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Center for Computational Systems Medicine level2
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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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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:CPSF6-COL9A1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CPSF6-COL9A1
FusionPDB ID: 19146
FusionGDB2.0 ID: 19146
HgeneTgene
Gene symbol

CPSF6

COL9A1

Gene ID

11052

1297

Gene namecleavage and polyadenylation specific factor 6collagen type IX alpha 1 chain
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7DJ149L1.1.2|EDM6|MED|STL4
Cytomap

12q15

6q13

Type of geneprotein-codingprotein-coding
Descriptioncleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage collagen alpha-1(IX) chainalpha-1(IX) collagen chaincartilage-specific short collagencollagen IX, alpha-1 polypeptidecollagen, type IX, alpha 1
Modification date2020031320200313
UniProtAcc

Q16630

P20849

Ensembl transtripts involved in fusion geneENST idsENST00000550987, ENST00000266679, 
ENST00000435070, ENST00000456847, 
ENST00000551516, 		ENST00000320755, 
ENST00000357250, ENST00000370499, 
ENST00000489611, ENST00000370496, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score69 X 12 X 19=157327 X 5 X 4=140
# samples 718
** MAII scorelog2(71/15732*10)=-4.46973925655087
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/140*10)=-0.807354922057604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CPSF6 [Title/Abstract] AND COL9A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CPSF6(69633486)-COL9A1(70926784), # samples:4
Anticipated loss of major functional domain due to fusion event.CPSF6-COL9A1 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.
CPSF6-COL9A1 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.
CPSF6-COL9A1 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.
CPSF6-COL9A1 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.
CPSF6-COL9A1 seems lost the major protein functional domain in Hgene 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
HgeneCPSF6

GO:0006397

mRNA processing

14690600

HgeneCPSF6

GO:0051262

protein tetramerization

20695905

HgeneCPSF6

GO:0051290

protein heterotetramerization

23187700

HgeneCPSF6

GO:1990120

messenger ribonucleoprotein complex assembly

29276085


check buttonFusion gene breakpoints across CPSF6 (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 COL9A1 (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
ChimerDB4SARCTCGA-FX-A2QS-01ACPSF6chr12

69633486

-COL9A1chr6

70926784

-
ChimerDB4SARCTCGA-FX-A2QS-01ACPSF6chr12

69633486

+COL9A1chr6

70926784

-
ChimerDB4SARCTCGA-FX-A2QSCPSF6chr12

69633486

+COL9A1chr6

70926784

-


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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)
ENST00000435070CPSF6chr1269633486+ENST00000357250COL9A1chr670926784-219117043813999
ENST00000435070CPSF6chr1269633486+ENST00000370499COL9A1chr670926784-12111703312110
ENST00000456847CPSF6chr1269633486+ENST00000357250COL9A1chr670926784-21281073757699
ENST00000456847CPSF6chr1269633486+ENST00000370499COL9A1chr670926784-11481073757699
ENST00000266679CPSF6chr1269633486+ENST00000357250COL9A1chr670926784-2112913596099
ENST00000266679CPSF6chr1269633486+ENST00000370499COL9A1chr670926784-1132913596099
ENST00000551516CPSF6chr1269633486+ENST00000357250COL9A1chr670926784-2086653333499
ENST00000551516CPSF6chr1269633486+ENST00000370499COL9A1chr670926784-1106653333499

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
ENST00000435070ENST00000357250CPSF6chr1269633486+COL9A1chr670926784-0.070489470.9295106
ENST00000435070ENST00000370499CPSF6chr1269633486+COL9A1chr670926784-0.066966730.9330332
ENST00000456847ENST00000357250CPSF6chr1269633486+COL9A1chr670926784-0.0907824860.9092175
ENST00000456847ENST00000370499CPSF6chr1269633486+COL9A1chr670926784-0.0874730350.9125269
ENST00000266679ENST00000357250CPSF6chr1269633486+COL9A1chr670926784-0.0494363050.9505637
ENST00000266679ENST00000370499CPSF6chr1269633486+COL9A1chr670926784-0.0873372260.91266274
ENST00000551516ENST00000357250CPSF6chr1269633486+COL9A1chr670926784-0.169857130.8301429
ENST00000551516ENST00000370499CPSF6chr1269633486+COL9A1chr670926784-0.1862070.81379294

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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

>19146_19146_1_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000266679_COL9A1_chr6_70926784_ENST00000357250_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

>19146_19146_2_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000266679_COL9A1_chr6_70926784_ENST00000370499_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

>19146_19146_3_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000435070_COL9A1_chr6_70926784_ENST00000357250_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

>19146_19146_4_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000435070_COL9A1_chr6_70926784_ENST00000370499_length(amino acids)=110AA_BP=0
MLADQPAWCRRLAHRNREAQEVPGVQALQEFLPPLGGLAHRLGHFCHSWQGLGHLVELFADIRVNVYVVHAVRHLPSASAAAAAAASCRS

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

>19146_19146_5_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000456847_COL9A1_chr6_70926784_ENST00000357250_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

>19146_19146_6_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000456847_COL9A1_chr6_70926784_ENST00000370499_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

>19146_19146_7_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000551516_COL9A1_chr6_70926784_ENST00000357250_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

>19146_19146_8_CPSF6-COL9A1_CPSF6_chr12_69633486_ENST00000551516_COL9A1_chr6_70926784_ENST00000370499_length(amino acids)=99AA_BP=1
MPQLWMVFLTQAPSPGVVHADSHAAVSLSRVRPFVKCSLTSLHGAGGWLTETGKPRRSRGSRHSRNSCHPWGASLTVSAISAIAGRAWVT

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

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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/chr12:69633486/chr6:70926784)
- 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
CPSF6

Q16630

COL9A1

P20849

FUNCTION: Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:9659921, PubMed:8626397, PubMed:14690600, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:9659921, PubMed:8626397, PubMed:14690600). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elements localized upstream of pA signals and promotes RNA looping, and hence activates directly the mRNA 3'-processing machinery (PubMed:15169763, PubMed:29276085, PubMed:21295486). Plays a role in mRNA export (PubMed:19864460). {ECO:0000269|PubMed:14690600, ECO:0000269|PubMed:15169763, ECO:0000269|PubMed:19864460, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:21295486, ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085, ECO:0000269|PubMed:8626397, ECO:0000269|PubMed:9659921}.; FUNCTION: (Microbial infection) Binds HIV-1 capsid-nucleocapsid (HIV-1 CA-NC) complexes and might thereby promote the integration of the virus in the nucleus of dividing cells (in vitro). {ECO:0000269|PubMed:24130490}.FUNCTION: Structural component of hyaline cartilage and vitreous of the eye.

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
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032655_712617.3333333333334679.0DomainNote=Collagen-like 7
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032713_755617.3333333333334679.0DomainNote=Collagen-like 8
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032790_847617.3333333333334679.0DomainNote=Collagen-like 9
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032848_899617.3333333333334679.0DomainNote=Collagen-like 10
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011269_3240329.0DomainNote=Collagen-like 1
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011325_3560329.0DomainNote=Collagen-like 2
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011358_4030329.0DomainNote=Collagen-like 3
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011416_4720329.0DomainNote=Collagen-like 4
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011473_5160329.0DomainNote=Collagen-like 5
TgeneCOL9A1chr12:69633486chr6:70926784ENST0000037049601150_2440329.0DomainNote=Laminin G-like
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011587_6430329.0DomainNote=Collagen-like 6
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011655_7120329.0DomainNote=Collagen-like 7
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011713_7550329.0DomainNote=Collagen-like 8
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011790_8470329.0DomainNote=Collagen-like 9
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011848_8990329.0DomainNote=Collagen-like 10
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032757_786617.3333333333334679.0RegionNote=Nonhelical region (NC2)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032787_901617.3333333333334679.0RegionNote=Triple-helical region (COL1)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032902_921617.3333333333334679.0RegionNote=Nonhelical region (NC1)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638902_921860.3333333333334922.0RegionNote=Nonhelical region (NC1)
TgeneCOL9A1chr12:69633486chr6:70926784ENST0000037049601124_2680329.0RegionNote=Nonhelical region (NC4)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011269_4050329.0RegionNote=Triple-helical region (COL3)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011406_4170329.0RegionNote=Nonhelical region (NC3)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011418_7560329.0RegionNote=Triple-helical region (COL2)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011757_7860329.0RegionNote=Nonhelical region (NC2)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011787_9010329.0RegionNote=Triple-helical region (COL1)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000370496011902_9210329.0RegionNote=Nonhelical region (NC1)

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111208_39820.0701.3333333333334Compositional biasNote=Pro-rich
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111490_55120.0701.3333333333334Compositional biasNote=Arg-rich
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110208_39820.02111.0Compositional biasNote=Pro-rich
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110490_55120.02111.0Compositional biasNote=Arg-rich
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111202_20620.0701.3333333333334MotifGAR
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110202_20620.02111.0MotifGAR
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111358_55120.0701.3333333333334Region(Microbial infection) Binds to HIV-1 capsid protein p24 (CA)
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111404_55120.0701.3333333333334RegionSufficient for nuclear speckle localization
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111405_55120.0701.3333333333334RegionNecessary for RNA-binding
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+111510_55120.0701.3333333333334RegionSufficient for nuclear targeting
HgeneCPSF6chr12:69633486chr6:70926784ENST00000266679+11181_16120.0701.3333333333334RegionNecessary for nuclear paraspeckles localization
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110358_55120.02111.0Region(Microbial infection) Binds to HIV-1 capsid protein p24 (CA)
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110404_55120.02111.0RegionSufficient for nuclear speckle localization
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110405_55120.02111.0RegionNecessary for RNA-binding
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+110510_55120.02111.0RegionSufficient for nuclear targeting
HgeneCPSF6chr12:69633486chr6:70926784ENST00000435070+11081_16120.02111.0RegionNecessary for nuclear paraspeckles localization
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032269_324617.3333333333334679.0DomainNote=Collagen-like 1
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032325_356617.3333333333334679.0DomainNote=Collagen-like 2
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032358_403617.3333333333334679.0DomainNote=Collagen-like 3
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032416_472617.3333333333334679.0DomainNote=Collagen-like 4
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032473_516617.3333333333334679.0DomainNote=Collagen-like 5
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000320755303250_244617.3333333333334679.0DomainNote=Laminin G-like
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032587_643617.3333333333334679.0DomainNote=Collagen-like 6
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638269_324860.3333333333334922.0DomainNote=Collagen-like 1
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638325_356860.3333333333334922.0DomainNote=Collagen-like 2
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638358_403860.3333333333334922.0DomainNote=Collagen-like 3
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638416_472860.3333333333334922.0DomainNote=Collagen-like 4
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638473_516860.3333333333334922.0DomainNote=Collagen-like 5
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000357250363850_244860.3333333333334922.0DomainNote=Laminin G-like
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638587_643860.3333333333334922.0DomainNote=Collagen-like 6
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638655_712860.3333333333334922.0DomainNote=Collagen-like 7
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638713_755860.3333333333334922.0DomainNote=Collagen-like 8
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638790_847860.3333333333334922.0DomainNote=Collagen-like 9
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638848_899860.3333333333334922.0DomainNote=Collagen-like 10
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000320755303224_268617.3333333333334679.0RegionNote=Nonhelical region (NC4)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032269_405617.3333333333334679.0RegionNote=Triple-helical region (COL3)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032406_417617.3333333333334679.0RegionNote=Nonhelical region (NC3)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003207553032418_756617.3333333333334679.0RegionNote=Triple-helical region (COL2)
TgeneCOL9A1chr12:69633486chr6:70926784ENST00000357250363824_268860.3333333333334922.0RegionNote=Nonhelical region (NC4)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638269_405860.3333333333334922.0RegionNote=Triple-helical region (COL3)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638406_417860.3333333333334922.0RegionNote=Nonhelical region (NC3)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638418_756860.3333333333334922.0RegionNote=Triple-helical region (COL2)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638757_786860.3333333333334922.0RegionNote=Nonhelical region (NC2)
TgeneCOL9A1chr12:69633486chr6:70926784ENST000003572503638787_901860.3333333333334922.0RegionNote=Triple-helical region (COL1)


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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 >>>36_CPSF6_69633486_COL9A1_70926784_ranked_0.pdbCPSF66963348669633486ENST00000370499COL9A1chr670926784-
MLADQPAWCRRLAHRNREAQEVPGVQALQEFLPPLGGLAHRLGHFCHSWQGLGHLVELFADIRVNVYVVHAVRHLPSASAAAAAAASCRS
110


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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.
CPSF6_pLDDT.png
all structure
all structure
COL9A1_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.
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

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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
CPSF6
COL9A1


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 CPSF6-COL9A1


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 CPSF6-COL9A1


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