ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for TRIP12

Gene summary

Gene information	Gene symbol	TRIP12
	Gene ID	9320
	Gene name	thyroid hormone receptor interactor 12
	Synonyms	MRD49\|TRIP-12\|TRIPC\|ULF
	Cytomap	2q36.3
	Type of gene	protein-coding
	Description	E3 ubiquitin-protein ligase TRIP12E3 ubiquitin-protein ligase for ArfHECT-type E3 ubiquitin transferase TRIP12TR-interacting protein 12probable E3 ubiquitin-protein ligase TRIP12thyroid receptor interacting protein 12
	Modification date	20200313
	UniProtAcc	C9JLD7, C9JLJ5, C9JSX9, F8W9P3, G5E9G6, H7C1L9, H7C2Y1, L0R5E3, Q14669, Q57Z94,
	Context

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

Gene	GO ID	GO term	PubMed ID
TRIP12	GO:0000209	protein polyubiquitination	30982744
TRIP12	GO:0006511	ubiquitin-dependent protein catabolic process	18627766\|20208519\|30982744

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Gene structures and expression levels for TRIP12

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.

ENSG00000153827

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	UP	ENST00000389045.7	TRIP12-204:protein_coding:TRIP12	4.695373e+02	9.156271e-01	6.673948e-05	5.251621e-04
CB	UP	ENST00000389044.8	TRIP12-203:protein_coding:TRIP12	1.216566e+02	1.135425e+00	5.100118e-03	2.000384e-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 TRIP12

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_101132	chr2	229829193:229829288:229830756:229830821:229836848:229836984	229830756:229830821
exon_skip_104852	chr2	229769231:229769325:229771519:229771632:229774097:229774261	229771519:229771632
exon_skip_120401	chr2	229810957:229811045:229811136:229811204:229813870:229814031	229811136:229811204
exon_skip_126076	chr2	229859376:229859574:229860406:229860531:229879982:229880128	229860406:229860531
exon_skip_143535	chr2	229795179:229795330:229796591:229796782:229797690:229797831	229796591:229796782
exon_skip_153005	chr2	229879982:229880128:229900737:229900858:229921880:229921903	229900737:229900858
exon_skip_164790	chr2	229771519:229771632:229774097:229774261:229777315:229777407	229774097:229774261
exon_skip_185496	chr2	229811136:229811204:229813870:229814031:229814233:229814325	229813870:229814031
exon_skip_193820	chr2	229788798:229788940:229789611:229789762:229791124:229791251	229789611:229789762
exon_skip_242161	chr2	229771519:229771632:229774097:229774261:229777315:229777479	229774097:229774261
exon_skip_243482	chr2	229840822:229840927:229858772:229859574:229879982:229880128	229858772:229859574
exon_skip_24909	chr2	229879982:229880128:229900737:229900858:229921880:229921994	229900737:229900858
exon_skip_255103	chr2	229798875:229799049:229799283:229799383:229802252:229802459	229799283:229799383
exon_skip_256175	chr2	229774097:229774261:229777315:229777479:229778433:229778465	229777315:229777479
exon_skip_25928	chr2	229829193:229829288:229830756:229830839:229836848:229836984	229830756:229830839
exon_skip_262972	chr2	229803571:229803689:229803999:229804227:229805730:229805802	229803999:229804227
exon_skip_272205	chr2	229830756:229830839:229836848:229836984:229840822:229840927	229836848:229836984
exon_skip_296453	chr2	229859521:229859574:229860406:229860531:229879982:229880128	229860406:229860531
exon_skip_55759	chr2	229785757:229785855:229787505:229787661:229788798:229788940	229787505:229787661
exon_skip_62634	chr2	229859376:229859574:229879982:229880128:229921880:229921903	229879982:229880128
exon_skip_85056	chr2	229796591:229796782:229797690:229797831:229798875:229799049	229797690:229797831
exon_skip_89433	chr2	229767441:229767750:229768616:229768719:229769231:229769325	229768616:229768719

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 TRIP12

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
ENST00000283943	229787505	229787661	Frame-shift
ENST00000283943	229797690	229797831	Frame-shift
ENST00000283943	229799283	229799383	Frame-shift
ENST00000283943	229858772	229859574	Frame-shift
ENST00000283943	229771519	229771632	In-frame
ENST00000283943	229774097	229774261	In-frame
ENST00000283943	229777315	229777479	In-frame
ENST00000283943	229796591	229796782	In-frame
ENST00000283943	229813870	229814031	In-frame
ENST00000283943	229830756	229830821	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
ENST00000283943	229787505	229787661	Frame-shift
ENST00000283943	229799283	229799383	Frame-shift
ENST00000283943	229858772	229859574	Frame-shift
ENST00000283943	229774097	229774261	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
ENST00000283943	229768616	229768719	Frame-shift
ENST00000283943	229787505	229787661	Frame-shift
ENST00000283943	229789611	229789762	Frame-shift
ENST00000283943	229797690	229797831	Frame-shift
ENST00000283943	229799283	229799383	Frame-shift
ENST00000283943	229803999	229804227	Frame-shift
ENST00000283943	229858772	229859574	Frame-shift
ENST00000283943	229771519	229771632	In-frame
ENST00000283943	229774097	229774261	In-frame
ENST00000283943	229811136	229811204	In-frame
ENST00000283943	229813870	229814031	In-frame
ENST00000283943	229830756	229830821	In-frame

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Infer the effects of exon skipping event on protein functional features for TRIP12

p-ENSG00000153827_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
ENST00000283943	9891	1992	229830756	229830821	1324	1388	381	403
ENST00000283943	9891	1992	229813870	229814031	1860	2020	560	613
ENST00000283943	9891	1992	229796591	229796782	3579	3769	1133	1196
ENST00000283943	9891	1992	229777315	229777479	5319	5482	1713	1767
ENST00000283943	9891	1992	229774097	229774261	5484	5647	1768	1822
ENST00000283943	9891	1992	229771519	229771632	5649	5761	1823	1860

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
ENST00000283943	9891	1992	229774097	229774261	5484	5647	1768	1822

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
ENST00000283943	9891	1992	229830756	229830821	1324	1388	381	403
ENST00000283943	9891	1992	229813870	229814031	1860	2020	560	613
ENST00000283943	9891	1992	229811136	229811204	2022	2089	614	636
ENST00000283943	9891	1992	229774097	229774261	5484	5647	1768	1822
ENST00000283943	9891	1992	229771519	229771632	5649	5761	1823	1860

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
Q14669	381	403	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	381	403	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	381	403	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	560	613	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	560	613	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	560	613	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1133	1196	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1133	1196	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1133	1196	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1713	1767	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1713	1767	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1713	1767	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1713	1767	1449	1992	Natural variant	ID=VAR_080435;Note=In MRD49. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28251352;Dbxref=PMID:28251352
Q14669	1768	1822	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1768	1822	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	1449	1992	Natural variant	ID=VAR_080435;Note=In MRD49. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28251352;Dbxref=PMID:28251352
Q14669	1823	1860	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1823	1860	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1823	1860	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1823	1860	1449	1992	Natural variant	ID=VAR_080435;Note=In MRD49. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28251352;Dbxref=PMID:28251352
Q14669	1823	1860	1840	1840	Natural variant	ID=VAR_080438;Note=In MRD49. S->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077

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
Q14669	1768	1822	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1768	1822	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	1449	1992	Natural variant	ID=VAR_080435;Note=In MRD49. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28251352;Dbxref=PMID:28251352

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
Q14669	381	403	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	381	403	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	381	403	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	560	613	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	560	613	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	560	613	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	614	636	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	614	636	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	614	636	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1768	1822	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1768	1822	1449	1992	Natural variant	ID=VAR_080435;Note=In MRD49. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28251352;Dbxref=PMID:28251352
Q14669	1823	1860	2	1992	Chain	ID=PRO_0000173872;Note=E3 ubiquitin-protein ligase TRIP12
Q14669	1823	1860	338	1992	Natural variant	ID=VAR_080432;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1823	1860	352	1992	Natural variant	ID=VAR_080433;Note=In MRD49%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077
Q14669	1823	1860	1449	1992	Natural variant	ID=VAR_080435;Note=In MRD49. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28251352;Dbxref=PMID:28251352
Q14669	1823	1860	1840	1840	Natural variant	ID=VAR_080438;Note=In MRD49. S->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27848077;Dbxref=PMID:27848077

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3'-UTR located exon skipping events that lost miRNA binding sites in TRIP12

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 TRIP12

- 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 TRIP12

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

ADstage

MSBB

IFG

exon_skip_126076

-3.799126e-01

4.613718e-02

chr2

229859376

229859574

229860406

229860531

229879982

229880128

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TRIP12

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 TRIP12

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM45	exon_skip_126076	5.095016e-01	9.448913e-12
FL	HNRNPA0	exon_skip_126076	4.207480e-01	9.107192e-10
FL	RBM45	exon_skip_126076	4.064271e-01	3.737358e-09
HCC	PTBP1	exon_skip_296453	-4.768797e-01	1.110265e-16
IFG	PTBP1	exon_skip_126076	-4.286541e-01	2.284943e-02
PCC	PTBP1	exon_skip_126076	-5.703365e-01	7.989497e-19
TC	PTBP1	exon_skip_126076	-4.816346e-01	1.136133e-10

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RelatedDrugs for TRIP12

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 TRIP12

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 TRIP12

Gene structures and expression levels for TRIP12

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TRIP12

Open reading frame (ORF) annotation in the exon skipping event for TRIP12

Infer the effects of exon skipping event on protein functional features for TRIP12

3'-UTR located exon skipping events that lost miRNA binding sites in TRIP12

SNVs in the skipped exons for TRIP12

AD stage-associated exon skippint events for TRIP12

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TRIP12

Correlation with RNA binding proteins (RBPs) for TRIP12

RelatedDrugs for TRIP12

RelatedDiseases for TRIP12