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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:CTNNA1-COTL1 (FusionGDB2 ID:20251)

Fusion Gene Summary for CTNNA1-COTL1

check button Fusion gene summary
Fusion gene informationFusion gene name: CTNNA1-COTL1
Fusion gene ID: 20251
HgeneTgene
Gene symbol

CTNNA1

COTL1

Gene ID

1495

23406

Gene namecatenin alpha 1coactosin like F-actin binding protein 1
SynonymsCAP102|MDPT2CLP
Cytomap

5q31.2

16q24.1

Type of geneprotein-codingprotein-coding
Descriptioncatenin alpha-1alpha-E-catenincatenin (cadherin-associated protein), alpha 1, 102kDaepididymis secretory sperm binding proteinrenal carcinoma antigen NY-REN-13coactosin-like proteincoactosin-like 1epididymis secretory sperm binding protein
Modification date2020031320200313
UniProtAcc.

Q14019

Ensembl transtripts involved in fusion geneENST00000355078, ENST00000302763, 
ENST00000518825, ENST00000520400, 
ENST00000540387, 
ENST00000262428, 
ENST00000567278, ENST00000564057, 
Fusion gene scores* DoF score25 X 19 X 12=570011 X 6 X 5=330
# samples 3412
** MAII scorelog2(34/5700*10)=-4.06735526780176
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/330*10)=-1.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTNNA1 [Title/Abstract] AND COTL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTNNA1(138119061)-COTL1(84600561), # samples:2
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
HgeneCTNNA1

GO:0071681

cellular response to indole-3-methanol

10868478


check buttonFusion gene breakpoints across CTNNA1 (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 COTL1 (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
ChimerDB4PRADTCGA-V1-A9ZR-01ACTNNA1chr5

138119061

+COTL1chr16

84600561

-
ChimerDB4PRADTCGA-V1-A9ZR-01ACTNNA1chr5

138119061

-COTL1chr16

84600561

-


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Fusion Gene ORF analysis for CTNNA1-COTL1

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-3CDSENST00000355078ENST00000262428CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-5UTRENST00000355078ENST00000567278CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-5UTRENST00000355078ENST00000564057CTNNA1chr5

138119061

+COTL1chr16

84600561

-
In-frameENST00000302763ENST00000262428CTNNA1chr5

138119061

+COTL1chr16

84600561

-
5CDS-5UTRENST00000302763ENST00000567278CTNNA1chr5

138119061

+COTL1chr16

84600561

-
5CDS-5UTRENST00000302763ENST00000564057CTNNA1chr5

138119061

+COTL1chr16

84600561

-
In-frameENST00000518825ENST00000262428CTNNA1chr5

138119061

+COTL1chr16

84600561

-
5CDS-5UTRENST00000518825ENST00000567278CTNNA1chr5

138119061

+COTL1chr16

84600561

-
5CDS-5UTRENST00000518825ENST00000564057CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-3CDSENST00000520400ENST00000262428CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-5UTRENST00000520400ENST00000567278CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-5UTRENST00000520400ENST00000564057CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-3CDSENST00000540387ENST00000262428CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-5UTRENST00000540387ENST00000567278CTNNA1chr5

138119061

+COTL1chr16

84600561

-
intron-5UTRENST00000540387ENST00000564057CTNNA1chr5

138119061

+COTL1chr16

84600561

-

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)
ENST00000302763CTNNA1chr5138119061+ENST00000262428COTL1chr1684600561-1753391479141112
ENST00000518825CTNNA1chr5138119061+ENST00000262428COTL1chr1684600561-166530339153112

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
ENST00000302763ENST00000262428CTNNA1chr5138119061+COTL1chr1684600561-0.028026570.9719734
ENST00000518825ENST00000262428CTNNA1chr5138119061+COTL1chr1684600561-0.03869630.9613037

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Fusion Genomic Features for CTNNA1-COTL1


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 CTNNA1-COTL1


check button Go to

FGviewer for the breakpoints of chr5:138119061-chr16:84600561

.
- 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
.COTL1

Q14019

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 F-actin in a calcium-independent manner. Has no direct effect on actin depolymerization. Acts as a chaperone for ALOX5 (5LO), influencing both its stability and activity in leukotrienes synthesis. {ECO:0000269|PubMed:11583571, ECO:0000269|PubMed:19807693}.

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
HgeneCTNNA1chr5:138119061chr16:84600561ENST00000302763+3182_228100.33333333333333907.0RegionNote=Involved in homodimerization
HgeneCTNNA1chr5:138119061chr16:84600561ENST00000540387+1122_2280537.0RegionNote=Involved in homodimerization
TgeneCOTL1chr5:138119061chr16:84600561ENST00000262428242_130106.0143.0DomainADF-H
TgeneCOTL1chr5:138119061chr16:84600561ENST000002624282466_75106.0143.0RegionNote=Flexible and important for F-actin binding


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Fusion Gene Sequence for CTNNA1-COTL1


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.
>In-frame_ENST00000302763_ENST00000262428_TCGA-V1-A9ZR-01A_CTNNA1_chr5_138119061_+_COTL1_chr16_84600561_length(transcript)=1753nt_BP=391nt
TCCTCCTCCTAGCCGGACTGGAGGGAGACAAAGCAGCGCCCGTCTGCTTCGGGCCTCTGGAATTTAGCGCTCGCCCAGCTAGCCGCAGAA
ATGACTGCTGTCCATGCAGGCAACATAAACTTCAAGTGGGATCCTAAAAGTCTAGAGATCAGGACTCTGGCAGTTGAGAGACTGTTGGAG
CCTCTTGTTACACAGGTTACAACCCTTGTAAACACCAATAGTAAAGGGCCCTCTAATAAGAAGAGAGGTCGTTCTAAGAAGGCCCATGTT
TTGGCTGCATCTGTTGAACAAGCAACTGAGAATTTCTTGGAGAAGGGGGATAAAATTGCGAAGGAGAGCCAGTTTCTCAAGGAGGAGCTT
GTGGCTGCTGTAGAAGATGTTCGAAAACAAGAATTTCGCTAAGGAGTTTGTGATCAGTGATCGGAAGGAGCTGGAGGAAGATTTCATCAA
GAGCGAGCTGAAGAAGGCGGGGGGAGCCAATTACGACGCCCAGACGGAGTAACCCCAGCCCCCGCCACACCACCCCTTGCCAAAGTCATC
TGCCTGCTCCCCGGGGGAGAGGACCGCCGGCCTCAGCTACTAGCCCACCAGCCCACCAGGGAGAAAAGAAGCCATGAGAGGCAGCGCCCG
CCACCCTGTGTCCACAGCCCCCACCTTCCCGCTTCCCTTAGAACCCTGCCGTGTCCTATCTCATGACGCTCATGGAACCTCTTTCTTTGA
TCTTCTTTTTCTTTTCTCCCCCTCTTTTTTGTTCTAAAGAAAAGTCATTTTGATGCAAGGTCCTGCCTGCCATCAGATCCGAGGTGCCTC
CTGCAGTGACCCCTTTTCCTGGCATTTCTCTTCCACGCGACGAGGTCTGCCTAGTGAGATCTGCATGACCTCACGTTGCTTTCCAGAGCC
CGGGCCTATTTTGCCATCTCAGTTTTCCTGGACCCTGCTTCCTGTGTACCACTGAGGGGCAGCTGGGCCAGGAGCTGTGCCCGGTGCCTG
CAGCCTTCATAAGCACACACGTCCATTCCCTACTAAGGCCCAGACCTCCTGGTATCTGCCCCGGGCTCCCTCATCCCACCTCCATCCGGA
GTTGCCTAAGATGCATGTCCAGCATAGGCAGGATTGCTCGGTGGTGAGAAGGTTAGGTCCGGCTCAGACTGAATAAGAAGAGATAAAATT
TGCCTTAAAACTTACCTGGCAGTGGCTTTGCTGCACGGTCTGAAACCACCTGTTCCCACCCTCTTGACCGAAATTTCCTTGTGACACAGA
GAAGGGCAAAGGTCTGAGCCCAGAGTTGACGGAGGGAGTATTTCAGGGTTCACTTCAGGGGCTCCCAAAGCGACAAGATCGTTAGGGAGA
GAGGCCCAGGGTGGGGACTGGGAATTTAAGGAGAGCTGGGAACGGATCCCTTAGGTTCAGGAAGCTTCTGTGTAAGCTGCGAGGATGGCT
TGGGCCGAAGGGTTGCTCTGCCCGCCGCGCTAGCTGTGAGCTGAGCAAAGCCCTGGGCTCACAGCACCCCAAAAGCCTGTGGCTTCAGTC
CTGCGTCTGCACCACACATTCAAAAGGATCGTTTTGTTTTGTTTTTAAAGAAAGGTGAGATTGGCTTGGTTCTTCATGAGCACATTTGAT
ATAGCTCTTTTTCTGTTTTTCCTTGCTCATTTCGTTTTGGGGAAGAAATCTGTACTGTATTGGGATTGTAAAGAACATCTCTGCACTCAG

>In-frame_ENST00000302763_ENST00000262428_TCGA-V1-A9ZR-01A_CTNNA1_chr5_138119061_+_COTL1_chr16_84600561_length(amino acids)=112AA_start in transcript=479_stop in transcript=141
MAPPAFFSSLLMKSSSSSFRSLITNSLAKFLFSNIFYSSHKLLLEKLALLRNFIPLLQEILSCLFNRCSQNMGLLRTTSLLIRGPFTIGV

--------------------------------------------------------------
>In-frame_ENST00000518825_ENST00000262428_TCGA-V1-A9ZR-01A_CTNNA1_chr5_138119061_+_COTL1_chr16_84600561_length(transcript)=1665nt_BP=303nt
AAATGACTGCTGTCCATGCAGGCAACATAAACTTCAAGTGGGATCCTAAAAGTCTAGAGATCAGGACTCTGGCAGTTGAGAGACTGTTGG
AGCCTCTTGTTACACAGGTTACAACCCTTGTAAACACCAATAGTAAAGGGCCCTCTAATAAGAAGAGAGGTCGTTCTAAGAAGGCCCATG
TTTTGGCTGCATCTGTTGAACAAGCAACTGAGAATTTCTTGGAGAAGGGGGATAAAATTGCGAAGGAGAGCCAGTTTCTCAAGGAGGAGC
TTGTGGCTGCTGTAGAAGATGTTCGAAAACAAGAATTTCGCTAAGGAGTTTGTGATCAGTGATCGGAAGGAGCTGGAGGAAGATTTCATC
AAGAGCGAGCTGAAGAAGGCGGGGGGAGCCAATTACGACGCCCAGACGGAGTAACCCCAGCCCCCGCCACACCACCCCTTGCCAAAGTCA
TCTGCCTGCTCCCCGGGGGAGAGGACCGCCGGCCTCAGCTACTAGCCCACCAGCCCACCAGGGAGAAAAGAAGCCATGAGAGGCAGCGCC
CGCCACCCTGTGTCCACAGCCCCCACCTTCCCGCTTCCCTTAGAACCCTGCCGTGTCCTATCTCATGACGCTCATGGAACCTCTTTCTTT
GATCTTCTTTTTCTTTTCTCCCCCTCTTTTTTGTTCTAAAGAAAAGTCATTTTGATGCAAGGTCCTGCCTGCCATCAGATCCGAGGTGCC
TCCTGCAGTGACCCCTTTTCCTGGCATTTCTCTTCCACGCGACGAGGTCTGCCTAGTGAGATCTGCATGACCTCACGTTGCTTTCCAGAG
CCCGGGCCTATTTTGCCATCTCAGTTTTCCTGGACCCTGCTTCCTGTGTACCACTGAGGGGCAGCTGGGCCAGGAGCTGTGCCCGGTGCC
TGCAGCCTTCATAAGCACACACGTCCATTCCCTACTAAGGCCCAGACCTCCTGGTATCTGCCCCGGGCTCCCTCATCCCACCTCCATCCG
GAGTTGCCTAAGATGCATGTCCAGCATAGGCAGGATTGCTCGGTGGTGAGAAGGTTAGGTCCGGCTCAGACTGAATAAGAAGAGATAAAA
TTTGCCTTAAAACTTACCTGGCAGTGGCTTTGCTGCACGGTCTGAAACCACCTGTTCCCACCCTCTTGACCGAAATTTCCTTGTGACACA
GAGAAGGGCAAAGGTCTGAGCCCAGAGTTGACGGAGGGAGTATTTCAGGGTTCACTTCAGGGGCTCCCAAAGCGACAAGATCGTTAGGGA
GAGAGGCCCAGGGTGGGGACTGGGAATTTAAGGAGAGCTGGGAACGGATCCCTTAGGTTCAGGAAGCTTCTGTGTAAGCTGCGAGGATGG
CTTGGGCCGAAGGGTTGCTCTGCCCGCCGCGCTAGCTGTGAGCTGAGCAAAGCCCTGGGCTCACAGCACCCCAAAAGCCTGTGGCTTCAG
TCCTGCGTCTGCACCACACATTCAAAAGGATCGTTTTGTTTTGTTTTTAAAGAAAGGTGAGATTGGCTTGGTTCTTCATGAGCACATTTG
ATATAGCTCTTTTTCTGTTTTTCCTTGCTCATTTCGTTTTGGGGAAGAAATCTGTACTGTATTGGGATTGTAAAGAACATCTCTGCACTC

>In-frame_ENST00000518825_ENST00000262428_TCGA-V1-A9ZR-01A_CTNNA1_chr5_138119061_+_COTL1_chr16_84600561_length(amino acids)=112AA_start in transcript=391_stop in transcript=53
MAPPAFFSSLLMKSSSSSFRSLITNSLAKFLFSNIFYSSHKLLLEKLALLRNFIPLLQEILSCLFNRCSQNMGLLRTTSLLIRGPFTIGV

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

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Fusion Gene PPI Analysis for CTNNA1-COTL1


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
HgeneCTNNA1chr5:138119061chr16:84600561ENST00000302763+318325_394100.33333333333333907.0alpha-actinin
HgeneCTNNA1chr5:138119061chr16:84600561ENST00000540387+112325_3940537.0alpha-actinin
HgeneCTNNA1chr5:138119061chr16:84600561ENST00000302763+31897_148100.33333333333333907.0JUP and CTNNB1
HgeneCTNNA1chr5:138119061chr16:84600561ENST00000540387+11297_1480537.0JUP and CTNNB1


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 CTNNA1-COTL1


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 CTNNA1-COTL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCTNNA1C1708349Hereditary Diffuse Gastric Cancer3ORPHANET
HgeneCTNNA1C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneCTNNA1C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneCTNNA1C0238198Gastrointestinal Stromal Tumors1CTD_human
HgeneCTNNA1C1837029Macular Dystrophy, Butterfly-Shaped Pigmentary, 21CTD_human;UNIPROT
HgeneCTNNA1C1868569Patterned dystrophy of retinal pigment epithelium1CTD_human
HgeneCTNNA1C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneCTNNA1C2713368Hematopoetic Myelodysplasia1CTD_human
HgeneCTNNA1C3179349Gastrointestinal Stromal Sarcoma1CTD_human
HgeneCTNNA1C3463824MYELODYSPLASTIC SYNDROME1CTD_human
HgeneCTNNA1C4511237Butterfly-shaped pigmentary macular dystrophy1ORPHANET
TgeneCOTL1C0006142Malignant neoplasm of breast1CTD_human
TgeneCOTL1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneCOTL1C0678222Breast Carcinoma1CTD_human
TgeneCOTL1C1257931Mammary Neoplasms, Human1CTD_human
TgeneCOTL1C1458155Mammary Neoplasms1CTD_human
TgeneCOTL1C4704874Mammary Carcinoma, Human1CTD_human