710:236176860	ENSG00000116962.10	ENST00000264187.6
exon_skip_38375	1	236176710:236176860:236180447:236180573:236187369:236187510	236180447:236180573	ENSG00000116962.10	ENST00000264187.6
exon_skip_38378	1	236180447:236180573:236187369:236187513:236189195:236189441	236187369:236187513	ENSG00000116962.10	ENST00000264187.6
exon_skip_38380	1	236192849:236193050:236195700:236195952:236201403:236201553	236195700:236195952	ENSG00000116962.10	ENST00000264187.6,ENST00000366595.3
exon_skip_38381	1	236195700:236195952:236201403:236201553:236205209:236205592	236201403:236201553	ENSG00000116962.10	ENST00000264187.6,ENST00000366595.3
exon_skip_38384	1	236201403:236201553:236205209:236205592:236208756:236208983	236205209:236205592	ENSG00000116962.10	ENST00000264187.6,ENST00000366595.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NID1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_38358	1	236148678:236148805:236154185:236154358:236156944:236157172	236154185:236154358	ENSG00000116962.10	ENST00000366595.3,ENST00000264187.6
exon_skip_38359	1	236154185:236154358:236156944:236157172:236175220:236175343	236156944:236157172	ENSG00000116962.10	ENST00000264187.6
exon_skip_38361	1	236156944:236157172:236175220:236175343:236176710:236176860	236175220:236175343	ENSG00000116962.10	ENST00000264187.6
exon_skip_38370	1	236175220:236175343:236176710:236176860:236180447:236180573	236176710:236176860	ENSG00000116962.10	ENST00000264187.6
exon_skip_38375	1	236176710:236176860:236180447:236180573:236187369:236187510	236180447:236180573	ENSG00000116962.10	ENST00000264187.6
exon_skip_38378	1	236180447:236180573:236187369:236187513:236189195:236189441	236187369:236187513	ENSG00000116962.10	ENST00000264187.6
exon_skip_38380	1	236192849:236193050:236195700:236195952:236201403:236201553	236195700:236195952	ENSG00000116962.10	ENST00000366595.3,ENST00000264187.6
exon_skip_38381	1	236195700:236195952:236201403:236201553:236205209:236205592	236201403:236201553	ENSG00000116962.10	ENST00000366595.3,ENST00000264187.6
exon_skip_38384	1	236201403:236201553:236205209:236205592:236208756:236208983	236205209:236205592	ENSG00000116962.10	ENST00000366595.3,ENST00000264187.6

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 NID1

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
ENST00000264187	236154185	236154358	Frame-shift
ENST00000264187	236205209	236205592	Frame-shift
ENST00000264187	236156944	236157172	In-frame
ENST00000264187	236175220	236175343	In-frame
ENST00000264187	236176710	236176860	In-frame
ENST00000264187	236180447	236180573	In-frame
ENST00000264187	236187369	236187513	In-frame
ENST00000264187	236195700	236195952	In-frame
ENST00000264187	236201403	236201553	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
ENST00000264187	236154185	236154358	Frame-shift
ENST00000264187	236205209	236205592	Frame-shift
ENST00000264187	236156944	236157172	In-frame
ENST00000264187	236175220	236175343	In-frame
ENST00000264187	236176710	236176860	In-frame
ENST00000264187	236180447	236180573	In-frame
ENST00000264187	236187369	236187513	In-frame
ENST00000264187	236195700	236195952	In-frame
ENST00000264187	236201403	236201553	In-frame

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Infer the effects of exon skipping event on protein functional features for NID1

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
ENST00000264187	5881	1247	236201403	236201553	1219	1368	378	428
ENST00000264187	5881	1247	236195700	236195952	1369	1620	428	512
ENST00000264187	5881	1247	236187369	236187513	2068	2211	661	709
ENST00000264187	5881	1247	236180447	236180573	2212	2337	709	751
ENST00000264187	5881	1247	236176710	236176860	2338	2487	751	801
ENST00000264187	5881	1247	236175220	236175343	2488	2610	801	842
ENST00000264187	5881	1247	236156944	236157172	2611	2838	842	918

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
ENST00000264187	5881	1247	236201403	236201553	1219	1368	378	428
ENST00000264187	5881	1247	236195700	236195952	1369	1620	428	512
ENST00000264187	5881	1247	236187369	236187513	2068	2211	661	709
ENST00000264187	5881	1247	236180447	236180573	2212	2337	709	751
ENST00000264187	5881	1247	236176710	236176860	2338	2487	751	801
ENST00000264187	5881	1247	236175220	236175343	2488	2610	801	842
ENST00000264187	5881	1247	236156944	236157172	2611	2838	842	918

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
P14543	378	428	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	378	428	390	403	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	397	412	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	411	618	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	414	425	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	386	426	Domain	Note=EGF-like 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	378	428	387	387	Natural variant	ID=VAR_055763;Note=R->H;Dbxref=dbSNP:rs16833154
P14543	428	512	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	428	512	411	618	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	428	512	430	667	Domain	Note=Nidogen G2 beta-barrel;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00348
P14543	661	709	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	661	709	672	685	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	661	709	679	695	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	661	709	697	708	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	661	709	430	667	Domain	Note=Nidogen G2 beta-barrel;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00348
P14543	661	709	668	709	Domain	Note=EGF-like 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	661	709	702	704	Motif	Note=Cell attachment site
P14543	661	709	669	669	Natural variant	ID=VAR_021904;Note=Q->R;Dbxref=dbSNP:rs3738534
P14543	709	751	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	709	751	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	709	751	714	727	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	709	751	721	736	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	709	751	738	750	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	709	751	668	709	Domain	Note=EGF-like 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	709	751	710	751	Domain	Note=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	751	801	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	751	801	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	751	801	762	777	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	751	801	769	787	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	751	801	789	800	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	751	801	710	751	Domain	Note=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	751	801	758	801	Domain	Note=EGF-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	801	842	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	801	842	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	801	842	806	817	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	801	842	811	826	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	801	842	828	839	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	801	842	758	801	Domain	Note=EGF-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	801	842	802	840	Domain	Note=EGF-like 5%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	801	842	807	807	Natural variant	ID=VAR_058124;Note=Q->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.6;Dbxref=dbSNP:rs3738531
P14543	842	918	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	842	918	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	842	918	849	878	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	842	918	889	896	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	842	918	898	919	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	842	918	846	919	Domain	Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00500

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
P14543	378	428	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	378	428	390	403	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	397	412	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	411	618	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	414	425	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	378	428	386	426	Domain	Note=EGF-like 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	378	428	387	387	Natural variant	ID=VAR_055763;Note=R->H;Dbxref=dbSNP:rs16833154
P14543	428	512	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	428	512	411	618	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	428	512	430	667	Domain	Note=Nidogen G2 beta-barrel;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00348
P14543	661	709	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	661	709	672	685	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	661	709	679	695	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	661	709	697	708	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	661	709	430	667	Domain	Note=Nidogen G2 beta-barrel;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00348
P14543	661	709	668	709	Domain	Note=EGF-like 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	661	709	702	704	Motif	Note=Cell attachment site
P14543	661	709	669	669	Natural variant	ID=VAR_021904;Note=Q->R;Dbxref=dbSNP:rs3738534
P14543	709	751	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	709	751	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	709	751	714	727	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	709	751	721	736	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	709	751	738	750	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	709	751	668	709	Domain	Note=EGF-like 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	709	751	710	751	Domain	Note=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	751	801	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	751	801	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	751	801	762	777	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	751	801	769	787	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	751	801	789	800	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	751	801	710	751	Domain	Note=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	751	801	758	801	Domain	Note=EGF-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	801	842	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	801	842	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	801	842	806	817	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	801	842	811	826	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	801	842	828	839	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	801	842	758	801	Domain	Note=EGF-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	801	842	802	840	Domain	Note=EGF-like 5%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076
P14543	801	842	807	807	Natural variant	ID=VAR_058124;Note=Q->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.6;Dbxref=dbSNP:rs3738531
P14543	842	918	710	842	Alternative sequence	ID=VSP_017254;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.6;Dbxref=PMID:15489334
P14543	842	918	29	1247	Chain	ID=PRO_0000007669;Note=Nidogen-1
P14543	842	918	849	878	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	842	918	889	896	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	842	918	898	919	Disulfide bond	Ontology_term=ECO:0000250;evidence=ECO:0000250
P14543	842	918	846	919	Domain	Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00500

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SNVs in the skipped exons for NID1

- 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.

NID1_LIHC_exon_skip_38384_psi_boxplot.png
boxplot

NID1_LUAD_exon_skip_38384_psi_boxplot.png
boxplot

NID1_SKCM_exon_skip_38384_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
LIHC	TCGA-DD-A1EG-01	exon_skip_38359	236156945	236157172	236156947	236156947	Frame_Shift_Del	G	-	p.P918fs
LIHC	TCGA-DD-A3A0-01	exon_skip_38359	236156945	236157172	236156947	236156947	Frame_Shift_Del	G	-	p.P918fs
UCEC	TCGA-AP-A0LT-01	exon_skip_38359	236156945	236157172	236156947	236156947	Frame_Shift_Del	G	-	p.P918fs
LIHC	TCGA-DD-A3A0-01	exon_skip_38359	236156945	236157172	236157116	236157116	Frame_Shift_Del	C	-	p.A862fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_38378	236187370	236187513	236187431	236187431	Frame_Shift_Del	G	-	p.P689fs
LIHC	TCGA-DD-A1EG-01	exon_skip_38380	236195701	236195952	236195837	236195837	Frame_Shift_Del	C	-	p.G467fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_38380	236195701	236195952	236195888	236195888	Frame_Shift_Del	G	-	p.P450fs
LIHC	TCGA-DD-A3A0-01	exon_skip_38381	236201404	236201553	236201533	236201533	Frame_Shift_Del	A	-	p.S386fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_38381	236201404	236201553	236201550	236201550	Frame_Shift_Del	A	-	p.F380fs
LIHC	TCGA-DD-A1EG-01	exon_skip_38384	236205210	236205592	236205383	236205383	Frame_Shift_Del	C	-	p.G322fs
LIHC	TCGA-DD-A1EG-01	exon_skip_38384	236205210	236205592	236205398	236205398	Frame_Shift_Del	T	-	p.K316fs
LIHC	TCGA-BC-A10T-01	exon_skip_38361	236175221	236175343	236175322	236175323	Frame_Shift_Ins	-	T	p.P809fs
KIRC	TCGA-BP-5181-01	exon_skip_38380	236195701	236195952	236195855	236195856	Frame_Shift_Ins	-	T	p.C461fs
THYM	TCGA-ZT-A8OM-01	exon_skip_38378	236187370	236187513	236187374	236187374	Nonsense_Mutation	G	T	p.C708X
STAD	TCGA-BR-8368-01	exon_skip_38381	236201404	236201553	236201453	236201453	Nonsense_Mutation	G	T	p.C412*
STAD	TCGA-BR-8368-01	exon_skip_38381	236201404	236201553	236201453	236201453	Nonsense_Mutation	G	T	p.C412X
BLCA	TCGA-G2-A3IE-01	exon_skip_38384	236205210	236205592	236205225	236205225	Nonsense_Mutation	C	A	p.E374*
LUAD	TCGA-38-7271-01	exon_skip_38384	236205210	236205592	236205429	236205429	Nonsense_Mutation	C	A	p.E306*
LUAD	TCGA-55-1594-01	exon_skip_38384	236205210	236205592	236205495	236205495	Nonsense_Mutation	C	A	p.E284*
SKCM	TCGA-FW-A3R5-06	exon_skip_38384	236205210	236205592	236205562	236205562	Nonsense_Mutation	C	T	p.W261*
SKCM	TCGA-FW-A3R5-06	exon_skip_38384	236205210	236205592	236205562	236205562	Nonsense_Mutation	C	T	p.W261X
SKCM	TCGA-FW-A3R5-06	exon_skip_38384	236205210	236205592	236205563	236205563	Nonsense_Mutation	C	T	p.W261*
SKCM	TCGA-FW-A3R5-06	exon_skip_38384	236205210	236205592	236205563	236205563	Nonsense_Mutation	C	T	p.W261X
UCEC	TCGA-AX-A063-01	exon_skip_38361	236175221	236175343	236175219	236175219	Splice_Site	A	T	e12+2
CHOL	TCGA-W5-AA39-01	exon_skip_38361	236175221	236175343	236175345	236175345	Splice_Site	T	C	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-55-1594-01
	Cancer type: LUAD
	ESID: exon_skip_38384
	Skipped exon start: 236205210
	Skipped exon end: 236205592
	Mutation start: 236205495
	Mutation end: 236205495
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.E284*
exon_skip_109033_LUAD_TCGA-55-1594-01.png
exon_skip_110964_LUAD_TCGA-55-1594-01.png
exon_skip_38384_LUAD_TCGA-55-1594-01.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
TUHR4TKB_KIDNEY	236154186	236154358	236154297	236154297	Frame_Shift_Del	G	-	p.P939fs
LS411N_LARGE_INTESTINE	236154186	236154358	236154337	236154337	Frame_Shift_Del	G	-	p.P926fs
BICR18_UPPER_AERODIGESTIVE_TRACT	236187370	236187513	236187434	236187434	Frame_Shift_Del	A	-	p.G688fs
CW2_LARGE_INTESTINE	236154186	236154358	236154228	236154229	Frame_Shift_Ins	-	T	p.N962fs
BICR18_UPPER_AERODIGESTIVE_TRACT	236187370	236187513	236187426	236187427	Frame_Shift_Ins	-	T	p.T691fs
NCIH1155_LUNG	236154186	236154358	236154191	236154191	Missense_Mutation	C	T	p.V975I
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236154186	236154358	236154238	236154238	Missense_Mutation	A	C	p.L959R
CROAP3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236154186	236154358	236154269	236154269	Missense_Mutation	C	A	p.A949S
KARPAS1106P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236154186	236154358	236154269	236154269	Missense_Mutation	C	A	p.A949S
U698M_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236154186	236154358	236154269	236154269	Missense_Mutation	C	A	p.A949S
HCC366_LUNG	236156945	236157172	236156998	236156998	Missense_Mutation	C	T	p.R901H
MDAPCA2B_PROSTATE	236156945	236157172	236157005	236157005	Missense_Mutation	C	T	p.V899M
HCT15_LARGE_INTESTINE	236156945	236157172	236157029	236157029	Missense_Mutation	C	T	p.G891S
T84_LARGE_INTESTINE	236156945	236157172	236157033	236157033	Missense_Mutation	G	C	p.C889W
NCIH1869_LUNG	236175221	236175343	236175308	236175308	Missense_Mutation	C	T	p.D814N
HARA_LUNG	236176711	236176860	236176759	236176759	Missense_Mutation	T	A	p.T786S
HEC1_ENDOMETRIUM	236176711	236176860	236176795	236176795	Missense_Mutation	G	A	p.R774W
LNZTA3WT4_CENTRAL_NERVOUS_SYSTEM	236180448	236180573	236180487	236180487	Missense_Mutation	C	T	p.V739M
LNZ308_CENTRAL_NERVOUS_SYSTEM	236180448	236180573	236180487	236180487	Missense_Mutation	C	T	p.V739M
NCIH522_LUNG	236180448	236180573	236180493	236180493	Missense_Mutation	C	T	p.E737K
EN_ENDOMETRIUM	236180448	236180573	236180499	236180499	Missense_Mutation	G	A	p.R735C
PC9_LUNG	236180448	236180573	236180528	236180528	Missense_Mutation	G	A	p.T725I
PC14_LUNG	236180448	236180573	236180528	236180528	Missense_Mutation	G	A	p.T725I
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236187370	236187513	236187400	236187400	Missense_Mutation	C	T	p.G700S
TTC466_BONE	236187370	236187513	236187417	236187417	Missense_Mutation	G	A	p.T694I
GSU_STOMACH	236187370	236187513	236187441	236187441	Missense_Mutation	C	T	p.R686H
CORL321_PLEURA	236187370	236187513	236187457	236187457	Missense_Mutation	T	C	p.T681A
GP2D_LARGE_INTESTINE	236187370	236187513	236187489	236187489	Missense_Mutation	T	C	p.N670S
GP5D_LARGE_INTESTINE	236187370	236187513	236187489	236187489	Missense_Mutation	T	C	p.N670S
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236195701	236195952	236195739	236195739	Missense_Mutation	A	G	p.V500A
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236195701	236195952	236195818	236195818	Missense_Mutation	T	C	p.S474G
NCIH2004RT_SOFT_TISSUE	236195701	236195952	236195854	236195854	Missense_Mutation	C	T	p.V462I
HCC515_LUNG	236195701	236195952	236195866	236195866	Missense_Mutation	G	T	p.L458I
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236195701	236195952	236195944	236195944	Missense_Mutation	G	T	p.Q432K
MFM223_BREAST	236201404	236201553	236201449	236201449	Missense_Mutation	A	C	p.C414G
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236201404	236201553	236201515	236201515	Missense_Mutation	T	C	p.N392D
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236205210	236205592	236205239	236205239	Missense_Mutation	T	C	p.D369G
HEC6_ENDOMETRIUM	236205210	236205592	236205312	236205312	Missense_Mutation	G	A	p.P345S
NCIH810_LUNG	236205210	236205592	236205335	236205335	Missense_Mutation	G	T	p.A337E
LS411N_LARGE_INTESTINE	236205210	236205592	236205386	236205386	Missense_Mutation	C	A	p.R320M
K562_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	236205210	236205592	236205406	236205406	Missense_Mutation	G	T	p.F313L
HOS_BONE	236205210	236205592	236205468	236205468	Missense_Mutation	C	T	p.D293N
WM793_SKIN	236205210	236205592	236205530	236205530	Missense_Mutation	T	C	p.N272S
DU145_PROSTATE	236205210	236205592	236205549	236205549	Missense_Mutation	C	A	p.G266W
MFE319_ENDOMETRIUM	236187370	236187513	236187382	236187382	Nonsense_Mutation	G	A	p.R706*
HT115_LARGE_INTESTINE	236187370	236187513	236187394	236187394	Nonsense_Mutation	G	A	p.R702*
SNU245_BILIARY_TRACT	236156945	236157172	236156946	236156946	Splice_Site	C	T	p.P918P
EKVX_LUNG	236180448	236180573	236180444	236180456	Splice_Site	TTACCCACACACG	-	p.TCVG749fs
OC316_OVARY	236195701	236195952	236195702	236195702	Splice_Site	G	A	p.T512T
OC314_OVARY	236195701	236195952	236195702	236195702	Splice_Site	G	A	p.T512T

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NID1

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 NID1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NID1

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RelatedDrugs for NID1

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
	P14543	DB00013	Urokinase	Nidogen-1	biotech	approved\|investigational\|withdrawn

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RelatedDiseases for NID1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
NID1	C0023893	Liver Cirrhosis, Experimental	1	CTD_human
NID1	C0043094	Weight Gain	1	CTD_human

	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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