ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MEIS1

Gene summary

Gene information	Gene symbol	MEIS1
	Gene ID	4211
	Gene name	Meis homeobox 1
	Synonyms	-
	Cytomap	2p14
	Type of gene	protein-coding
	Description	homeobox protein Meis1Meis1, myeloid ecotropic viral integration site 1 homologWUGSC:H_NH0444B04.1leukemogenic homolog protein
	Modification date	20180523
	UniProtAcc	O00470
	Context	PubMed: MEIS1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene

GO ID

GO term

PubMed ID

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Exon skipping events across known transcript of Ensembl for MEIS1 from UCSC genome browser

Skipped exons in TCGA and GTEx 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.

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Gene isoform structures and expression levels for MEIS1

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for MEIS1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_326061	2	66662689:66663000:66664868:66665095:66666974:66667099	66664868:66665095	ENSG00000143995.15	ENST00000272369.9,ENST00000407092.2,ENST00000488550.1,ENST00000560281.2
exon_skip_326064	2	66664938:66665095:66666974:66667116:66667693:66667744	66666974:66667116	ENSG00000143995.15	ENST00000490726.1,ENST00000272369.9,ENST00000398506.2,ENST00000407092.2,ENST00000488550.1,ENST00000444274.2,ENST00000560281.2
exon_skip_326067	2	66666452:66666803:66666974:66667116:66667693:66667744	66666974:66667116	ENSG00000143995.15	ENST00000495021.2
exon_skip_326068	2	66668545:66668596:66670033:66670180:66691240:66691352	66670033:66670180	ENSG00000143995.15	ENST00000272369.9,ENST00000398506.2,ENST00000437869.1,ENST00000495021.2,ENST00000407092.2,ENST00000488550.1,ENST00000444274.2,ENST00000560281.2
exon_skip_326073	2	66670096:66670180:66691240:66691352:66739280:66739323	66691240:66691352	ENSG00000143995.15	ENST00000409622.1,ENST00000606455.1,ENST00000272369.9,ENST00000398506.2,ENST00000495021.2,ENST00000407092.2,ENST00000488550.1,ENST00000498705.1,ENST00000560281.2
exon_skip_326074	2	66670096:66670180:66691240:66691352:66775074:66775151	66691240:66691352	ENSG00000143995.15	ENST00000444274.2
exon_skip_326077	2	66672324:66672428:66681840:66681926:66691240:66691352	66681840:66681926	ENSG00000143995.15	ENST00000475239.1
exon_skip_326081	2	66691240:66691352:66739280:66739426:66775074:66775151	66739280:66739426	ENSG00000143995.15	ENST00000606455.1,ENST00000272369.9,ENST00000398506.2,ENST00000495021.2,ENST00000475239.1,ENST00000407092.2,ENST00000488550.1,ENST00000560281.2
exon_skip_326082	2	66723157:66723332:66739280:66739426:66775074:66775151	66739280:66739426	ENSG00000143995.15	ENST00000542964.1
exon_skip_326086	2	66775074:66775151:66789213:66789251:66794584:66794632	66789213:66789251	ENSG00000143995.15	ENST00000606455.1
exon_skip_326090	2	66795798:66795888:66796181:66796277:66798377:66798383	66796181:66796277	ENSG00000143995.15	ENST00000409517.1,ENST00000272369.9,ENST00000495021.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MEIS1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_326061	2	66662689:66663000:66664868:66665095:66666974:66667099	66664868:66665095	ENSG00000143995.15	ENST00000560281.2,ENST00000272369.9,ENST00000407092.2,ENST00000488550.1
exon_skip_326064	2	66664938:66665095:66666974:66667116:66667693:66667744	66666974:66667116	ENSG00000143995.15	ENST00000560281.2,ENST00000272369.9,ENST00000407092.2,ENST00000488550.1,ENST00000490726.1,ENST00000398506.2,ENST00000444274.2
exon_skip_326067	2	66666452:66666803:66666974:66667116:66667693:66667744	66666974:66667116	ENSG00000143995.15	ENST00000495021.2
exon_skip_326068	2	66668545:66668596:66670033:66670180:66691240:66691352	66670033:66670180	ENSG00000143995.15	ENST00000560281.2,ENST00000272369.9,ENST00000407092.2,ENST00000488550.1,ENST00000398506.2,ENST00000444274.2,ENST00000495021.2,ENST00000437869.1
exon_skip_326073	2	66670096:66670180:66691240:66691352:66739280:66739323	66691240:66691352	ENSG00000143995.15	ENST00000560281.2,ENST00000272369.9,ENST00000407092.2,ENST00000488550.1,ENST00000398506.2,ENST00000495021.2,ENST00000409622.1,ENST00000498705.1,ENST00000606455.1
exon_skip_326074	2	66670096:66670180:66691240:66691352:66775074:66775151	66691240:66691352	ENSG00000143995.15	ENST00000444274.2
exon_skip_326081	2	66691240:66691352:66739280:66739426:66775074:66775151	66739280:66739426	ENSG00000143995.15	ENST00000560281.2,ENST00000272369.9,ENST00000407092.2,ENST00000488550.1,ENST00000398506.2,ENST00000495021.2,ENST00000606455.1,ENST00000475239.1
exon_skip_326082	2	66723157:66723332:66739280:66739426:66775074:66775151	66739280:66739426	ENSG00000143995.15	ENST00000542964.1
exon_skip_326086	2	66775074:66775151:66789213:66789251:66794584:66794632	66789213:66789251	ENSG00000143995.15	ENST00000606455.1
exon_skip_326090	2	66795798:66795888:66796181:66796277:66798377:66798383	66796181:66796277	ENSG00000143995.15	ENST00000272369.9,ENST00000495021.2,ENST00000409517.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for MEIS1

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000272369	66796181	66796277	3UTR-3CDS
ENST00000272369	66664868	66665095	Frame-shift
ENST00000272369	66666974	66667116	Frame-shift
ENST00000272369	66691240	66691352	Frame-shift
ENST00000272369	66739280	66739426	Frame-shift
ENST00000272369	66670033	66670180	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000272369	66796181	66796277	3UTR-3CDS
ENST00000272369	66664868	66665095	Frame-shift
ENST00000272369	66666974	66667116	Frame-shift
ENST00000272369	66691240	66691352	Frame-shift
ENST00000272369	66739280	66739426	Frame-shift
ENST00000272369	66670033	66670180	In-frame

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Infer the effects of exon skipping event on protein functional features for MEIS1

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000272369	4308	390	66670033	66670180	941	1087	161	210

Loci of skipped exons in GTEx 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
ENST00000272369	4308	390	66670033	66670180	941	1087	161	210

Lost protein functional features of individual exon skipping events in TCGA.

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
O00470	161	210	1	390	Chain	ID=PRO_0000049105;Note=Homeobox protein Meis1
O00470	161	210	194	240	Compositional bias	Note=Ser/Thr-rich

Lost protein functional features of individual exon skipping events in GTEx.

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
O00470	161	210	1	390	Chain	ID=PRO_0000049105;Note=Homeobox protein Meis1
O00470	161	210	194	240	Compositional bias	Note=Ser/Thr-rich

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SNVs in the skipped exons for MEIS1

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A39Y-01	exon_skip_326061	66664869	66665095	66664881	66664881	Frame_Shift_Del	C	-	p.P9fs
LIHC	TCGA-DD-A39Y-01	exon_skip_326061	66664869	66665095	66664890	66664890	Frame_Shift_Del	G	-	p.G13fs
LIHC	TCGA-DD-A3A0-01	exon_skip_326061	66664869	66665095	66664890	66664890	Frame_Shift_Del	G	-	p.G13fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_326061	66664869	66665095	66664929	66664929	Frame_Shift_Del	G	-	p.G25fs
COAD	TCGA-AZ-6598-01	exon_skip_326067 exon_skip_326064	66666975	66667116	66667034	66667034	Frame_Shift_Del	C	-	p.T100fs
COAD	TCGA-A6-6781-01	exon_skip_326081 exon_skip_326082	66739281	66739426	66739308	66739308	Frame_Shift_Del	C	-	p.S257fs
LIHC	TCGA-DD-A1EG-01	exon_skip_326081 exon_skip_326082	66739281	66739426	66739346	66739346	Frame_Shift_Del	A	-	p.K271fs
COAD	TCGA-A6-6780-01	exon_skip_326067 exon_skip_326064	66666975	66667116	66667033	66667034	Frame_Shift_Ins	-	C	p.T100fs
LIHC	TCGA-BC-A10T-01	exon_skip_326081 exon_skip_326082	66739281	66739426	66739382	66739383	Frame_Shift_Ins	-	T	p.S282fs
BLCA	TCGA-XF-A9T0-01	exon_skip_326061	66664869	66665095	66665001	66665001	Nonsense_Mutation	C	T	p.Q49*
KIRC	TCGA-CJ-4902-01	exon_skip_326067 exon_skip_326064	66666975	66667116	66667009	66667009	Nonsense_Mutation	G	T	p.E92*
KIRC	TCGA-CJ-4902-01	exon_skip_326067 exon_skip_326064	66666975	66667116	66667009	66667009	Nonsense_Mutation	G	T	p.E92X
THYM	TCGA-ZB-A96G-01	exon_skip_326067 exon_skip_326064	66666975	66667116	66667042	66667042	Nonsense_Mutation	G	T	p.E103X
LUAD	TCGA-55-A492-01	exon_skip_326068	66670034	66670180	66670040	66670040	Nonsense_Mutation	G	T	p.E164*
HNSC	TCGA-D6-A6EP-01	exon_skip_326073 exon_skip_326074	66691241	66691352	66691249	66691249	Nonsense_Mutation	G	A	p.W213*
CHOL	TCGA-W5-AA36-01	exon_skip_326090	66796182	66796277	66796228	66796228	Nonsense_Mutation	G	A	p.W387X

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
SNUC5_LARGE_INTESTINE	66666975	66667116	66667034	66667034	Frame_Shift_Del	C	-	p.T100fs
SNUC2A_LARGE_INTESTINE	66670034	66670180	66670137	66670140	Frame_Shift_Del	CAGA	-	p.SD196fs
SNUC2B_LARGE_INTESTINE	66670034	66670180	66670137	66670140	Frame_Shift_Del	CAGA	-	p.SD196fs
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66739281	66739426	66739358	66739358	Frame_Shift_Del	A	-	p.K275fs
OVMANA_OVARY	66664869	66665095	66664872	66664872	Missense_Mutation	G	A	p.D6N
HS683_CENTRAL_NERVOUS_SYSTEM	66664869	66665095	66664912	66664912	Missense_Mutation	T	C	p.I19T
KYSE50_OESOPHAGUS	66664869	66665095	66664920	66664920	Missense_Mutation	A	G	p.T22A
NCIH2291_LUNG	66664869	66665095	66664936	66664936	Missense_Mutation	C	A	p.P27Q
MDAPCA2B_PROSTATE	66664869	66665095	66664962	66664962	Missense_Mutation	G	A	p.V36I
A2780_OVARY	66664869	66665095	66664984	66664984	Missense_Mutation	C	G	p.P43R
NCIH889_LUNG	66664869	66665095	66664984	66664984	Missense_Mutation	C	G	p.P43R
AGS_STOMACH	66666975	66667116	66666992	66666992	Missense_Mutation	T	C	p.L86P
SQ1_LUNG	66666975	66667116	66667024	66667024	Missense_Mutation	G	T	p.A97S
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66666975	66667116	66667060	66667060	Missense_Mutation	G	A	p.G109R
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66666975	66667116	66667060	66667060	Missense_Mutation	G	A	p.G109R
SW1783_CENTRAL_NERVOUS_SYSTEM	66670034	66670180	66670064	66670064	Missense_Mutation	C	T	p.R172W
SW954_VULVA	66670034	66670180	66670110	66670110	Missense_Mutation	T	C	p.I187T
BICR18_UPPER_AERODIGESTIVE_TRACT	66670034	66670180	66670151	66670151	Missense_Mutation	A	G	p.I201V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66670034	66670180	66670151	66670151	Missense_Mutation	A	G	p.I201V
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66670034	66670180	66670151	66670151	Missense_Mutation	A	G	p.I201V
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66670034	66670180	66670151	66670151	Missense_Mutation	A	G	p.I201V
K2_SKIN	66670034	66670180	66670154	66670154	Missense_Mutation	A	G	p.T202A
SNU1040_LARGE_INTESTINE	66670034	66670180	66670172	66670172	Missense_Mutation	A	G	p.T208A
LS411N_LARGE_INTESTINE	66691241	66691352	66691310	66691310	Missense_Mutation	G	A	p.G234S
A375_SKIN	66691241	66691352	66691338	66691338	Missense_Mutation	A	G	p.N243S
NCIH1651_LUNG	66691241	66691352	66691339	66691339	Missense_Mutation	C	A	p.N243K
NCIH650_LUNG	66739281	66739426	66739305	66739305	Missense_Mutation	C	A	p.A256D
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66739281	66739426	66739365	66739365	Missense_Mutation	G	A	p.R276H
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66739281	66739426	66739383	66739383	Missense_Mutation	T	C	p.V282A
NCIH1373_LUNG	66739281	66739426	66739400	66739400	Missense_Mutation	A	G	p.R288G
NCIH1373_LUNG	66739281	66739426	66739402	66739402	Missense_Mutation	G	T	p.R288S
HEC59_ENDOMETRIUM	66739281	66739426	66739408	66739408	Missense_Mutation	G	T	p.W290C
ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66666975	66667116	66666975	66666976	Splice_Site	AC	-	p.H81fs

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MEIS1

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MEIS1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MEIS1

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RelatedDrugs for MEIS1

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for MEIS1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MEIS1	C0035258	Restless Legs Syndrome	1	CTD_human
MEIS1	C1458155	Mammary Neoplasms	1	CTD_human

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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