ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MLF1

Gene summary

Gene information	Gene symbol	MLF1
	Gene ID	4291
	Gene name	myeloid leukemia factor 1
	Synonyms	-
	Cytomap	3q25.32
	Type of gene	protein-coding
	Description	myeloid leukemia factor 1myelodysplasia-myeloid leukemia factor 1testis tissue sperm-binding protein Li 49e
	Modification date	20180523
	UniProtAcc	P58340
	Context	PubMed: MLF1 [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
MLF1	GO:0007050	cell cycle arrest	15861129

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Exon skipping events across known transcript of Ensembl for MLF1 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 MLF1

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 MLF1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_379045	3	158288998:158289136:158291086:158291222:158310222:158310370	158291086:158291222	ENSG00000178053.13	ENST00000482628.1
exon_skip_379046	3	158289049:158289136:158300444:158300718:158310222:158310370	158300444:158300718	ENSG00000178053.13	ENST00000478894.2,ENST00000392822.3
exon_skip_379047	3	158289049:158289136:158306640:158306713:158310222:158310370	158306640:158306713	ENSG00000178053.13	ENST00000487838.1
exon_skip_379048	3	158288982:158289136:158306648:158306713:158310222:158310370	158306648:158306713	ENSG00000178053.13	ENST00000495452.1
exon_skip_379049	3	158289049:158289136:158310222:158310370:158314650:158314734	158310222:158310370	ENSG00000178053.13	ENST00000355893.5
exon_skip_379056	3	158288983:158289180:158306640:158306713:158310222:158310370	158306640:158306713	ENSG00000178053.13	ENST00000469452.1,ENST00000471745.1,ENST00000484955.1
exon_skip_379057	3	158288983:158289180:158310222:158310370:158314650:158314734	158310222:158310370	ENSG00000178053.13	ENST00000359117.5
exon_skip_379060	3	158288983:158289180:158314650:158314734:158315868:158315949	158314650:158314734	ENSG00000178053.13	ENST00000498592.1
exon_skip_379062	3	158310222:158310370:158311170:158311210:158314650:158314734	158311170:158311210	ENSG00000178053.13	ENST00000497004.1
exon_skip_379064	3	158310222:158310370:158311170:158311215:158314650:158314734	158311170:158311215	ENSG00000178053.13	ENST00000478894.2,ENST00000466246.1,ENST00000477042.1,ENST00000471745.1,ENST00000392822.3
exon_skip_379066	3	158310222:158310370:158314650:158314734:158315868:158315949	158314650:158314734	ENSG00000178053.13	ENST00000482628.1,ENST00000355893.5,ENST00000495452.1,ENST00000359117.5,ENST00000484955.1,ENST00000487838.1
exon_skip_379068	3	158314657:158314734:158315868:158315997:158317802:158317962	158315868:158315997	ENSG00000178053.13	ENST00000478894.2,ENST00000498592.1,ENST00000482628.1,ENST00000355893.5,ENST00000466246.1,ENST00000495452.1,ENST00000477042.1,ENST00000471745.1,ENST00000359117.5,ENST00000484955.1,ENST00000392822.3,ENST00000497004.1,ENST00000491767.1
exon_skip_379070	3	158317802:158317962:158320595:158320728:158322885:158322981	158320595:158320728	ENSG00000178053.13	ENST00000478894.2,ENST00000482628.1,ENST00000355893.5,ENST00000469452.1,ENST00000471745.1,ENST00000359117.5,ENST00000484955.1,ENST00000392822.3,ENST00000497004.1,ENST00000491767.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MLF1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_379045	3	158288998:158289136:158291086:158291222:158310222:158310370	158291086:158291222	ENSG00000178053.13	ENST00000482628.1
exon_skip_379046	3	158289049:158289136:158300444:158300718:158310222:158310370	158300444:158300718	ENSG00000178053.13	ENST00000478894.2,ENST00000392822.3
exon_skip_379047	3	158289049:158289136:158306640:158306713:158310222:158310370	158306640:158306713	ENSG00000178053.13	ENST00000487838.1
exon_skip_379048	3	158288982:158289136:158306648:158306713:158310222:158310370	158306648:158306713	ENSG00000178053.13	ENST00000495452.1
exon_skip_379049	3	158289049:158289136:158310222:158310370:158314650:158314734	158310222:158310370	ENSG00000178053.13	ENST00000355893.5
exon_skip_379056	3	158288983:158289180:158306640:158306713:158310222:158310370	158306640:158306713	ENSG00000178053.13	ENST00000484955.1,ENST00000471745.1,ENST00000469452.1
exon_skip_379057	3	158288983:158289180:158310222:158310370:158314650:158314734	158310222:158310370	ENSG00000178053.13	ENST00000359117.5
exon_skip_379060	3	158288983:158289180:158314650:158314734:158315868:158315949	158314650:158314734	ENSG00000178053.13	ENST00000498592.1
exon_skip_379062	3	158310222:158310370:158311170:158311210:158314650:158314734	158311170:158311210	ENSG00000178053.13	ENST00000497004.1
exon_skip_379064	3	158310222:158310370:158311170:158311215:158314650:158314734	158311170:158311215	ENSG00000178053.13	ENST00000477042.1,ENST00000471745.1,ENST00000478894.2,ENST00000392822.3,ENST00000466246.1
exon_skip_379066	3	158310222:158310370:158314650:158314734:158315868:158315949	158314650:158314734	ENSG00000178053.13	ENST00000355893.5,ENST00000484955.1,ENST00000359117.5,ENST00000495452.1,ENST00000482628.1,ENST00000487838.1
exon_skip_379068	3	158314657:158314734:158315868:158315997:158317802:158317962	158315868:158315997	ENSG00000178053.13	ENST00000491767.1,ENST00000355893.5,ENST00000484955.1,ENST00000359117.5,ENST00000498592.1,ENST00000477042.1,ENST00000495452.1,ENST00000471745.1,ENST00000497004.1,ENST00000482628.1,ENST00000478894.2,ENST00000392822.3,ENST00000466246.1
exon_skip_379070	3	158317802:158317962:158320595:158320728:158322885:158322981	158320595:158320728	ENSG00000178053.13	ENST00000491767.1,ENST00000355893.5,ENST00000484955.1,ENST00000359117.5,ENST00000471745.1,ENST00000497004.1,ENST00000469452.1,ENST00000482628.1,ENST00000478894.2,ENST00000392822.3

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 MLF1

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
ENST00000355893	158310222	158310370	Frame-shift
ENST00000355893	158320595	158320728	Frame-shift
ENST00000355893	158314650	158314734	In-frame
ENST00000355893	158315868	158315997	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
ENST00000355893	158310222	158310370	Frame-shift
ENST00000355893	158320595	158320728	Frame-shift
ENST00000355893	158314650	158314734	In-frame
ENST00000355893	158315868	158315997	In-frame

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Infer the effects of exon skipping event on protein functional features for MLF1

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
ENST00000355893	2220	268	158314650	158314734	334	417	65	93
ENST00000355893	2220	268	158315868	158315997	418	546	93	136

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
ENST00000355893	2220	268	158314650	158314734	334	417	65	93
ENST00000355893	2220	268	158315868	158315997	418	546	93	136

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
P58340	65	93	65	65	Alternative sequence	ID=VSP_043726;Note=In isoform 3 and isoform 4. T->TATSCSLVPFGDFGGM;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P58340	65	93	1	268	Chain	ID=PRO_0000220752;Note=Myeloid leukemia factor 1
P58340	65	93	50	125	Region	Note=Interaction with COPS3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15861129;Dbxref=PMID:15861129
P58340	93	136	94	136	Alternative sequence	ID=VSP_043131;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P58340	93	136	1	268	Chain	ID=PRO_0000220752;Note=Myeloid leukemia factor 1
P58340	93	136	50	125	Region	Note=Interaction with COPS3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15861129;Dbxref=PMID:15861129

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
P58340	65	93	65	65	Alternative sequence	ID=VSP_043726;Note=In isoform 3 and isoform 4. T->TATSCSLVPFGDFGGM;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P58340	65	93	1	268	Chain	ID=PRO_0000220752;Note=Myeloid leukemia factor 1
P58340	65	93	50	125	Region	Note=Interaction with COPS3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15861129;Dbxref=PMID:15861129
P58340	93	136	94	136	Alternative sequence	ID=VSP_043131;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
P58340	93	136	1	268	Chain	ID=PRO_0000220752;Note=Myeloid leukemia factor 1
P58340	93	136	50	125	Region	Note=Interaction with COPS3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15861129;Dbxref=PMID:15861129

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SNVs in the skipped exons for MLF1

- 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
BLCA	TCGA-S5-A6DX-01	exon_skip_379057 exon_skip_379049	158310223	158310370	158310242	158310242	Nonsense_Mutation	C	T	p.R23*
UCEC	TCGA-B5-A11E-01	exon_skip_379057 exon_skip_379049	158310223	158310370	158310254	158310254	Nonsense_Mutation	C	T	p.R27*
UCEC	TCGA-BS-A0TC-01	exon_skip_379057 exon_skip_379049	158310223	158310370	158310341	158310341	Nonsense_Mutation	G	T	p.G56*
SKCM	TCGA-FR-A3YO-06	exon_skip_379060 exon_skip_379066	158314651	158314734	158314672	158314672	Nonsense_Mutation	C	T	p.Q48*
SKCM	TCGA-FR-A3YO-06	exon_skip_379060 exon_skip_379066	158314651	158314734	158314672	158314672	Nonsense_Mutation	C	T	p.Q63X
CHOL	TCGA-W5-AA39-01	exon_skip_379068	158315869	158315997	158315944	158315944	Nonsense_Mutation	G	T	p.E150X
STAD	TCGA-F1-6874-01	exon_skip_379070	158320596	158320728	158320655	158320655	Nonsense_Mutation	C	T	p.R210*
STAD	TCGA-F1-6874-01	exon_skip_379070	158320596	158320728	158320655	158320655	Nonsense_Mutation	C	T	p.R241X
COAD	TCGA-AA-A00J-01	exon_skip_379070	158320596	158320728	158320712	158320712	Nonsense_Mutation	C	T	p.R219X

- 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
KINGS1_CENTRAL_NERVOUS_SYSTEM	158315869	158315997	158315907	158315910	Frame_Shift_Del	TTCT	-	p.CS106fs
NCIH1581_LUNG	158310223	158310370	158310239	158310239	Missense_Mutation	C	G	p.H22D
NCIH2077_LUNG	158310223	158310370	158310239	158310239	Missense_Mutation	C	G	p.H22D
HEC251_ENDOMETRIUM	158310223	158310370	158310363	158310363	Missense_Mutation	C	A	p.S63Y
LN443_CENTRAL_NERVOUS_SYSTEM	158314651	158314734	158314667	158314667	Missense_Mutation	C	A	p.S71Y
DOTC24510_CERVIX	158314651	158314734	158314702	158314702	Missense_Mutation	A	G	p.R83G
LB996RCC_KIDNEY	158314651	158314734	158314729	158314729	Missense_Mutation	A	G	p.N92D
HT115_LARGE_INTESTINE	158315869	158315997	158315887	158315887	Missense_Mutation	C	T	p.P100S
MAC2A_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	158315869	158315997	158315912	158315912	Missense_Mutation	C	T	p.S108F
HEC251_ENDOMETRIUM	158320596	158320728	158320661	158320661	Missense_Mutation	A	G	p.N212D
639V_URINARY_TRACT	158320596	158320728	158320667	158320667	Missense_Mutation	G	A	p.G214R
HEC251_ENDOMETRIUM	158315869	158315997	158315983	158315983	Nonsense_Mutation	C	T	p.R132*
NCIH835_LUNG	158320596	158320728	158320655	158320655	Nonsense_Mutation	C	T	p.R210*
HT115_LARGE_INTESTINE	158314651	158314734	158314734	158314734	Splice_Site	C	T	p.F93F

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MLF1

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
exon_skip_379070	3	158317802:158317962:158320595:158320728:158322885:158322981	158320595:158320728	ENST00000478894.2,ENST00000482628.1,ENST00000355893.5,ENST00000469452.1,ENST00000471745.1,ENST00000359117.5,ENST00000484955.1,ENST00000392822.3,ENST00000497004.1,ENST00000491767.1	HNSC	rs4875	chr3:158320597	T/C	1.27e-03
exon_skip_379070	3	158317802:158317962:158320595:158320728:158322885:158322981	158320595:158320728	ENST00000478894.2,ENST00000482628.1,ENST00000355893.5,ENST00000469452.1,ENST00000471745.1,ENST00000359117.5,ENST00000484955.1,ENST00000392822.3,ENST00000497004.1,ENST00000491767.1	LGG	rs4875	chr3:158320597	T/C	9.05e-04
exon_skip_379070	3	158317802:158317962:158320595:158320728:158322885:158322981	158320595:158320728	ENST00000478894.2,ENST00000482628.1,ENST00000355893.5,ENST00000469452.1,ENST00000471745.1,ENST00000359117.5,ENST00000484955.1,ENST00000392822.3,ENST00000497004.1,ENST00000491767.1	LUSC	rs4875	chr3:158320597	T/C	8.09e-04
exon_skip_379070	3	158317802:158317962:158320595:158320728:158322885:158322981	158320595:158320728	ENST00000478894.2,ENST00000482628.1,ENST00000355893.5,ENST00000469452.1,ENST00000471745.1,ENST00000359117.5,ENST00000484955.1,ENST00000392822.3,ENST00000497004.1,ENST00000491767.1	LUSC	rs4875	chr3:158320597	T/C	2.95e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MLF1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MLF1

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RelatedDrugs for MLF1

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 MLF1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MLF1	C0038356	Stomach 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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