ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for ANXA2

Gene summary

Gene information	Gene symbol	ANXA2
	Gene ID	302
	Gene name	annexin A2
	Synonyms	ANX2\|ANX2L4\|CAL1H\|HEL-S-270\|LIP2\|LPC2\|LPC2D\|P36\|PAP-IV
	Cytomap	15q22.2
	Type of gene	protein-coding
	Description	annexin A2annexin IIannexin-2calpactin I heavy chaincalpactin I heavy polypeptidecalpactin-1 heavy chainchromobindin 8epididymis secretory protein Li 270epididymis secretory sperm binding proteinlipocortin IIplacental anticoagulant protein IVpr
	Modification date	20200313
	UniProtAcc	A0A024R5Z7, H0YKL9, H0YKN4, H0YKS4, H0YKV8, H0YKX9, H0YKZ7, H0YL33, H0YLE2, H0YLV6, H0YM50, H0YMD0, H0YMD9, H0YMM1, H0YMT9, H0YMU9, H0YMW4, H0YN28, H0YN42, H0YN52, H0YNA0, H0YNB8, H0YNP5, P07355,
	Context

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

Gene	GO ID	GO term	PubMed ID
ANXA2	GO:0001921	positive regulation of receptor recycling	22848640
ANXA2	GO:0031340	positive regulation of vesicle fusion	2138016
ANXA2	GO:0032804	negative regulation of low-density lipoprotein particle receptor catabolic process	22848640
ANXA2	GO:0036035	osteoclast development	7961821
ANXA2	GO:1905581	positive regulation of low-density lipoprotein particle clearance	22848640
ANXA2	GO:1905597	positive regulation of low-density lipoprotein particle receptor binding	22848640
ANXA2	GO:1905602	positive regulation of receptor-mediated endocytosis involved in cholesterol transport	22848640

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Gene structures and expression levels for ANXA2

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.

ENSG00000182718

Differentially expressed gene analysis across multiple brain tissues between AD and control.

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
TC	UP	1.183977e+03	9.809723e-01	5.997910e-13	1.024576e-10

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
PG	UP	ENST00000396024.7	ANXA2-202:protein_coding:ANXA2	4.934520e+00	2.305029e+00	6.521623e-06	3.654553e-04
PG	UP	ENST00000421017.6	ANXA2-203:protein_coding:ANXA2	2.912791e+01	1.324438e+00	3.604282e-04	6.994593e-03
PG	UP	ENST00000560466.5	ANXA2-232:protein_coding:ANXA2	2.542017e+01	1.230376e+00	3.824052e-04	7.304612e-03
PG	UP	ENST00000666172.1	SPANXA2-OT1-205:lncRNA:SPANXA2	4.030931e+00	9.143260e-01	2.444409e-03	2.754165e-02
PG	UP	ENST00000560014.5	ANXA2-228:nonsense_mediated_decay:ANXA2	3.510056e+00	8.022776e-01	3.120023e-03	3.270075e-02
PG	UP	ENST00000559559.5	ANXA2-222:retained_intron:ANXA2	2.372212e+00	1.027895e+00	3.884487e-03	3.830184e-02
CB	UP	ENST00000558985.5	ANXA2-214:protein_coding:ANXA2	7.671845e+00	1.386652e+00	2.161608e-04	1.422705e-03
TC	UP	ENST00000451270.6	ANXA2-204:protein_coding:ANXA2	9.976113e+02	9.957569e-01	3.275914e-13	1.417049e-10
TC	UP	ENST00000561022.5	ANXA2-237:nonsense_mediated_decay:ANXA2	6.170534e+00	1.888733e+00	1.857619e-09	2.193361e-07
TC	UP	ENST00000421017.6	ANXA2-203:protein_coding:ANXA2	9.488825e+01	8.668741e-01	2.385134e-06	8.185866e-05
TC	UP	ENST00000558985.5	ANXA2-214:protein_coding:ANXA2	9.002573e+00	1.509991e+00	1.666610e-05	3.888926e-04
TC	UP	ENST00000560014.5	ANXA2-228:nonsense_mediated_decay:ANXA2	2.954739e+00	1.023289e+00	1.730758e-05	4.001953e-04
TC	UP	ENST00000559780.5	ANXA2-225:protein_coding:ANXA2	1.464375e+00	1.635610e+00	5.998028e-05	1.077249e-03
TC	UP	ENST00000559467.5	ANXA2-221:protein_coding:ANXA2	2.738983e+00	1.727696e+00	1.353175e-04	2.054495e-03
TC	UP	ENST00000558503.5	ANXA2-212:nonsense_mediated_decay:ANXA2	8.641101e-01	2.011947e+00	8.174307e-04	8.453051e-03
TC	UP	ENST00000559370.5	ANXA2-220:protein_coding:ANXA2	1.762482e+00	8.948173e-01	5.978716e-03	3.824443e-02
TC	UP	ENST00000557937.5	ANXA2-208:lncRNA:ANXA2	8.155373e-01	1.095157e+00	7.957154e-03	4.733027e-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 ANXA2

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_114797	chr15	60386028:60386086:60397258:60397338:60397943:60397964	60397258:60397338
exon_skip_135671	chr15	60360967:60361054:60364429:60364523:60386028:60386086	60364429:60364523
exon_skip_139334	chr15	60347404:60347689:60349075:60349197:60351193:60351251	60349075:60349197
exon_skip_143900	chr15	60386028:60386086:60393038:60393440:60397943:60397974	60393038:60393440
exon_skip_145376	chr15	60364429:60364523:60386028:60386086:60397258:60397338	60386028:60386086
exon_skip_146423	chr15	60360941:60361054:60364429:60364523:60386028:60386086	60364429:60364523
exon_skip_17588	chr15	60364429:60364523:60386028:60386086:60397943:60397986	60386028:60386086
exon_skip_178432	chr15	60386028:60386086:60396373:60396427:60397943:60397964	60396373:60396427
exon_skip_221011	chr15	60386033:60386086:60393038:60393440:60397943:60397964	60393038:60393440
exon_skip_230153	chr15	60364429:60364523:60397258:60397338:60397943:60397986	60397258:60397338
exon_skip_254696	chr15	60386028:60386086:60393038:60393440:60397943:60397964	60393038:60393440
exon_skip_258726	chr15	60364429:60364523:60374619:60374682:60382342:60382441	60374619:60374682
exon_skip_261565	chr15	60386033:60386086:60397258:60397338:60397943:60397964	60397258:60397338
exon_skip_26299	chr15	60386028:60386086:60396151:60396427:60397943:60397964	60396151:60396427
exon_skip_269816	chr15	60386028:60386086:60390213:60390317:60397943:60397986	60390213:60390317
exon_skip_271758	chr15	60364476:60364523:60382342:60382441:60386028:60386086	60382342:60382441
exon_skip_283388	chr15	60396373:60396427:60397258:60397338:60397943:60397964	60397258:60397338
exon_skip_39853	chr15	60364492:60364523:60382342:60382441:60386028:60386086	60382342:60382441
exon_skip_72783	chr15	60386028:60386086:60390213:60390317:60397943:60397964	60390213:60390317
exon_skip_81611	chr15	60357194:60357236:60360941:60361054:60364429:60364523	60360941:60361054
exon_skip_88064	chr15	60386028:60386086:60396151:60396427:60397258:60397338	60396151:60396427
exon_skip_88549	chr15	60396373:60396427:60397258:60397338:60397943:60397986	60397258:60397338
exon_skip_96545	chr15	60347337:60347689:60349075:60349197:60351193:60351251	60349075:60349197

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 ANXA2

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
ENST00000421017	60397258	60397338	3UTR-3UTR
ENST00000396024	60382342	60382441	Frame-shift
ENST00000421017	60382342	60382441	Frame-shift
ENST00000451270	60382342	60382441	Frame-shift
ENST00000396024	60349075	60349197	In-frame
ENST00000421017	60349075	60349197	In-frame
ENST00000451270	60349075	60349197	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
ENST00000421017	60397258	60397338	3UTR-3UTR
ENST00000396024	60382342	60382441	Frame-shift
ENST00000421017	60382342	60382441	Frame-shift
ENST00000451270	60382342	60382441	Frame-shift

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
ENST00000421017	60397258	60397338	3UTR-3UTR
ENST00000396024	60382342	60382441	Frame-shift
ENST00000421017	60382342	60382441	Frame-shift
ENST00000451270	60382342	60382441	Frame-shift
ENST00000396024	60360941	60361054	In-frame
ENST00000421017	60360941	60361054	In-frame
ENST00000451270	60360941	60361054	In-frame

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Infer the effects of exon skipping event on protein functional features for ANXA2

p-ENSG00000182718_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
ENST00000396024	1693	339	60349075	60349197	998	1119	279	319
ENST00000421017	1461	339	60349075	60349197	974	1095	279	319
ENST00000451270	1452	339	60349075	60349197	950	1071	279	319

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
ENST00000396024	1693	339	60360941	60361054	404	516	81	118
ENST00000421017	1461	339	60360941	60361054	380	492	81	118
ENST00000451270	1452	339	60360941	60361054	356	468	81	118

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
P07355	279	319	279	282	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	279	282	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	279	282	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	2	339	Chain	ID=PRO_0000067470;Note=Annexin A2
P07355	279	319	2	339	Chain	ID=PRO_0000067470;Note=Annexin A2
P07355	279	319	2	339	Chain	ID=PRO_0000067470;Note=Annexin A2
P07355	279	319	285	295	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	285	295	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	285	295	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	300	311	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	300	311	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	300	311	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	315	322	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	315	322	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	315	322	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	274	334	Repeat	Note=Annexin 4
P07355	279	319	274	334	Repeat	Note=Annexin 4
P07355	279	319	274	334	Repeat	Note=Annexin 4
P07355	279	319	293	293	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P07355	279	319	293	293	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P07355	279	319	293	293	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P07355	279	319	296	298	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	296	298	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	279	319	296	298	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV

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
P07355	81	118	2	339	Chain	ID=PRO_0000067470;Note=Annexin A2
P07355	81	118	2	339	Chain	ID=PRO_0000067470;Note=Annexin A2
P07355	81	118	2	339	Chain	ID=PRO_0000067470;Note=Annexin A2
P07355	81	118	83	90	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	83	90	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	83	90	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	93	103	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	93	103	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	93	103	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	106	117	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	106	117	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	106	117	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2HYV
P07355	81	118	77	81	Mutagenesis	Note=Strongly decreases interaction with PCSK9. RRTKK->AATAA;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18799458,ECO:0000269\|PubMed:22848640;Dbxref=PMID:18799458,PMID:22848640
P07355	81	118	77	81	Mutagenesis	Note=Strongly decreases interaction with PCSK9. RRTKK->AATAA;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18799458,ECO:0000269\|PubMed:22848640;Dbxref=PMID:18799458,PMID:22848640
P07355	81	118	77	81	Mutagenesis	Note=Strongly decreases interaction with PCSK9. RRTKK->AATAA;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18799458,ECO:0000269\|PubMed:22848640;Dbxref=PMID:18799458,PMID:22848640
P07355	81	118	80	84	Mutagenesis	Note=No effect on interaction with PCSK9. KKELA->GKPLD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18799458;Dbxref=PMID:18799458
P07355	81	118	80	84	Mutagenesis	Note=No effect on interaction with PCSK9. KKELA->GKPLD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18799458;Dbxref=PMID:18799458
P07355	81	118	80	84	Mutagenesis	Note=No effect on interaction with PCSK9. KKELA->GKPLD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18799458;Dbxref=PMID:18799458
P07355	81	118	88	88	Mutagenesis	Note=Strongly decreases interaction with PCSK9%3B when associated with 77-A--A-80. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18799458;Dbxref=PMID:18799458
P07355	81	118	88	88	Mutagenesis	Note=Strongly decreases interaction with PCSK9%3B when associated with 77-A--A-80. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18799458;Dbxref=PMID:18799458
P07355	81	118	88	88	Mutagenesis	Note=Strongly decreases interaction with PCSK9%3B when associated with 77-A--A-80. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18799458;Dbxref=PMID:18799458
P07355	81	118	98	98	Natural variant	ID=VAR_012982;Note=Polymorphism%3B does not affect interaction with PCSK9. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:22848640;Dbxref=dbSNP:rs17845226,PMID:15489334,PMID:22848640
P07355	81	118	98	98	Natural variant	ID=VAR_012982;Note=Polymorphism%3B does not affect interaction with PCSK9. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:22848640;Dbxref=dbSNP:rs17845226,PMID:15489334,PMID:22848640
P07355	81	118	98	98	Natural variant	ID=VAR_012982;Note=Polymorphism%3B does not affect interaction with PCSK9. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:22848640;Dbxref=dbSNP:rs17845226,PMID:15489334,PMID:22848640
P07355	81	118	42	102	Repeat	Note=Annexin 1
P07355	81	118	42	102	Repeat	Note=Annexin 1
P07355	81	118	42	102	Repeat	Note=Annexin 1
P07355	81	118	114	174	Repeat	Note=Annexin 2
P07355	81	118	114	174	Repeat	Note=Annexin 2
P07355	81	118	114	174	Repeat	Note=Annexin 2

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3'-UTR located exon skipping events that lost miRNA binding sites in ANXA2

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	ENST00000421017	60397258	60397338	hsa-miR-6794-3p	chr15:60397303-60397310	8mer-1a	chr15:60397294-60397315	145.00	-16.83
MSBB	ENST00000421017	60397258	60397338	hsa-miR-6794-3p	chr15:60397303-60397310	8mer-1a	chr15:60397294-60397315	145.00	-16.83
ROSMAP	ENST00000421017	60397258	60397338	hsa-miR-6794-3p	chr15:60397303-60397310	8mer-1a	chr15:60397294-60397315	145.00	-16.83

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SNVs in the skipped exons for ANXA2

- 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 ANXA2

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 ANXA2

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 ANXA2

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for ANXA2

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P07355	approved	DB00031	Tenecteplase	biotech	P07355
P07355	approved\|investigational\|vet_approved	DB00591	Fluocinolone acetonide	small molecule	P07355

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RelatedDiseases for ANXA2

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 ANXA2

Gene structures and expression levels for ANXA2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ANXA2

Open reading frame (ORF) annotation in the exon skipping event for ANXA2

Infer the effects of exon skipping event on protein functional features for ANXA2

3'-UTR located exon skipping events that lost miRNA binding sites in ANXA2

SNVs in the skipped exons for ANXA2

AD stage-associated exon skippint events for ANXA2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ANXA2

Correlation with RNA binding proteins (RBPs) for ANXA2

RelatedDrugs for ANXA2

RelatedDiseases for ANXA2