ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SND1

Gene summary

Gene information	Gene symbol	SND1
	Gene ID	27044
	Gene name	staphylococcal nuclease and tudor domain containing 1
	Synonyms	TDRD11\|Tudor-SN\|p100
	Cytomap	7q32.1
	Type of gene	protein-coding
	Description	staphylococcal nuclease domain-containing protein 1EBNA2 coactivator p100testis tissue sperm-binding protein Li 82Ptudor domain-containing protein 11
	Modification date	20200313
	UniProtAcc	A0A140VK49, H7C597, Q7KZF4,
	Context

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

Gene	GO ID	GO term	PubMed ID
SND1	GO:0010587	miRNA catabolic process	28546213

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Gene structures and expression levels for SND1

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.

ENSG00000197157

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
CB	DOWN	ENST00000489417.5	SND1-214:retained_intron:SND1	4.065214e+02	-1.141178e+00	1.676373e-10	9.758178e-09
CB	DOWN	ENST00000479086.1	TYSND1-203:lncRNA:TYSND1	1.175087e+02	-2.081198e+00	6.756934e-06	7.567683e-05
CB	DOWN	ENST00000470463.1	SND1-208:lncRNA:SND1	9.558342e+00	-8.067782e-01	4.979520e-04	2.870142e-03
TC	DOWN	ENST00000489417.5	SND1-214:retained_intron:SND1	2.904673e+02	-8.818444e-01	2.375110e-07	1.252245e-05

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 SND1

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_11618	chr7	128084724:128084847:128085711:128085780:128086938:128087051	128085711:128085780
exon_skip_132111	chr7	127807484:127807573:127844324:127844424:127887902:127887949	127844324:127844424
exon_skip_1552	chr7	128086938:128087051:128089489:128089692:128091837:128091881	128089489:128089692
exon_skip_172121	chr7	127904747:127904819:127928060:127928186:127929188:127929227	127928060:127928186
exon_skip_174620	chr7	127990947:127991056:128074502:128074690:128081360:128081501	128074502:128074690
exon_skip_189624	chr7	127904747:127904819:127928060:127928186:127929188:127929329	127928060:127928186
exon_skip_205569	chr7	127990947:127991056:128008034:128008144:128074502:128074690	128008034:128008144
exon_skip_205731	chr7	127694828:127694948:127698875:127698953:127701163:127701213	127698875:127698953
exon_skip_216968	chr7	127904626:127904819:127928060:127928186:127929188:127929227	127928060:127928186
exon_skip_45745	chr7	127707557:127707647:127721287:127721400:127807484:127807573	127721287:127721400
exon_skip_58716	chr7	127887912:127888012:127904747:127904819:127929188:127929227	127904747:127904819
exon_skip_91598	chr7	127844324:127844424:127887902:127888012:127904747:127904819	127887902:127888012

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

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Open reading frame (ORF) annotation in the exon skipping event for SND1

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
ENST00000354725	127698875	127698953	Frame-shift
ENST00000354725	127844324	127844424	Frame-shift
ENST00000354725	127904747	127904819	Frame-shift
ENST00000354725	127721287	127721400	In-frame
ENST00000354725	128074502	128074690	In-frame
ENST00000354725	128089489	128089692	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
ENST00000354725	127844324	127844424	Frame-shift
ENST00000354725	128074502	128074690	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
ENST00000354725	127698875	127698953	Frame-shift
ENST00000354725	127844324	127844424	Frame-shift
ENST00000354725	127904747	127904819	Frame-shift
ENST00000354725	128085711	128085780	Frame-shift
ENST00000354725	127721287	127721400	In-frame
ENST00000354725	127887902	127888012	In-frame
ENST00000354725	128074502	128074690	In-frame
ENST00000354725	128089489	128089692	In-frame

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Infer the effects of exon skipping event on protein functional features for SND1

p-ENSG00000197157_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
ENST00000354725	3493	910	127721287	127721400	1234	1346	346	384
ENST00000354725	3493	910	128074502	128074690	1975	2162	593	656
ENST00000354725	3493	910	128089489	128089692	2614	2816	806	874

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
ENST00000354725	3493	910	128074502	128074690	1975	2162	593	656

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
ENST00000354725	3493	910	127721287	127721400	1234	1346	346	384
ENST00000354725	3493	910	127887902	127888012	1539	1648	448	484
ENST00000354725	3493	910	128074502	128074690	1975	2162	593	656
ENST00000354725	3493	910	128089489	128089692	2614	2816	806	874

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
Q7KZF4	346	384	341	351	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	355	359	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	365	370	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	346	384	341	496	Domain	Note=TNase-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00272
Q7KZF4	346	384	384	386	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	352	354	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	593	601	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	607	613	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	627	630	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	593	656	525	660	Domain	Note=TNase-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00272
Q7KZF4	593	656	618	624	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	632	634	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	640	653	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	656	658	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	641	641	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q7KZF4	593	656	645	645	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q7KZF4	806	874	824	832	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	835	837	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	839	844	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	860	863	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	806	874	807	821	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	851	857	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	869	871	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	872	887	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	845	847	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O

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
Q7KZF4	593	656	593	601	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	607	613	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	627	630	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	593	656	525	660	Domain	Note=TNase-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00272
Q7KZF4	593	656	618	624	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	632	634	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	640	653	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	656	658	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	641	641	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q7KZF4	593	656	645	645	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163

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
Q7KZF4	346	384	341	351	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	355	359	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	365	370	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	346	384	341	496	Domain	Note=TNase-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00272
Q7KZF4	346	384	384	386	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	346	384	352	354	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	448	484	459	462	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	448	484	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	448	484	341	496	Domain	Note=TNase-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00272
Q7KZF4	448	484	450	456	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	448	484	476	488	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	593	601	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	607	613	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	627	630	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	593	656	525	660	Domain	Note=TNase-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00272
Q7KZF4	593	656	618	624	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	632	634	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	640	653	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	656	658	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3BDL
Q7KZF4	593	656	641	641	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q7KZF4	593	656	645	645	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q7KZF4	806	874	824	832	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	835	837	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	839	844	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	860	863	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	2	910	Chain	ID=PRO_0000183180;Note=Staphylococcal nuclease domain-containing protein 1
Q7KZF4	806	874	807	821	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	851	857	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	869	871	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	872	887	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O
Q7KZF4	806	874	845	847	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5M9O

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3'-UTR located exon skipping events that lost miRNA binding sites in SND1

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 SND1

- 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 SND1

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 SND1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for SND1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SND1

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 SND1

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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Gene summary for SND1

Gene structures and expression levels for SND1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SND1

Open reading frame (ORF) annotation in the exon skipping event for SND1

Infer the effects of exon skipping event on protein functional features for SND1

3'-UTR located exon skipping events that lost miRNA binding sites in SND1

SNVs in the skipped exons for SND1

AD stage-associated exon skippint events for SND1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SND1

Correlation with RNA binding proteins (RBPs) for SND1

RelatedDrugs for SND1

RelatedDiseases for SND1