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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:STIM1-CLIP1 (FusionGDB2 ID:86790)

Fusion Gene Summary for STIM1-CLIP1

check button Fusion gene summary
Fusion gene informationFusion gene name: STIM1-CLIP1
Fusion gene ID: 86790
HgeneTgene
Gene symbol

STIM1

CLIP1

Gene ID

6786

6249

Gene namestromal interaction molecule 1CAP-Gly domain containing linker protein 1
SynonymsD11S4896E|GOK|IMD10|STRMK|TAM|TAM1CLIP|CLIP-170|CLIP170|CYLN1|RSN
Cytomap

11p15.4

12q24.31

Type of geneprotein-codingprotein-coding
Descriptionstromal interaction molecule 1CAP-Gly domain-containing linker protein 1cytoplasmic linker protein 1cytoplasmic linker protein 170 alpha-2cytoplasmic linker protein CLIP-170restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)
Modification date2020032920200313
UniProtAcc.

P30622

Ensembl transtripts involved in fusion geneENST00000300737, ENST00000527651, 
ENST00000527484, ENST00000533977, 
ENST00000361654, ENST00000545889, 
ENST00000302528, ENST00000358808, 
ENST00000537178, ENST00000540338, 
ENST00000536634, ENST00000540539, 
Fusion gene scores* DoF score21 X 13 X 12=327612 X 12 X 6=864
# samples 2313
** MAII scorelog2(23/3276*10)=-3.83222959069663
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/864*10)=-2.73251968913501
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STIM1 [Title/Abstract] AND CLIP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSTIM1(3877639)-CLIP1(122773088), # samples:4
Anticipated loss of major functional domain due to fusion event.STIM1-CLIP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
STIM1-CLIP1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
STIM1-CLIP1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneSTIM1

GO:0002115

store-operated calcium entry

28219928

HgeneSTIM1

GO:0005513

detection of calcium ion

16005298

HgeneSTIM1

GO:0032237

activation of store-operated calcium channel activity

16005298|26322679|28219928

HgeneSTIM1

GO:0045762

positive regulation of adenylate cyclase activity

19171672

HgeneSTIM1

GO:0051924

regulation of calcium ion transport

16005298


check buttonFusion gene breakpoints across STIM1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CLIP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4UCECTCGA-D1-A3DG-01ASTIM1chr11

3877639

+CLIP1chr12

122773088

-
ChimerDB4UCECTCGA-D1-A3DGSTIM1chr11

3877639

+CLIP1chr12

122773088

-
ChimerDB4UCECTCGA-D1-A3DG-01ASTIM1chr11

3877639

+CLIP1chr12

122773088

-
ChimerDB4UCECTCGA-D1-A3DG-01ASTIM1chr11

3877639

-CLIP1chr12

122773088

-


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Fusion Gene ORF analysis for STIM1-CLIP1

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
Frame-shiftENST00000300737ENST00000361654STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000300737ENST00000545889STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000300737ENST00000302528STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000300737ENST00000358808STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000300737ENST00000537178STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000300737ENST00000540338STIM1chr11

3877639

+CLIP1chr12

122773088

-
5CDS-intronENST00000300737ENST00000536634STIM1chr11

3877639

+CLIP1chr12

122773088

-
5CDS-intronENST00000300737ENST00000540539STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000527651ENST00000361654STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000527651ENST00000545889STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000527651ENST00000302528STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000527651ENST00000358808STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000527651ENST00000537178STIM1chr11

3877639

+CLIP1chr12

122773088

-
Frame-shiftENST00000527651ENST00000540338STIM1chr11

3877639

+CLIP1chr12

122773088

-
5CDS-intronENST00000527651ENST00000536634STIM1chr11

3877639

+CLIP1chr12

122773088

-
5CDS-intronENST00000527651ENST00000540539STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000527484ENST00000361654STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000527484ENST00000545889STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000527484ENST00000302528STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000527484ENST00000358808STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000527484ENST00000537178STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000527484ENST00000540338STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-intronENST00000527484ENST00000536634STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-intronENST00000527484ENST00000540539STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000533977ENST00000361654STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000533977ENST00000545889STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000533977ENST00000302528STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000533977ENST00000358808STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000533977ENST00000537178STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-3CDSENST00000533977ENST00000540338STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-intronENST00000533977ENST00000536634STIM1chr11

3877639

+CLIP1chr12

122773088

-
intron-intronENST00000533977ENST00000540539STIM1chr11

3877639

+CLIP1chr12

122773088

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for STIM1-CLIP1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for STIM1-CLIP1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CLIP1

P30622

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Binds to the plus end of microtubules and regulates the dynamics of the microtubule cytoskeleton. Promotes microtubule growth and microtubule bundling. Links cytoplasmic vesicles to microtubules and thereby plays an important role in intracellular vesicle trafficking. Plays a role macropinocytosis and endosome trafficking. {ECO:0000269|PubMed:12433698, ECO:0000269|PubMed:17563362, ECO:0000269|PubMed:17889670}.

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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Fusion Gene Sequence for STIM1-CLIP1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for STIM1-CLIP1


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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Related Drugs for STIM1-CLIP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for STIM1-CLIP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSTIM1C1861451Stormorken Syndrome5GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSTIM1C4011726MYOPATHY, TUBULAR AGGREGATE, 14GENOMICS_ENGLAND;UNIPROT
HgeneSTIM1C2748557Immune dysfunction with T-cell inactivation due to calcium entry defect 23CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSTIM1C0020538Hypertensive disease1CTD_human
HgeneSTIM1C0024121Lung Neoplasms1CTD_human
HgeneSTIM1C0027659Neoplasms, Experimental1CTD_human
HgeneSTIM1C0087031Juvenile-Onset Still Disease1CTD_human
HgeneSTIM1C0242379Malignant neoplasm of lung1CTD_human
HgeneSTIM1C0410207Tubular Aggregate Myopathy1CTD_human;ORPHANET
HgeneSTIM1C0494261Combined immunodeficiency1GENOMICS_ENGLAND
HgeneSTIM1C3495559Juvenile arthritis1CTD_human
HgeneSTIM1C3495676Anorectal Malformations1GENOMICS_ENGLAND
HgeneSTIM1C3714758Juvenile psoriatic arthritis1CTD_human
HgeneSTIM1C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneSTIM1C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human