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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:STIM1-VHL

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: STIM1-VHL
FusionPDB ID: 87409
FusionGDB2.0 ID: 87409
HgeneTgene
Gene symbol

STIM1

VHL

Gene ID

6786

7428

Gene namestromal interaction molecule 1von Hippel-Lindau tumor suppressor
SynonymsD11S4896E|GOK|IMD10|STRMK|TAM|TAM1HRCA1|RCA1|VHL1|pVHL
Cytomap

11p15.4

3p25.3

Type of geneprotein-codingprotein-coding
Descriptionstromal interaction molecule 1von Hippel-Lindau disease tumor suppressorelongin binding proteinprotein G7von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase
Modification date2020032920200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000300737, ENST00000527651, 
ENST00000527484, ENST00000533977, 
ENST00000477538, ENST00000256474, 
ENST00000345392, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score21 X 13 X 12=32764 X 3 X 3=36
# samples 234
** MAII scorelog2(23/3276*10)=-3.83222959069663
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)STIM1(3877639)-VHL(10191471), # samples:2
Anticipated loss of major functional domain due to fusion event.STIM1-VHL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
STIM1-VHL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
STIM1-VHL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
STIM1-VHL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

TgeneVHL

GO:0016567

protein ubiquitination

24899725

TgeneVHL

GO:0061428

negative regulation of transcription from RNA polymerase II promoter in response to hypoxia

11641274


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.
all structure

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


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUSCTCGA-66-2766-01ASTIM1chr11

3877639

-VHLchr3

10191471

+
ChimerDB4LUSCTCGA-66-2766-01ASTIM1chr11

3877639

+VHLchr3

10191471

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000300737STIM1chr113877639+ENST00000256474VHLchr310191471+31427081564187
ENST00000300737STIM1chr113877639+ENST00000345392VHLchr310191471+30047081564187
ENST00000527651STIM1chr113877639+ENST00000256474VHLchr310191471+266222874406110
ENST00000527651STIM1chr113877639+ENST00000345392VHLchr310191471+252422874406110

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
ENST00000300737ENST00000256474STIM1chr113877639+VHLchr310191471+0.0263266880.9736733
ENST00000300737ENST00000345392STIM1chr113877639+VHLchr310191471+0.0516485160.9483515
ENST00000527651ENST00000256474STIM1chr113877639+VHLchr310191471+0.0350878950.9649121
ENST00000527651ENST00000345392STIM1chr113877639+VHLchr310191471+0.0301559180.96984404

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>87409_87409_1_STIM1-VHL_STIM1_chr11_3877639_ENST00000300737_VHL_chr3_10191471_ENST00000256474_length(amino acids)=187AA_BP=
LDLGTASRLGTGLGGGADLGLGGPGSRRRPRPQDPAGRTPSPASAARRSSAGRGQVPPSRLSSLLFSSSSTSVPAETPAAPFRRGVVICG
ADSSPAATLPEVSGSGTSSGRRSPGGPTVGPEEPALLPHPNLEHLTFGCWRGQARGWLDSCGAARASCLETVGCTPGLLALPLGSRGVHI

--------------------------------------------------------------

>87409_87409_2_STIM1-VHL_STIM1_chr11_3877639_ENST00000300737_VHL_chr3_10191471_ENST00000345392_length(amino acids)=187AA_BP=
LDLGTASRLGTGLGGGADLGLGGPGSRRRPRPQDPAGRTPSPASAARRSSAGRGQVPPSRLSSLLFSSSSTSVPAETPAAPFRRGVVICG
ADSSPAATLPEVSGSGTSSGRRSPGGPTVGPEEPALLPHPNLEHLTFGCWRGQARGWLDSCGAARASCLETVGCTPGLLALPLGSRGVHI

--------------------------------------------------------------

>87409_87409_3_STIM1-VHL_STIM1_chr11_3877639_ENST00000527651_VHL_chr3_10191471_ENST00000256474_length(amino acids)=110AA_BP=46
MRPRVMDVCVRLALWLLWGLLLHQGQSLSHSHSEKATGTSSGANSEESTAAVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPN

--------------------------------------------------------------

>87409_87409_4_STIM1-VHL_STIM1_chr11_3877639_ENST00000527651_VHL_chr3_10191471_ENST00000345392_length(amino acids)=110AA_BP=46
MRPRVMDVCVRLALWLLWGLLLHQGQSLSHSHSEKATGTSSGANSEESTAAVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPN

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:3877639/chr3:10191471)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+11276_8746.333333333333336686.0Calcium binding.
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112248_44246.333333333333336686.0Coiled coilOntology_term=ECO:0000269,ECO:0000269,ECO:0000269
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112270_33646.333333333333336686.0Compositional biasNote=Glu-rich
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112600_62946.333333333333336686.0Compositional biasNote=Pro/Ser-rich
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112672_68546.333333333333336686.0Compositional biasNote=Lys-rich
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112132_20046.333333333333336686.0DomainSAM
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+11263_9846.333333333333336686.0DomainNote=EF-hand
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112642_64546.333333333333336686.0MotifNote=Microtubule tip localization signal
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112334_44446.333333333333336686.0RegionNote=SOAR/CAD
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112235_68546.333333333333336686.0Topological domainCytoplasmic
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+11223_21346.333333333333336686.0Topological domainExtracellular
HgeneSTIM1chr11:3877639chr3:10191471ENST00000300737+112214_23446.333333333333336686.0TransmembraneHelical
TgeneVHLchr11:3877639chr3:10191471ENST0000025647413100_155154.33333333333334214.0RegionNote=Involved in binding to CCT complex
TgeneVHLchr11:3877639chr3:10191471ENST000002564741314_53154.33333333333334214.0RegionNote=8 X 5 AA tandem repeats of G-[PAVG]-E-E-[DAYSLE]
TgeneVHLchr11:3877639chr3:10191471ENST0000034539202100_155113.33333333333333173.0RegionNote=Involved in binding to CCT complex
TgeneVHLchr11:3877639chr3:10191471ENST000003453920214_53113.33333333333333173.0RegionNote=8 X 5 AA tandem repeats of G-[PAVG]-E-E-[DAYSLE]
TgeneVHLchr11:3877639chr3:10191471ENST000002564741314_18154.33333333333334214.0RepeatNote=1
TgeneVHLchr11:3877639chr3:10191471ENST000002564741319_23154.33333333333334214.0RepeatNote=2
TgeneVHLchr11:3877639chr3:10191471ENST000002564741324_28154.33333333333334214.0RepeatNote=3
TgeneVHLchr11:3877639chr3:10191471ENST000002564741329_33154.33333333333334214.0RepeatNote=4
TgeneVHLchr11:3877639chr3:10191471ENST000002564741334_38154.33333333333334214.0RepeatNote=5
TgeneVHLchr11:3877639chr3:10191471ENST000002564741339_43154.33333333333334214.0RepeatNote=6
TgeneVHLchr11:3877639chr3:10191471ENST000002564741344_48154.33333333333334214.0RepeatNote=7
TgeneVHLchr11:3877639chr3:10191471ENST000002564741349_53154.33333333333334214.0RepeatNote=8
TgeneVHLchr11:3877639chr3:10191471ENST000003453920214_18113.33333333333333173.0RepeatNote=1
TgeneVHLchr11:3877639chr3:10191471ENST000003453920219_23113.33333333333333173.0RepeatNote=2
TgeneVHLchr11:3877639chr3:10191471ENST000003453920224_28113.33333333333333173.0RepeatNote=3
TgeneVHLchr11:3877639chr3:10191471ENST000003453920229_33113.33333333333333173.0RepeatNote=4
TgeneVHLchr11:3877639chr3:10191471ENST000003453920234_38113.33333333333333173.0RepeatNote=5
TgeneVHLchr11:3877639chr3:10191471ENST000003453920239_43113.33333333333333173.0RepeatNote=6
TgeneVHLchr11:3877639chr3:10191471ENST000003453920244_48113.33333333333333173.0RepeatNote=7
TgeneVHLchr11:3877639chr3:10191471ENST000003453920249_53113.33333333333333173.0RepeatNote=8


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
STIM1
VHL


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to STIM1-VHL


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to STIM1-VHL


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource