ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for HNRNPD

Gene summary

Gene information	Gene symbol	HNRNPD
	Gene ID	3184
	Gene name	heterogeneous nuclear ribonucleoprotein D
	Synonyms	AUF1\|AUF1A\|HNRPD\|P37\|hnRNPD0
	Cytomap	4q21.22
	Type of gene	protein-coding
	Description	heterogeneous nuclear ribonucleoprotein D0ARE-binding protein AUFI, type AAU-rich element RNA binding protein 1, 37kDahnRNP D0
	Modification date	20180523
	UniProtAcc	Q14103
	Context	PubMed: HNRNPD [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 HNRNPD 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 HNRNPD

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 HNRNPD

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_430416	4	83274986:83275307:83276047:83276154:83276456:83276554	83276047:83276154	ENSG00000138668.14	ENST00000514671.1
exon_skip_430422	4	83274986:83275307:83276456:83276554:83277689:83277836	83276456:83276554	ENSG00000138668.14	ENST00000313899.7,ENST00000543098.1,ENST00000352301.4
exon_skip_430423	4	83274986:83275307:83276456:83276554:83277948:83278048	83276456:83276554	ENSG00000138668.14	ENST00000353341.4
exon_skip_430434	4	83276456:83276554:83277689:83277836:83277948:83278048	83277689:83277836	ENSG00000138668.14	ENST00000313899.7,ENST00000513584.1,ENST00000543098.1,ENST00000541060.1,ENST00000352301.4
exon_skip_430444	4	83276456:83276554:83277948:83278048:83278465:83278545	83277948:83278048	ENSG00000138668.14	ENST00000514671.1,ENST00000353341.4,ENST00000508119.1
exon_skip_430451	4	83278589:83278597:83279811:83279973:83280623:83280792	83279811:83279973	ENSG00000138668.14	ENST00000313899.7,ENST00000509263.1,ENST00000514671.1,ENST00000353341.4,ENST00000507010.1,ENST00000543098.1,ENST00000352301.4,ENST00000515432.1
exon_skip_430453	4	83278589:83278597:83279811:83279973:83294598:83294639	83279811:83279973	ENSG00000138668.14	ENST00000513584.1,ENST00000541060.1
exon_skip_430461	4	83279910:83279973:83280623:83280792:83292680:83292737	83280623:83280792	ENSG00000138668.14	ENST00000313899.7,ENST00000509263.1,ENST00000353341.4,ENST00000507010.1
exon_skip_430462	4	83279910:83279973:83280623:83280792:83294598:83294639	83280623:83280792	ENSG00000138668.14	ENST00000503822.1,ENST00000543098.1,ENST00000352301.4
exon_skip_430482	4	83280721:83280792:83292680:83292737:83294598:83294639	83292680:83292737	ENSG00000138668.14	ENST00000509107.1,ENST00000353341.4,ENST00000507010.1
exon_skip_430491	4	83280721:83280792:83294598:83294930:83295271:83295297	83294598:83294930	ENSG00000138668.14	ENST00000503822.1
exon_skip_430500	4	83292680:83292737:83294598:83294890:83295271:83295297	83294598:83294890	ENSG00000138668.14	ENST00000507010.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for HNRNPD

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_430416	4	83274986:83275307:83276047:83276154:83276456:83276554	83276047:83276154	ENSG00000138668.14	ENST00000514671.1
exon_skip_430422	4	83274986:83275307:83276456:83276554:83277689:83277836	83276456:83276554	ENSG00000138668.14	ENST00000313899.7,ENST00000352301.4,ENST00000543098.1
exon_skip_430423	4	83274986:83275307:83276456:83276554:83277948:83278048	83276456:83276554	ENSG00000138668.14	ENST00000353341.4
exon_skip_430434	4	83276456:83276554:83277689:83277836:83277948:83278048	83277689:83277836	ENSG00000138668.14	ENST00000313899.7,ENST00000352301.4,ENST00000543098.1,ENST00000541060.1,ENST00000513584.1
exon_skip_430444	4	83276456:83276554:83277948:83278048:83278465:83278545	83277948:83278048	ENSG00000138668.14	ENST00000353341.4,ENST00000514671.1,ENST00000508119.1
exon_skip_430451	4	83278589:83278597:83279811:83279973:83280623:83280792	83279811:83279973	ENSG00000138668.14	ENST00000313899.7,ENST00000353341.4,ENST00000514671.1,ENST00000352301.4,ENST00000543098.1,ENST00000509263.1,ENST00000507010.1,ENST00000515432.1
exon_skip_430453	4	83278589:83278597:83279811:83279973:83294598:83294639	83279811:83279973	ENSG00000138668.14	ENST00000541060.1,ENST00000513584.1
exon_skip_430461	4	83279910:83279973:83280623:83280792:83292680:83292737	83280623:83280792	ENSG00000138668.14	ENST00000313899.7,ENST00000353341.4,ENST00000509263.1,ENST00000507010.1
exon_skip_430462	4	83279910:83279973:83280623:83280792:83294598:83294639	83280623:83280792	ENSG00000138668.14	ENST00000352301.4,ENST00000543098.1,ENST00000503822.1
exon_skip_430482	4	83280721:83280792:83292680:83292737:83294598:83294639	83292680:83292737	ENSG00000138668.14	ENST00000353341.4,ENST00000507010.1,ENST00000509107.1
exon_skip_430491	4	83280721:83280792:83294598:83294930:83295271:83295297	83294598:83294930	ENSG00000138668.14	ENST00000503822.1
exon_skip_430500	4	83292680:83292737:83294598:83294890:83295271:83295297	83294598:83294890	ENSG00000138668.14	ENST00000507010.1

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 HNRNPD

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
ENST00000313899	83276456	83276554	5CDS-5UTR
ENST00000313899	83280623	83280792	Frame-shift
ENST00000313899	83277689	83277836	In-frame
ENST00000313899	83279811	83279973	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
ENST00000313899	83276456	83276554	5CDS-5UTR
ENST00000313899	83280623	83280792	Frame-shift
ENST00000313899	83277689	83277836	In-frame
ENST00000313899	83279811	83279973	In-frame

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

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
ENST00000313899	3050	355	83279811	83279973	738	899	153	207
ENST00000313899	3050	355	83277689	83277836	1132	1278	284	333

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
ENST00000313899	3050	355	83279811	83279973	738	899	153	207
ENST00000313899	3050	355	83277689	83277836	1132	1278	284	333

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

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

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SNVs in the skipped exons for HNRNPD

- 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.

- 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_430422 exon_skip_430423	83276457	83276554	83276496	83276496	Frame_Shift_Del	T	-	p.K353fs
LIHC	TCGA-DD-A1EG-01	exon_skip_430422 exon_skip_430423	83276457	83276554	83276540	83276540	Frame_Shift_Del	A	-	p.Y339fs
LIHC	TCGA-DD-A1EG-01	exon_skip_430444	83277949	83278048	83277993	83277993	Frame_Shift_Del	C	-	p.G270fs
LUAD	TCGA-44-2656-01	exon_skip_430444	83277949	83278048	83278025	83278025	Frame_Shift_Del	C	-	p.S259fs
LGG	TCGA-DU-6392-01	exon_skip_430451 exon_skip_430453	83279812	83279973	83279883	83279883	Frame_Shift_Del	T	-	p.I184fs
UCEC	TCGA-BG-A0LX-01	exon_skip_430451 exon_skip_430453	83279812	83279973	83279883	83279883	Frame_Shift_Del	T	-	p.I184fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_430451 exon_skip_430453	83279812	83279973	83279914	83279914	Frame_Shift_Del	T	-	p.K173fs
UCEC	TCGA-D1-A0ZP-01	exon_skip_430500	83294599	83294890	83294711	83294711	Frame_Shift_Del	C	-	p.A41fs
UCEC	TCGA-D1-A0ZP-01	exon_skip_430491	83294599	83294930	83294711	83294711	Frame_Shift_Del	C	-	p.A41fs
BLCA	TCGA-ZF-A9RC-01	exon_skip_430434	83277690	83277836	83277772	83277773	Frame_Shift_Ins	-	C	p.G306fs
LIHC	TCGA-CC-A3M9-01	exon_skip_430444	83277949	83278048	83278019	83278020	Frame_Shift_Ins	-	C	p.A261fs
LIHC	TCGA-CC-A3M9-01	exon_skip_430444	83277949	83278048	83278019	83278020	Frame_Shift_Ins	-	C	p.E261fs
LIHC	TCGA-BC-A112-01	exon_skip_430451 exon_skip_430453	83279812	83279973	83279826	83279827	Frame_Shift_Ins	-	A	p.LW202fs
HNSC	TCGA-CV-7183-01	exon_skip_430461 exon_skip_430462	83280624	83280792	83280734	83280735	Frame_Shift_Ins	-	C	p.Y116fs
PRAD	TCGA-EJ-8474-01	exon_skip_430461 exon_skip_430462	83280624	83280792	83280638	83280638	Nonsense_Mutation	C	A	p.E149*
PRAD	TCGA-EJ-8474-01	exon_skip_430461 exon_skip_430462	83280624	83280792	83280638	83280638	Nonsense_Mutation	C	A	p.E149X
BLCA	TCGA-ZF-A9R2-01	exon_skip_430461 exon_skip_430462	83280624	83280792	83280673	83280673	Nonsense_Mutation	G	C	p.S137*
DLBC	TCGA-FA-A6HN-01	exon_skip_430500	83294599	83294890	83294756	83294756	Nonsense_Mutation	G	A	p.Q26X
DLBC	TCGA-FA-A6HN-01	exon_skip_430491	83294599	83294930	83294756	83294756	Nonsense_Mutation	G	A	p.Q26X

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

Depth of coverage in three exons

Mutation description

- 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
LS411N_LARGE_INTESTINE	83279812	83279973	83279883	83279883	Frame_Shift_Del	T	-	p.I184fs
HCT15_LARGE_INTESTINE	83279812	83279973	83279877	83279878	Frame_Shift_Ins	-	A	p.V186fs
MKN45_STOMACH	83294599	83294890	83294787	83294792	In_Frame_Del	TGCCGC	-	p.AA14del
MKN45_STOMACH	83294599	83294930	83294787	83294792	In_Frame_Del	TGCCGC	-	p.AA14del
PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	83294599	83294890	83294781	83294782	In_Frame_Ins	-	GCCGTT	p.17_17A>ATA
PL21_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	83294599	83294930	83294781	83294782	In_Frame_Ins	-	GCCGTT	p.17_17A>ATA
P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	83276457	83276554	83276492	83276492	Missense_Mutation	A	G	p.Y355H
SNU475_LIVER	83277690	83277836	83277743	83277743	Missense_Mutation	C	T	p.G316E
PECAPJ49_UPPER_AERODIGESTIVE_TRACT	83277690	83277836	83277776	83277776	Missense_Mutation	T	C	p.Y305C
ESO26_OESOPHAGUS	83277949	83278048	83277954	83277954	Missense_Mutation	C	A	p.G283V
MCC13_SKIN	83277949	83278048	83277960	83277960	Missense_Mutation	C	T	p.G281E
KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	83279812	83279973	83279858	83279858	Missense_Mutation	T	A	p.D192V
HEC251_ENDOMETRIUM	83279812	83279973	83279914	83279914	Missense_Mutation	T	G	p.K173N
HEC251_ENDOMETRIUM	83280624	83280792	83280643	83280643	Missense_Mutation	T	G	p.E147A
HCC2998_LARGE_INTESTINE	83280624	83280792	83280749	83280749	Missense_Mutation	C	T	p.D112N
BICR18_UPPER_AERODIGESTIVE_TRACT	83292681	83292737	83292700	83292700	Missense_Mutation	T	C	p.T91A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	83292681	83292737	83292700	83292700	Missense_Mutation	T	C	p.T91A
BICR18_UPPER_AERODIGESTIVE_TRACT	83292681	83292737	83292712	83292712	Missense_Mutation	A	T	p.S87T
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	83292681	83292737	83292712	83292712	Missense_Mutation	A	T	p.S87T
BHT101_THYROID	83292681	83292737	83292714	83292714	Missense_Mutation	T	G	p.H86P
NCIH1836_LUNG	83294599	83294890	83294701	83294701	Missense_Mutation	C	A	p.G44V
NCIH1836_LUNG	83294599	83294930	83294701	83294701	Missense_Mutation	C	A	p.G44V
SNU1105_CENTRAL_NERVOUS_SYSTEM	83294599	83294890	83294767	83294767	Missense_Mutation	G	A	p.S22L
SNU1105_CENTRAL_NERVOUS_SYSTEM	83294599	83294930	83294767	83294767	Missense_Mutation	G	A	p.S22L
NB1_AUTONOMIC_GANGLIA	83277949	83278048	83278003	83278003	Nonsense_Mutation	G	A	p.Q267*
BICR18_UPPER_AERODIGESTIVE_TRACT	83276457	83276554	83276553	83276553	Splice_Site	G	A	p.N334N

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

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 HNRNPD

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

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RelatedDrugs for HNRNPD

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 HNRNPD

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 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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Gene summary for HNRNPD

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

Gene isoform structures and expression levels for HNRNPD

Exon skipping events with PSIs in TCGA for HNRNPD

Exon skipping events with PSIs in GTEx for HNRNPD

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

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

SNVs in the skipped exons for HNRNPD

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

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

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

RelatedDrugs for HNRNPD

RelatedDiseases for HNRNPD