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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:CLIP1-CRCP (FusionGDB2 ID:17155)

Fusion Gene Summary for CLIP1-CRCP

check button Fusion gene summary
Fusion gene informationFusion gene name: CLIP1-CRCP
Fusion gene ID: 17155
HgeneTgene
Gene symbol

CLIP1

CRCP

Gene ID

6249

27297

Gene nameCAP-Gly domain containing linker protein 1CGRP receptor component
SynonymsCLIP|CLIP-170|CLIP170|CYLN1|RSNC17|CGRP-RCP|CGRPRCP|POLR3I|POLR3J|RCP|RCP9|RPC9
Cytomap

12q24.31

7q11.21

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)DNA-directed RNA polymerase III subunit RPC9CGRP-receptor component proteinRNA polymerase III subunit C9calcitonin gene-related peptide-receptor component protein
Modification date2020031320200322
UniProtAcc

P30622

O75575

Ensembl transtripts involved in fusion geneENST00000358808, ENST00000361654, 
ENST00000537178, ENST00000302528, 
ENST00000536634, ENST00000540338, 
ENST00000540539, ENST00000545889, 
ENST00000338592, ENST00000395326, 
ENST00000398684, ENST00000415001, 
ENST00000431089, ENST00000492264, 
Fusion gene scores* DoF score22 X 22 X 13=62926 X 5 X 4=120
# samples 317
** MAII scorelog2(31/6292*10)=-4.34317855014145
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointCLIP1(122907067)-CRCP(65610429), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneCRCP

GO:0006383

transcription by RNA polymerase III

12482973


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 CRCP (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
ChimerDB4BLCATCGA-BT-A3PHCLIP1chr12

122907067

-CRCPchr7

65610429

+


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Fusion Gene ORF analysis for CLIP1-CRCP

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
5UTR-3CDSENST00000358808ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000358808ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000358808ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000358808ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000358808ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000361654ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000361654ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000361654ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000361654ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000361654ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000537178ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000537178ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000537178ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000537178ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-3CDSENST00000537178ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-intronENST00000358808ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-intronENST00000361654ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
5UTR-intronENST00000537178ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000302528ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000302528ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000302528ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000302528ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000302528ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000536634ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000536634ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000536634ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000536634ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000536634ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540338ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540338ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540338ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540338ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540338ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540539ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540539ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540539ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540539ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000540539ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000545889ENST00000338592CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000545889ENST00000395326CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000545889ENST00000398684CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000545889ENST00000415001CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-3CDSENST00000545889ENST00000431089CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-intronENST00000302528ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-intronENST00000536634ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-intronENST00000540338ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-intronENST00000540539ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+
intron-intronENST00000545889ENST00000492264CLIP1chr12

122907067

-CRCPchr7

65610429

+

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 CLIP1-CRCP


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)
CLIP1chr12122907067-CRCPchr765610429+1.93E-121
CLIP1chr12122907067-CRCPchr765610429+1.93E-121

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.
genomic feature of top 1%

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Fusion Protein Features for CLIP1-CRCP


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/:122907067/:65610429)
- 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

CRCP

O75575

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: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway (By similarity). {ECO:0000250}.; FUNCTION: Accessory protein for the calcitonin gene-related peptide (CGRP) receptor. It modulates CGRP responsiveness in a variety of tissues.

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 CLIP1-CRCP


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 CLIP1-CRCP


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 CLIP1-CRCP


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 CLIP1-CRCP


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