ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RNH1

Gene summary

Gene information	Gene symbol	RNH1
	Gene ID	6050
	Gene name	ribonuclease/angiogenin inhibitor 1
	Synonyms	RAI\|RNH
	Cytomap	11p15.5
	Type of gene	protein-coding
	Description	ribonuclease inhibitorplacental RNase inhibitorplacental ribonuclease inhibitortesticular tissue protein Li 164
	Modification date	20200327
	UniProtAcc	A0A024RC87, A0A0J9YXC4, E9PIK5, E9PIM9, E9PLZ3, E9PMA9, E9PMI1, E9PMJ3, E9PMN0, E9PR82, H0YCR7, O60930, P13489,
	Context

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

Gene	GO ID	GO term	PubMed ID
RNH1	GO:0045765	regulation of angiogenesis	3470787

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Gene structures and expression levels for RNH1

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.

ENSG00000023191

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
PCC	UP	ENST00000525701.5	RNH1-210:nonsense_mediated_decay:RNH1	2.176724e+01	9.445553e-01	1.037399e-05	1.302884e-03
CB	DOWN	ENST00000397604.7	RNH1-203:protein_coding:RNH1	3.994723e+02	-8.177090e-01	1.547982e-07	3.071785e-06
CB	UP	ENST00000524780.5	RNH1-208:retained_intron:RNH1	9.056712e+00	1.861556e+00	4.528738e-03	1.814213e-02

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 RNH1

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_146570	chr11	499829:499999:500484:500654:502062:502181	500484:500654
exon_skip_162051	chr11	502214:502249:504824:504996:506609:506759	504824:504996
exon_skip_187944	chr11	502137:502181:504824:504996:507113:507195	504824:504996
exon_skip_230089	chr11	502214:502249:504824:504996:507113:507195	504824:504996
exon_skip_286078	chr11	502214:502249:504824:504888:506609:506759	504824:504888
exon_skip_293894	chr11	500635:500654:502062:502249:507113:507195	502062:502249
exon_skip_84924	chr11	500635:500654:502062:502181:507113:507195	502062:502181

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_162051	Mayo_CB	5.452439e-01	7.154054e-01	-1.701615e-01	9.562894e-06
exon_skip_162051	Mayo_TC	6.724390e-01	7.793333e-01	-1.068943e-01	4.883657e-04

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Open reading frame (ORF) annotation in the exon skipping event for RNH1

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
ENST00000354420	504824	504996	3UTR-3UTR
ENST00000397615	504824	504996	3UTR-3UTR
ENST00000533410	504824	504996	3UTR-3UTR
ENST00000354420	500484	500654	In-frame
ENST00000356187	500484	500654	In-frame
ENST00000397604	500484	500654	In-frame
ENST00000397614	500484	500654	In-frame
ENST00000397615	500484	500654	In-frame
ENST00000438658	500484	500654	In-frame
ENST00000533410	500484	500654	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
ENST00000354420	504824	504996	3UTR-3UTR
ENST00000397615	504824	504996	3UTR-3UTR
ENST00000533410	504824	504996	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
ENST00000356187	502062	502249	3UTR-3CDS
ENST00000397604	502062	502181	3UTR-3CDS
ENST00000354420	504824	504996	3UTR-3UTR
ENST00000397615	504824	504996	3UTR-3UTR
ENST00000533410	504824	504996	3UTR-3UTR

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Infer the effects of exon skipping event on protein functional features for RNH1

p-ENSG00000023191_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
ENST00000354420	1911	461	500484	500654	471	640	34	90
ENST00000356187	1808	461	500484	500654	377	546	34	90
ENST00000397604	1739	461	500484	500654	262	431	34	90
ENST00000397614	1881	461	500484	500654	402	571	34	90
ENST00000397615	2031	461	500484	500654	554	723	34	90
ENST00000438658	1742	461	500484	500654	298	467	34	90
ENST00000533410	1846	461	500484	500654	400	569	34	90

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
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	31	38	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	60	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	2	461	Chain	ID=PRO_0000097343;Note=Ribonuclease inhibitor
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	42	53	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	69	78	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1Z7X
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	82	82	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	20	48	Repeat	Note=LRR 1
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	49	76	Repeat	Note=LRR 2
P13489	34	90	77	105	Repeat	Note=LRR 3
P13489	34	90	77	105	Repeat	Note=LRR 3
P13489	34	90	77	105	Repeat	Note=LRR 3
P13489	34	90	77	105	Repeat	Note=LRR 3
P13489	34	90	77	105	Repeat	Note=LRR 3
P13489	34	90	77	105	Repeat	Note=LRR 3
P13489	34	90	77	105	Repeat	Note=LRR 3

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

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3'-UTR located exon skipping events that lost miRNA binding sites in RNH1

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	ENST00000533410	504824	504996	hsa-miR-4513	chr11:504975-504982	8mer-1a	chr11:504959-504982	156.00	-26.22
Mayo	ENST00000533410	504824	504996	hsa-miR-3529-3p	chr11:504880-504887	8mer-1a	chr11:504862-504887	159.00	-17.03
Mayo	ENST00000533410	504824	504996	hsa-miR-4439	chr11:504976-504983	8mer-1a	chr11:504961-504983	154.00	-24.84
Mayo	ENST00000533410	504824	504996	hsa-miR-3136-5p	chr11:504976-504983	8mer-1a	chr11:504961-504983	154.00	-24.84
Mayo	ENST00000533410	504824	504996	hsa-miR-1224-5p	chr11:504942-504949	8mer-1a	chr11:504929-504949	152.00	-27.06
Mayo	ENST00000533410	504824	504996	hsa-miR-5690	chr11:504885-504892	8mer-1a	chr11:504873-504894	149.00	-17.02
Mayo	ENST00000533410	504824	504996	hsa-miR-3925-3p	chr11:504849-504856	8mer-1a	chr11:504848-504869	148.00	-17.39
Mayo	ENST00000533410	504824	504996	hsa-miR-6855-3p	chr11:504975-504982	8mer-1a	chr11:504959-504982	156.00	-26.22
MSBB	ENST00000533410	504824	504996	hsa-miR-4513	chr11:504975-504982	8mer-1a	chr11:504959-504982	156.00	-26.22
MSBB	ENST00000533410	504824	504996	hsa-miR-3529-3p	chr11:504880-504887	8mer-1a	chr11:504862-504887	159.00	-17.03
MSBB	ENST00000533410	504824	504996	hsa-miR-4439	chr11:504976-504983	8mer-1a	chr11:504961-504983	154.00	-24.84
MSBB	ENST00000533410	504824	504996	hsa-miR-3136-5p	chr11:504976-504983	8mer-1a	chr11:504961-504983	154.00	-24.84
MSBB	ENST00000533410	504824	504996	hsa-miR-1224-5p	chr11:504942-504949	8mer-1a	chr11:504929-504949	152.00	-27.06
MSBB	ENST00000533410	504824	504996	hsa-miR-5690	chr11:504885-504892	8mer-1a	chr11:504873-504894	149.00	-17.02
MSBB	ENST00000533410	504824	504996	hsa-miR-3925-3p	chr11:504849-504856	8mer-1a	chr11:504848-504869	148.00	-17.39
MSBB	ENST00000533410	504824	504996	hsa-miR-6855-3p	chr11:504975-504982	8mer-1a	chr11:504959-504982	156.00	-26.22
ROSMAP	ENST00000533410	504824	504996	hsa-miR-4513	chr11:504975-504982	8mer-1a	chr11:504959-504982	156.00	-26.22
ROSMAP	ENST00000533410	504824	504996	hsa-miR-3529-3p	chr11:504880-504887	8mer-1a	chr11:504862-504887	159.00	-17.03
ROSMAP	ENST00000533410	504824	504996	hsa-miR-4439	chr11:504976-504983	8mer-1a	chr11:504961-504983	154.00	-24.84
ROSMAP	ENST00000533410	504824	504996	hsa-miR-3136-5p	chr11:504976-504983	8mer-1a	chr11:504961-504983	154.00	-24.84
ROSMAP	ENST00000533410	504824	504996	hsa-miR-1224-5p	chr11:504942-504949	8mer-1a	chr11:504929-504949	152.00	-27.06
ROSMAP	ENST00000533410	504824	504996	hsa-miR-5690	chr11:504885-504892	8mer-1a	chr11:504873-504894	149.00	-17.02
ROSMAP	ENST00000533410	504824	504996	hsa-miR-3925-3p	chr11:504849-504856	8mer-1a	chr11:504848-504869	148.00	-17.39
ROSMAP	ENST00000533410	504824	504996	hsa-miR-6855-3p	chr11:504975-504982	8mer-1a	chr11:504959-504982	156.00	-26.22

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SNVs in the skipped exons for RNH1

- 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 RNH1

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 RNH1

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
CB	exon_skip_187944	rs7944548	chr11:502217	1.684039e-04	2.614567e-02
HCC	exon_skip_187944	rs11823647	chr11:454980	9.524152e-06	1.198866e-03
HCC	exon_skip_187944	rs7935013	chr11:467339	9.682201e-06	1.215880e-03
HCC	exon_skip_230089	rs1044707	chr11:491334	2.441242e-05	2.735090e-03
HCC	exon_skip_187944	rs7944548	chr11:502217	3.625658e-05	3.831092e-03
HCC	exon_skip_230089	rs7924341	chr11:440343	8.606727e-05	8.028893e-03
HCC	exon_skip_230089	rs12418639	chr11:473300	2.657718e-04	2.043415e-02
PCC	exon_skip_187944	rs7935013	chr11:467339	7.219344e-05	1.328826e-02
PCC	exon_skip_187944	rs7944548	chr11:502217	2.563973e-04	3.634051e-02
DLPFC	exon_skip_187944	rs7935013	chr11:467339	4.879173e-07	7.732749e-05
DLPFC	exon_skip_187944	rs7944548	chr11:502217	4.756215e-06	5.841857e-04
DLPFC	exon_skip_187944	rs12628	chr11:534242	1.259381e-05	1.379480e-03
DLPFC	exon_skip_187944	rs11823647	chr11:454980	1.291778e-05	1.408502e-03

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Correlation with RNA binding proteins (RBPs) for RNH1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM45	exon_skip_197042	5.130390e-01	1.025064e-11
CB	CNOT4	exon_skip_162051	-5.223578e-01	2.673454e-12
CB	TRA2A	exon_skip_162051	-5.324671e-01	8.415250e-13
CB	RBM45	exon_skip_162051	6.479782e-01	6.071059e-20
CB	NUP42	exon_skip_162051	4.552737e-01	2.352906e-09
CB	RBM45	exon_skip_230089	4.540549e-01	2.072449e-09
CB	TRA2A	exon_skip_206285	-4.030404e-01	1.053461e-05
IFG	CNOT4	exon_skip_197042	-5.169426e-01	8.144098e-03
IFG	UNK	exon_skip_197042	-6.269002e-01	7.980113e-04
IFG	TRA2A	exon_skip_197042	-6.419089e-01	5.422130e-04
IFG	PCBP2	exon_skip_197042	-5.056764e-01	9.915439e-03
IFG	RBM45	exon_skip_197042	-4.558059e-01	2.202808e-02
IFG	PABPC1	exon_skip_197042	-4.586221e-01	2.111953e-02
IFG	PABPN1L	exon_skip_187944	4.420982e-01	2.094734e-02
IFG	HNRNPK	exon_skip_187944	4.586461e-01	1.611968e-02
IFG	PCBP2	exon_skip_187944	4.589519e-01	1.603997e-02
TC	NOVA1	exon_skip_197042	4.566413e-01	1.450062e-09
TC	ILF2	exon_skip_286078	4.113139e-01	3.369280e-06
TC	NOVA1	exon_skip_286078	4.497255e-01	2.882087e-07
TC	NOVA1	exon_skip_162051	5.099682e-01	8.981896e-12
TC	NUP42	exon_skip_158721	4.214753e-01	1.476866e-06
TC	NOVA1	exon_skip_158721	4.876934e-01	1.399112e-08

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RelatedDrugs for RNH1

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 RNH1

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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