ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RUNX1

Gene summary

Gene information	Gene symbol	RUNX1
	Gene ID	861
	Gene name	RUNX family transcription factor 1
	Synonyms	AML1\|AML1-EVI-1\|AMLCR1\|CBF2alpha\|CBFA2\|EVI-1\|PEBP2aB\|PEBP2alpha
	Cytomap	21q22.12
	Type of gene	protein-coding
	Description	runt-related transcription factor 1AML1-EVI-1 fusion proteinPEA2-alpha BPEBP2-alpha BSL3-3 enhancer factor 1 alpha B subunitSL3/AKV core-binding factor alpha B subunitacute myeloid leukemia 1 proteincore-binding factor, runt domain, alpha subunit 2
	Modification date	20200322
	UniProtAcc	A0A023PPR2, A0A0C4DG58, A8MZI9, C9JWM1, H9KVB1, Q01196, Q2TAM6, U5P039, V9GYT3, V9GYT5, X5C3Z9, X5C404, X5C9T0, X5C9T4, X5CC24, X5CC30, X5CR08, X5CR12, X5CR15, X5CT67, X5CT71,
	Context

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

Gene	GO ID	GO term	PubMed ID
RUNX1	GO:0030097	hemopoiesis	21873977
RUNX1	GO:0045893	positive regulation of transcription, DNA-templated	10207087\|14970218
RUNX1	GO:0045944	positive regulation of transcription by RNA polymerase II	9199349\|10207087\|14970218\|21873977

Top

Gene structures and expression levels for RUNX1

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.

ENSG00000159216

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

Landscape of isoform expressions across multiple brain tissues between AD and control.

Top

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RUNX1

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

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

Top

Open reading frame (ORF) annotation in the exon skipping event for RUNX1

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
ENST00000344691	34834410	34834601	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
ENST00000344691	34834410	34834601	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
ENST00000344691	34834410	34834601	In-frame

Top

Infer the effects of exon skipping event on protein functional features for RUNX1

p-ENSG00000159216_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
ENST00000344691	7291	453	34834410	34834601	2111	2301	177	241

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
ENST00000344691	7291	453	34834410	34834601	2111	2301	177	241

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
ENST00000344691	7291	453	34834410	34834601	2111	2301	177	241

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
Q01196	177	241	137	242	Alternative sequence	ID=VSP_005920;Note=In isoform AML-1FC. VGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQD->VDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQDTRQIQPSPPWSYDQSYQYLGSIASPSVHPATPI;O
Q01196	177	241	178	224	Alternative sequence	ID=VSP_005923;Note=In isoform AML-1FA. RHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRA->SKCIHLGLVHPPGWYTLQAGILRDHVSDSLGSTFPPGGWQAPVKPKS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	178	188	Alternative sequence	ID=VSP_005921;Note=In isoform AML-1FB. RHRQKLDDQTK->NSLTWPRYPHI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	189	453	Alternative sequence	ID=VSP_005922;Note=In isoform AML-1FB. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	225	453	Alternative sequence	ID=VSP_005924;Note=In isoform AML-1FA. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	1	453	Chain	ID=PRO_0000174655;Note=Runt-related transcription factor 1
Q01196	177	241	187	453	Compositional bias	Note=Pro/Ser/Thr-rich
Q01196	177	241	50	178	Domain	Note=Runt;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00399
Q01196	177	241	175	177	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1CMO
Q01196	177	241	193	193	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q01196	177	241	212	212	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569
Q01196	177	241	145	453	Mutagenesis	Note=No DNA-binding. Missing
Q01196	177	241	177	177	Mutagenesis	Note=Strongly reduces DNA-binding. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11276260;Dbxref=PMID:11276260
Q01196	177	241	168	177	Region	Note=Interaction with DNA
Q01196	177	241	177	178	Site	Note=Breakpoint for translocation to form AML1-EMV-1 (or AML1-EAP) in CML and T-MDS%2C to form AML1-MTG8 (ETO) in AML-M2%2C to form AML1-CBFA2T3 in therapy-related myeloid malignancies%2C to form AML1-MECOM in CML and to form type I MACROD1-RUNX1 fusion p
Q01196	177	241	241	242	Site	Note=Breakpoint for translocation to form AML1-EAP in T-MDS and CML%2C to form type II MACROD1-RUNX1 fusion protein and to form RUNX1-CBFA2T2 in acute myeloid leukemia;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20520637;Dbxref=PMID:20520637

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
Q01196	177	241	137	242	Alternative sequence	ID=VSP_005920;Note=In isoform AML-1FC. VGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQD->VDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQDTRQIQPSPPWSYDQSYQYLGSIASPSVHPATPI;O
Q01196	177	241	178	224	Alternative sequence	ID=VSP_005923;Note=In isoform AML-1FA. RHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRA->SKCIHLGLVHPPGWYTLQAGILRDHVSDSLGSTFPPGGWQAPVKPKS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	178	188	Alternative sequence	ID=VSP_005921;Note=In isoform AML-1FB. RHRQKLDDQTK->NSLTWPRYPHI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	189	453	Alternative sequence	ID=VSP_005922;Note=In isoform AML-1FB. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	225	453	Alternative sequence	ID=VSP_005924;Note=In isoform AML-1FA. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	1	453	Chain	ID=PRO_0000174655;Note=Runt-related transcription factor 1
Q01196	177	241	187	453	Compositional bias	Note=Pro/Ser/Thr-rich
Q01196	177	241	50	178	Domain	Note=Runt;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00399
Q01196	177	241	175	177	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1CMO
Q01196	177	241	193	193	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q01196	177	241	212	212	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569
Q01196	177	241	145	453	Mutagenesis	Note=No DNA-binding. Missing
Q01196	177	241	177	177	Mutagenesis	Note=Strongly reduces DNA-binding. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11276260;Dbxref=PMID:11276260
Q01196	177	241	168	177	Region	Note=Interaction with DNA
Q01196	177	241	177	178	Site	Note=Breakpoint for translocation to form AML1-EMV-1 (or AML1-EAP) in CML and T-MDS%2C to form AML1-MTG8 (ETO) in AML-M2%2C to form AML1-CBFA2T3 in therapy-related myeloid malignancies%2C to form AML1-MECOM in CML and to form type I MACROD1-RUNX1 fusion p
Q01196	177	241	241	242	Site	Note=Breakpoint for translocation to form AML1-EAP in T-MDS and CML%2C to form type II MACROD1-RUNX1 fusion protein and to form RUNX1-CBFA2T2 in acute myeloid leukemia;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20520637;Dbxref=PMID:20520637

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
Q01196	177	241	137	242	Alternative sequence	ID=VSP_005920;Note=In isoform AML-1FC. VGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQD->VDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQDTRQIQPSPPWSYDQSYQYLGSIASPSVHPATPI;O
Q01196	177	241	178	224	Alternative sequence	ID=VSP_005923;Note=In isoform AML-1FA. RHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRA->SKCIHLGLVHPPGWYTLQAGILRDHVSDSLGSTFPPGGWQAPVKPKS;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	178	188	Alternative sequence	ID=VSP_005921;Note=In isoform AML-1FB. RHRQKLDDQTK->NSLTWPRYPHI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	189	453	Alternative sequence	ID=VSP_005922;Note=In isoform AML-1FB. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	225	453	Alternative sequence	ID=VSP_005924;Note=In isoform AML-1FA. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q01196	177	241	1	453	Chain	ID=PRO_0000174655;Note=Runt-related transcription factor 1
Q01196	177	241	187	453	Compositional bias	Note=Pro/Ser/Thr-rich
Q01196	177	241	50	178	Domain	Note=Runt;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00399
Q01196	177	241	175	177	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1CMO
Q01196	177	241	193	193	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q01196	177	241	212	212	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:23186163,ECO:0000244\|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569
Q01196	177	241	145	453	Mutagenesis	Note=No DNA-binding. Missing
Q01196	177	241	177	177	Mutagenesis	Note=Strongly reduces DNA-binding. R->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11276260;Dbxref=PMID:11276260
Q01196	177	241	168	177	Region	Note=Interaction with DNA
Q01196	177	241	177	178	Site	Note=Breakpoint for translocation to form AML1-EMV-1 (or AML1-EAP) in CML and T-MDS%2C to form AML1-MTG8 (ETO) in AML-M2%2C to form AML1-CBFA2T3 in therapy-related myeloid malignancies%2C to form AML1-MECOM in CML and to form type I MACROD1-RUNX1 fusion p
Q01196	177	241	241	242	Site	Note=Breakpoint for translocation to form AML1-EAP in T-MDS and CML%2C to form type II MACROD1-RUNX1 fusion protein and to form RUNX1-CBFA2T2 in acute myeloid leukemia;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20520637;Dbxref=PMID:20520637

Top

3'-UTR located exon skipping events that lost miRNA binding sites in RUNX1

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

Top

SNVs in the skipped exons for RUNX1

- 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

Top

AD stage-associated exon skippint events for RUNX1

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

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RUNX1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

Top

Correlation with RNA binding proteins (RBPs) for RUNX1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

Top

RelatedDrugs for RUNX1

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

RelatedDiseases for RUNX1

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

Home

Download

Statistics

Landscape

Help

Contact

Gene summary for RUNX1

Gene structures and expression levels for RUNX1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RUNX1

Open reading frame (ORF) annotation in the exon skipping event for RUNX1

Infer the effects of exon skipping event on protein functional features for RUNX1

3'-UTR located exon skipping events that lost miRNA binding sites in RUNX1

SNVs in the skipped exons for RUNX1

AD stage-associated exon skippint events for RUNX1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RUNX1

Correlation with RNA binding proteins (RBPs) for RUNX1

RelatedDrugs for RUNX1

RelatedDiseases for RUNX1