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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 36086

FusionGeneSummary for SRSF1_LMO4

check button Fusion gene summary
Fusion gene informationFusion gene name: SRSF1_LMO4
Fusion gene ID: 36086
HgeneTgene
Gene symbol

SRSF1

LMO4

Gene ID

6426

8543

Gene nameserine and arginine rich splicing factor 1LIM domain only 4
SynonymsASF|SF2|SF2p33|SFRS1|SRp30a-
Cytomap

17q22

1p22.3

Type of geneprotein-codingprotein-coding
Descriptionserine/arginine-rich splicing factor 1SR splicing factor 1alternative-splicing factor 1pre-mRNA-splicing factor SF2, P33 subunitsplicing factor 2splicing factor, arginine/serine-rich, 30-KD, ALIM domain transcription factor LMO4LIM domain only protein 4LIM-only 4 proteinLMO-4breast tumor autoantigen
Modification date2018052320180519
UniProtAcc

Q07955

P61968

Ensembl transtripts involved in fusion geneENST00000582730, ENST00000581497, 
ENST00000584773, ENST00000585096, 
ENST00000258962, 		ENST00000370544, 
ENST00000370542, ENST00000489303, 
Fusion gene scores* DoF score3 X 3 X 2=183 X 3 X 1=9
# samples 33
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SRSF1 [Title/Abstract] AND LMO4 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSRSF1

GO:0000380

alternative mRNA splicing, via spliceosome

8940107

HgeneSRSF1

GO:0000395

mRNA 5'-splice site recognition

8940107|9885563


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1CN301095SRSF1chr17

56083241

-LMO4chr1

87810839

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3UTRENST00000582730ENST00000370544SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000582730ENST00000370542SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-intronENST00000582730ENST00000489303SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000581497ENST00000370544SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000581497ENST00000370542SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-intronENST00000581497ENST00000489303SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000584773ENST00000370544SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000584773ENST00000370542SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-intronENST00000584773ENST00000489303SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000585096ENST00000370544SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000585096ENST00000370542SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-intronENST00000585096ENST00000489303SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000258962ENST00000370544SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-3UTRENST00000258962ENST00000370542SRSF1chr17

56083241

-LMO4chr1

87810839

+
intron-intronENST00000258962ENST00000489303SRSF1chr17

56083241

-LMO4chr1

87810839

+

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FusionProtFeatures for SRSF1_LMO4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SRSF1

Q07955

LMO4

P61968

Plays a role in preventing exon skipping, ensuring theaccuracy of splicing and regulating alternative splicing.Interacts with other spliceosomal components, via the RS domains,to form a bridge between the 5'- and 3'-splice site bindingcomponents, U1 snRNP and U2AF. Can stimulate binding of U1 snRNPto a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNAsequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or thedecamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'-CGAGGCG-3' motif in vitro. Three copies of the octamer constitutea powerful splicing enhancer in vitro, the ASF/SF2 splicingenhancer (ASE) which can specifically activate ASE-dependentsplicing. Isoform ASF-2 and isoform ASF-3 act as splicingrepressors. May function as export adapter involved in mRNAnuclear export through the TAP/NXF1 pathway.{ECO:0000269|PubMed:8139654}. Probable transcriptional factor. {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for SRSF1_LMO4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for SRSF1_LMO4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for SRSF1_LMO4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SRSF1_LMO4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSRSF1C0019693HIV Infections1CTD_human
HgeneSRSF1C0027627Neoplasm Metastasis1CTD_human
HgeneSRSF1C0036341Schizophrenia1CTD_human