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Center for Computational Systems Medicine level3
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Potential Active Site Information

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Potentially Interacting Small Molecules through Virtual Screening

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Biochemical Features of Small Molecules with ADME

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Drug Toxicity Information

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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:CLIP1-ROS1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CLIP1-ROS1
FusionPDB ID: 17164
FusionGDB2.0 ID: 17164
HgeneTgene
Gene symbol

CLIP1

ROS1

Gene ID

6249

6098

Gene nameCAP-Gly domain containing linker protein 1ROS proto-oncogene 1, receptor tyrosine kinase
SynonymsCLIP|CLIP-170|CLIP170|CYLN1|RSNMCF3|ROS|c-ros-1
Cytomap

12q24.31

6q22.1

Type of geneprotein-codingprotein-coding
DescriptionCAP-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)proto-oncogene tyrosine-protein kinase ROSROS proto-oncogene 1 , receptor tyrosine kinasec-ros oncogene 1 , receptor tyrosine kinaseproto-oncogene c-Ros-1transmembrane tyrosine-specific protein kinasev-ros avian UR2 sarcoma virus oncogene homolog 1
Modification date2020031320200314
UniProtAcc

P30622

P08922

Ensembl transtripts involved in fusion geneENST idsENST00000302528, ENST00000540338, 
ENST00000545889, ENST00000358808, 
ENST00000361654, ENST00000537178, 
ENST00000536634, ENST00000540539, 
ENST00000368507, ENST00000368508, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score22 X 22 X 13=629218 X 20 X 5=1800
# samples 3120
** MAII scorelog2(31/6292*10)=-4.34317855014145
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(20/1800*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CLIP1 [Title/Abstract] AND ROS1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)
Anticipated loss of major functional domain due to fusion event.CLIP1-ROS1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CLIP1-ROS1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CLIP1-ROS1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CLIP1-ROS1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CLIP1-ROS1 seems lost the major protein functional domain in Tgene partner, which is a kinase 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
TgeneROS1

GO:0001558

regulation of cell growth

16885344

TgeneROS1

GO:0006468

protein phosphorylation

16885344

TgeneROS1

GO:0032006

regulation of TOR signaling

16885344


check buttonFusion gene breakpoints across CLIP1 (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 ROS1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.


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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
ChimerKB3..CLIP1chr12

122794308

-ROS1chr6

117641193

-


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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)
ENST00000361654CLIP1chr12122794308-ENST00000368508ROS1chr6117641193-4861340217434281084
ENST00000361654CLIP1chr12122794308-ENST00000368507ROS1chr6117641193-4861340217434281084
ENST00000358808CLIP1chr12122794308-ENST00000368508ROS1chr6117641193-5175371615537421195
ENST00000358808CLIP1chr12122794308-ENST00000368507ROS1chr6117641193-5175371615537421195
ENST00000537178CLIP1chr12122794308-ENST00000368508ROS1chr6117641193-5133367421837001160
ENST00000537178CLIP1chr12122794308-ENST00000368507ROS1chr6117641193-5133367421837001160

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 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

>17164_17164_1_CLIP1-ROS1_CLIP1_chr12_122794308_ENST00000358808_ROS1_chr6_117641193_ENST00000368507_length(amino acids)=1195AA_BP=
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI
VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS
ATPPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCQPKYG
LFAPVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGTTALQEALKEK
QQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLETQTKLEHARIKELEQSLLFEKTKADKLQRELEDTRVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQE
ISSLQEKLEVTRTDHQREITSLKEHFGAREETHQKEIKALYTATEKLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEEL
KVSFSKGLGTETAEFAELKTQIEKMRLDYQHEIENLQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDT
LNKLQEAEIKVKELEVLQAKCNEQTKVIDNFTSQLKATEEKLLDLDALRKASSEGKSEMKKLRQQLEAAEKQIKHLEIEKNAESSKASSI
TRELQGRELKLTNLQENLSEVSQVKETLEKELQILKEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFRE
KDEREEQLIKAKEKLENDIAEIMKMSGDNSSQLTKMNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEK
KELERKLSDLEKKMETSHNQCQELKARYERATSETKTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDA
MQIMEQMTKEKTETLASLEDTKQTNAKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETLKQAAAQKSQQLSALQEENVK

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>17164_17164_2_CLIP1-ROS1_CLIP1_chr12_122794308_ENST00000358808_ROS1_chr6_117641193_ENST00000368508_length(amino acids)=1195AA_BP=
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI
VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS
ATPPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCQPKYG
LFAPVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGTTALQEALKEK
QQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLETQTKLEHARIKELEQSLLFEKTKADKLQRELEDTRVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQE
ISSLQEKLEVTRTDHQREITSLKEHFGAREETHQKEIKALYTATEKLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEEL
KVSFSKGLGTETAEFAELKTQIEKMRLDYQHEIENLQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDT
LNKLQEAEIKVKELEVLQAKCNEQTKVIDNFTSQLKATEEKLLDLDALRKASSEGKSEMKKLRQQLEAAEKQIKHLEIEKNAESSKASSI
TRELQGRELKLTNLQENLSEVSQVKETLEKELQILKEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFRE
KDEREEQLIKAKEKLENDIAEIMKMSGDNSSQLTKMNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEK
KELERKLSDLEKKMETSHNQCQELKARYERATSETKTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDA
MQIMEQMTKEKTETLASLEDTKQTNAKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETLKQAAAQKSQQLSALQEENVK

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>17164_17164_3_CLIP1-ROS1_CLIP1_chr12_122794308_ENST00000361654_ROS1_chr6_117641193_ENST00000368507_length(amino acids)=1084AA_BP=
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI
VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS
ATPPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCQPKYG
LFAPVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGTTALQEALKEK
QQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLEVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQEISSLQEKLEVTRTDHQREITSLKEHFGAREETHQK
EIKALYTATEKLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGLGTETAEFAELKTQIEKMRLDYQHEIEN
LQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDTLNKLQEAEIKASSITRELQGRELKLTNLQENLSEV
SQVKETLEKELQILKEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFREKDEREEQLIKAKEKLENDIAE
IMKMSGDNSSQLTKMNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEKKELERKLSDLEKKMETSHNQC
QELKARYERATSETKTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDT
KQTNAKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETLKQAAAQKSQQLSALQEENVKLAEELGRSRDEVTSHQKYSSN

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>17164_17164_4_CLIP1-ROS1_CLIP1_chr12_122794308_ENST00000361654_ROS1_chr6_117641193_ENST00000368508_length(amino acids)=1084AA_BP=
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI
VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS
ATPPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCQPKYG
LFAPVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGTTALQEALKEK
QQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLEVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQEISSLQEKLEVTRTDHQREITSLKEHFGAREETHQK
EIKALYTATEKLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGLGTETAEFAELKTQIEKMRLDYQHEIEN
LQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDTLNKLQEAEIKASSITRELQGRELKLTNLQENLSEV
SQVKETLEKELQILKEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFREKDEREEQLIKAKEKLENDIAE
IMKMSGDNSSQLTKMNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEKKELERKLSDLEKKMETSHNQC
QELKARYERATSETKTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDT
KQTNAKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETLKQAAAQKSQQLSALQEENVKLAEELGRSRDEVTSHQKYSSN

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>17164_17164_5_CLIP1-ROS1_CLIP1_chr12_122794308_ENST00000537178_ROS1_chr6_117641193_ENST00000368507_length(amino acids)=1160AA_BP=
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI
VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS
ATPPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCQPKYG
LFAPVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGTTALQEALKEK
QQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLEVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQEISSLQEKLEVTRTDHQREITSLKEHFGAREETHQK
EIKALYTATEKLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGLGTETAEFAELKTQIEKMRLDYQHEIEN
LQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDTLNKLQEAEIKVKELEVLQAKCNEQTKVIDNFTSQL
KATEEKLLDLDALRKASSEGKSEMKKLRQQLEAAEKQIKHLEIEKNAESSKASSITRELQGRELKLTNLQENLSEVSQVKETLEKELQIL
KEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFREKDEREEQLIKAKEKLENDIAEIMKMSGDNSSQLTK
MNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEKKELERKLSDLEKKMETSHNQCQELKARYERATSET
KTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDTKQTNAKLQNELDTL

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>17164_17164_6_CLIP1-ROS1_CLIP1_chr12_122794308_ENST00000537178_ROS1_chr6_117641193_ENST00000368508_length(amino acids)=1160AA_BP=
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGI
VLDEPIGKNDGSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLCTSTASMVSSSPSTPSNIPQKPSQPAAKEPS
ATPPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPLGKNDGAVAGTRYFQCQPKYG
LFAPVHKVTKIGFPSTTPAKAKANAVRRVMATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGTTALQEALKEK
QQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHDQHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLEVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQEISSLQEKLEVTRTDHQREITSLKEHFGAREETHQK
EIKALYTATEKLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGLGTETAEFAELKTQIEKMRLDYQHEIEN
LQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDTLNKLQEAEIKVKELEVLQAKCNEQTKVIDNFTSQL
KATEEKLLDLDALRKASSEGKSEMKKLRQQLEAAEKQIKHLEIEKNAESSKASSITRELQGRELKLTNLQENLSEVSQVKETLEKELQIL
KEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFREKDEREEQLIKAKEKLENDIAEIMKMSGDNSSQLTK
MNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEKKELERKLSDLEKKMETSHNQCQELKARYERATSET
KTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDTKQTNAKLQNELDTL

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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/chr12:/chr6:)
- 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
CLIP1

P30622

ROS1

P08922

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}.FUNCTION: Orphan receptor tyrosine kinase (RTK) that plays a role in epithelial cell differentiation and regionalization of the proximal epididymal epithelium. May activate several downstream signaling pathways related to cell differentiation, proliferation, growth and survival including the PI3 kinase-mTOR signaling pathway. Mediates the phosphorylation of PTPN11, an activator of this pathway. May also phosphorylate and activate the transcription factor STAT3 to control anchorage-independent cell growth. Mediates the phosphorylation and the activation of VAV3, a guanine nucleotide exchange factor regulating cell morphology. May activate other downstream signaling proteins including AKT1, MAPK1, MAPK3, IRS1 and PLCG2. {ECO:0000269|PubMed:11094073, ECO:0000269|PubMed:16885344}.

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


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file (795) >>>795.pdbFusion protein BP residue:
CIF file (795) >>>795.cif		CLIP1chr12122794308-ROS1chr6117641193-
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSET
QEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGIVLDEPIGKND
GSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLC
TSTASMVSSSPSTPSNIPQKPSQPAAKEPSATPPISNLTKTASESISNLS
EAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPL
GKNDGAVAGTRYFQCQPKYGLFAPVHKVTKIGFPSTTPAKAKANAVRRVM
ATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGT
TALQEALKEKQQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHD
QHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLEVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSL
SLLQEISSLQEKLEVTRTDHQREITSLKEHFGAREETHQKEIKALYTATE
KLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEELKVSFS
KGLGTETAEFAELKTQIEKMRLDYQHEIENLQNQQDSERAAHAKEMEALR
AKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDTLNKLQEAEIKASSIT
RELQGRELKLTNLQENLSEVSQVKETLEKELQILKEKFAEASEEAVSVQR
SMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFREKDEREEQLIKA
KEKLENDIAEIMKMSGDNSSQLTKMNDELRLKERDVEELQLKLTKANENA
SFLQKSIEDMTVKAEQSQQEAAKKHEEEKKELERKLSDLEKKMETSHNQC
QELKARYERATSETKTKHEEILQNLQKTLLDTEDKLKGAREENSGLLQEL
EELRKQADKAKAAQTAEDAMQIMEQMTKEKTETLASLEDTKQTNAKLQNE
LDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETLKQAAAQKSQQL
1084
3D view using mol* of 795 (AA BP:)
PDB file (836) >>>836.pdbFusion protein BP residue:
CIF file (836) >>>836.cif		CLIP1chr12122794308-ROS1chr6117641193-
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSET
QEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGIVLDEPIGKND
GSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLC
TSTASMVSSSPSTPSNIPQKPSQPAAKEPSATPPISNLTKTASESISNLS
EAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPL
GKNDGAVAGTRYFQCQPKYGLFAPVHKVTKIGFPSTTPAKAKANAVRRVM
ATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGT
TALQEALKEKQQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHD
QHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLEVATVSEKSRIMELEKDLALRVQEVAELRRRLESNKPAGDVDMSL
SLLQEISSLQEKLEVTRTDHQREITSLKEHFGAREETHQKEIKALYTATE
KLSKENESLKSKLEHANKENSDVIALWKSKLETAIASHQQAMEELKVSFS
KGLGTETAEFAELKTQIEKMRLDYQHEIENLQNQQDSERAAHAKEMEALR
AKLMKVIKEKENSLEAIRSKLDKAEDQHLVEMEDTLNKLQEAEIKVKELE
VLQAKCNEQTKVIDNFTSQLKATEEKLLDLDALRKASSEGKSEMKKLRQQ
LEAAEKQIKHLEIEKNAESSKASSITRELQGRELKLTNLQENLSEVSQVK
ETLEKELQILKEKFAEASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLE
KLRENLADMEAKFREKDEREEQLIKAKEKLENDIAEIMKMSGDNSSQLTK
MNDELRLKERDVEELQLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKK
HEEEKKELERKLSDLEKKMETSHNQCQELKARYERATSETKTKHEEILQN
LQKTLLDTEDKLKGAREENSGLLQELEELRKQADKAKAAQTAEDAMQIME
QMTKEKTETLASLEDTKQTNAKLQNELDTLKENNLKNVEELNKSKELLTV
ENQKMEEFRKEIETLKQAAAQKSQQLSALQEENVKLAEELGRSRDEVTSH
1160
3D view using mol* of 836 (AA BP:)
PDB file (845) >>>845.pdbFusion protein BP residue:
CIF file (845) >>>845.cif		CLIP1chr12122794308-ROS1chr6117641193-
MSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSET
QEEFVDDFRVGERVWVNGNKPGFIQFLGETQFAPGQWAGIVLDEPIGKND
GSVAGVRYFQCEPLKGIFTRPSKLTRKVQAEDEANGLQTTPASRATSPLC
TSTASMVSSSPSTPSNIPQKPSQPAAKEPSATPPISNLTKTASESISNLS
EAGSIKKGERELKIGDRVLVGGTKAGVVRFLGETDFAKGEWCGVELDEPL
GKNDGAVAGTRYFQCQPKYGLFAPVHKVTKIGFPSTTPAKAKANAVRRVM
ATTSASLKRSPSASSLSSMSSVASSVSSRPSRTGLLTETSSRYARKISGT
TALQEALKEKQQHIEQLLAERDLERAEVAKATSHVGEIEQELALARDGHD
QHVLELEAKMDQLRTMVEAADREKVELLNQLEEEKRKVEDLQFRVEEESI
TKGDLETQTKLEHARIKELEQSLLFEKTKADKLQRELEDTRVATVSEKSR
IMELEKDLALRVQEVAELRRRLESNKPAGDVDMSLSLLQEISSLQEKLEV
TRTDHQREITSLKEHFGAREETHQKEIKALYTATEKLSKENESLKSKLEH
ANKENSDVIALWKSKLETAIASHQQAMEELKVSFSKGLGTETAEFAELKT
QIEKMRLDYQHEIENLQNQQDSERAAHAKEMEALRAKLMKVIKEKENSLE
AIRSKLDKAEDQHLVEMEDTLNKLQEAEIKVKELEVLQAKCNEQTKVIDN
FTSQLKATEEKLLDLDALRKASSEGKSEMKKLRQQLEAAEKQIKHLEIEK
NAESSKASSITRELQGRELKLTNLQENLSEVSQVKETLEKELQILKEKFA
EASEEAVSVQRSMQETVNKLHQKEEQFNMLSSDLEKLRENLADMEAKFRE
KDEREEQLIKAKEKLENDIAEIMKMSGDNSSQLTKMNDELRLKERDVEEL
QLKLTKANENASFLQKSIEDMTVKAEQSQQEAAKKHEEEKKELERKLSDL
EKKMETSHNQCQELKARYERATSETKTKHEEILQNLQKTLLDTEDKLKGA
REENSGLLQELEELRKQADKAKAAQTAEDAMQIMEQMTKEKTETLASLED
TKQTNAKLQNELDTLKENNLKNVEELNKSKELLTVENQKMEEFRKEIETL
1195
3D view using mol* of 845 (AA BP:)


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
CLIP1_pLDDT.png
all structure
all structure
ROS1_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
CLIP1_ROS1_795_pLDDT.png (AA BP:)
all structure
CLIP1_ROS1_795_pLDDT_and_active_sites.png (AA BP:)
all structure
CLIP1_ROS1_795_violinplot.png (AA BP:)
all structure
CLIP1_ROS1_836_pLDDT.png (AA BP:)
all structure
CLIP1_ROS1_836_pLDDT_and_active_sites.png (AA BP:)
all structure
CLIP1_ROS1_836_violinplot.png (AA BP:)
all structure
CLIP1_ROS1_845_pLDDT.png (AA BP:)
all structure
CLIP1_ROS1_845_pLDDT_and_active_sites.png (AA BP:)
all structure
CLIP1_ROS1_845_violinplot.png (AA BP:)
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots
CLIP1_ROS1_836.png
all structure
CLIP1_ROS1_845.png
all structure

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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Fusion AA seq ID in FusionPDBSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
7950.9621830.966474.0260.5650.6410.8860.2311.0990.210.833Chain A: 131,132,133,134,207,208,209,210,211,212,2
31,233,238,239,240,275,276,278,279,280,936,939,940
,943,946,947,950,953,956,957,961
8360.6524470.601811.6620.57660.5230.77310.1461.09340.13350.4436Chain A: 28,29,30,31,165,166,167,168
8450.8098680.8025171.50.65660.59940.87130.25781.01910.2531.5495Chain A: 205,206,207,208,209,210,211,212,231,240,2
75,276,278,279,280

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Potentially Interacting Small Molecules through Virtual Screening


check button The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.
Fusion AA seq ID in FusionPDBZINC IDDrugBank IDDrug nameDocking scoreGlide gscore

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group

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Biochemical Features of Small Molecules


check button ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)
ZINC IDmol_MWdipoleSASAFOSAFISAPISAWPSAvolumedonorHBaccptHBIPHuman Oral AbsorptionPercent Human Oral AbsorptionRule Of FiveRule Of Three


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity


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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
CLIP1MTOR, IQGAP1, CDC42, RAC1, PAFAH1B1, Gorasp1, CALM1, BIN1, MAPRE1, TUBA1A, TUBB, AMOT, BUB3, MAEA, PSMC2, HDAC6, CADPS, CHD4, GPS1, DCTN1, DYNC1H1, Mapre1, Smurf2, PCGF1, DPPA4, NANOG, POU5F1, TSC22D2, GORASP1, BMP1, DAB2IP, RUNDC3A, BRCA1, ZNF598, UBE2M, KIAA1429, DCAF15, BICD1, REL, ORF3a, SERBP1, nsp2, CLIP4, NINL, ORF6, DDX58, AGAP3, CKAP2, CLASP1, CLASP2, DNAJA2, IKBKAP, ELP4, EXOC4, HINT1, HMMR, HNRNPA1L2, IARS2, KIF15, MAP7, MAST4, PLEKHA5, RPS6KA3, SIRT2, SLAIN1, TCHP, TEX9, BIRC6, CAMSAP1, DRG1, KIAA0368, MAP7D1, MAP7D2, MAP7D3, SF3B3, SLAIN2, MAPRE3, TRIM36, PPP2R2B, RABEP1, SRRT, OR2A4, GOT1, RABEP2, SYCE1, MBNL1, SSUH2, C18orf21, AGPAT1, CCR1, FBXO32, CDK1,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
CLIP1all structure
ROS1all structure


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 CLIP1-ROS1


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 CLIP1-ROS1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID
CLIP1ROS1Lung AdenocarcinomaMyCancerGenome
CLIP1ROS1Dedifferentiated LiposarcomaMyCancerGenome
CLIP1ROS1Breast Invasive Ductal CarcinomaMyCancerGenome
CLIP1ROS1Anaplastic GangliogliomaMyCancerGenome
CLIP1ROS1Cancer Of Unknown PrimaryMyCancerGenome

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneROS1C0007131Non-Small Cell Lung Carcinoma4CTD_human
TgeneROS1C0017638Glioma1CTD_human
TgeneROS1C0025202melanoma1CTD_human
TgeneROS1C0152013Adenocarcinoma of lung (disorder)1CGI;CTD_human
TgeneROS1C0259783mixed gliomas1CTD_human
TgeneROS1C0555198Malignant Glioma1CTD_human