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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:CTDSPL-TNRC6B

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CTDSPL-TNRC6B
	FusionPDB ID: 20212
	FusionGDB2.0 ID: 20212
		Hgene	Tgene
	Gene symbol	CTDSPL	TNRC6B
	Gene ID	10217	23112
	Gene name	CTD small phosphatase like	trinucleotide repeat containing adaptor 6B
	Synonyms	C3orf8\|HYA22\|PSR1\|RBSP3\|SCP3	-
	Cytomap	3p22.2	22q13.1
	Type of gene	protein-coding	protein-coding
	Description	CTD small phosphatase-like proteinCTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-likeCTDSP-likeNIF-like proteinNLI-interacting factor 1RB protein serine phosphatase from chromosome 3carboxy-terminal domain RNA poly	trinucleotide repeat-containing gene 6B proteintrinucleotide repeat containing 6B
	Modification date	20200313	20200313
	UniProtAcc	Q05D32	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000273179, ENST00000443503, ENST00000310189,	ENST00000497559, ENST00000301923, ENST00000335727, ENST00000402203, ENST00000454349,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 6 X 6=288	16 X 20 X 6=1920
	# samples	8	22
	** MAII score	log2(8/288*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(22/1920*10)=-3.12553088208386 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CTDSPL [Title/Abstract] AND TNRC6B [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CTDSPL(37988702)-TNRC6B(40717094), # samples:3
Anticipated loss of major functional domain due to fusion event.	CTDSPL-TNRC6B 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. CTDSPL-TNRC6B 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. CTDSPL-TNRC6B 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. CTDSPL-TNRC6B 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Fusion gene breakpoints across CTDSPL (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across TNRC6B (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

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	THYM	TCGA-XM-A8RF-01A	CTDSPL	chr3	37988702	-	TNRC6B	chr22	40717094	+
ChimerDB4	THYM	TCGA-XM-A8RF-01A	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+
ChimerDB4	THYM	TCGA-XM-A8RF	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000443503	CTDSPL	chr3	37988702	+	ENST00000301923	TNRC6B	chr22	40717094	+	13568	474	66	1001	311
ENST00000443503	CTDSPL	chr3	37988702	+	ENST00000402203	TNRC6B	chr22	40717094	+	1121	474	66	1001	311
ENST00000443503	CTDSPL	chr3	37988702	+	ENST00000454349	TNRC6B	chr22	40717094	+	13568	474	66	1001	311
ENST00000443503	CTDSPL	chr3	37988702	+	ENST00000335727	TNRC6B	chr22	40717094	+	13569	474	66	1001	311
ENST00000273179	CTDSPL	chr3	37988702	+	ENST00000301923	TNRC6B	chr22	40717094	+	13354	260	26	787	253
ENST00000273179	CTDSPL	chr3	37988702	+	ENST00000402203	TNRC6B	chr22	40717094	+	907	260	26	787	253
ENST00000273179	CTDSPL	chr3	37988702	+	ENST00000454349	TNRC6B	chr22	40717094	+	13354	260	26	787	253
ENST00000273179	CTDSPL	chr3	37988702	+	ENST00000335727	TNRC6B	chr22	40717094	+	13355	260	26	787	253

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000443503	ENST00000301923	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.01952042	0.9804796
ENST00000443503	ENST00000402203	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.10708357	0.89291644
ENST00000443503	ENST00000454349	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.01952042	0.9804796
ENST00000443503	ENST00000335727	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.01841947	0.98158056
ENST00000273179	ENST00000301923	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.018500816	0.98149925
ENST00000273179	ENST00000402203	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.08041126	0.91958874
ENST00000273179	ENST00000454349	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.018500816	0.98149925
ENST00000273179	ENST00000335727	CTDSPL	chr3	37988702	+	TNRC6B	chr22	40717094	+	0.017458232	0.9825418

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Fusion Amino Acid Sequences

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

>20212_20212_1_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000273179_TNRC6B_chr22_40717094_ENST00000301923_length(amino acids)=253AA_BP=78
MDGPAIITQVTNPKEDEGRLPGAGEKASQCNVSLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQ
HGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVG

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

>20212_20212_2_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000273179_TNRC6B_chr22_40717094_ENST00000335727_length(amino acids)=253AA_BP=78
MDGPAIITQVTNPKEDEGRLPGAGEKASQCNVSLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQ
HGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVG

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

>20212_20212_3_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000273179_TNRC6B_chr22_40717094_ENST00000402203_length(amino acids)=253AA_BP=78
MDGPAIITQVTNPKEDEGRLPGAGEKASQCNVSLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQ
HGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVG

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

>20212_20212_4_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000273179_TNRC6B_chr22_40717094_ENST00000454349_length(amino acids)=253AA_BP=78
MDGPAIITQVTNPKEDEGRLPGAGEKASQCNVSLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQ
HGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVG

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

>20212_20212_5_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000443503_TNRC6B_chr22_40717094_ENST00000301923_length(amino acids)=311AA_BP=136
MGRGPGPPLPERGAGRRARPGSGCERPPAPRPRAPRAAPPRAWLAGGRACGRPPRRAPMDGPAIITQVTNPKEDEGRLPGAGEKASQCNV
SLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTA
LHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVGPALNLFGGSTGLGQWSSSAGGSSGADLAGASL

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

>20212_20212_6_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000443503_TNRC6B_chr22_40717094_ENST00000335727_length(amino acids)=311AA_BP=136
MGRGPGPPLPERGAGRRARPGSGCERPPAPRPRAPRAAPPRAWLAGGRACGRPPRRAPMDGPAIITQVTNPKEDEGRLPGAGEKASQCNV
SLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTA
LHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVGPALNLFGGSTGLGQWSSSAGGSSGADLAGASL

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

>20212_20212_7_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000443503_TNRC6B_chr22_40717094_ENST00000402203_length(amino acids)=311AA_BP=136
MGRGPGPPLPERGAGRRARPGSGCERPPAPRPRAPRAAPPRAWLAGGRACGRPPRRAPMDGPAIITQVTNPKEDEGRLPGAGEKASQCNV
SLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTA
LHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVGPALNLFGGSTGLGQWSSSAGGSSGADLAGASL

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

>20212_20212_8_CTDSPL-TNRC6B_CTDSPL_chr3_37988702_ENST00000443503_TNRC6B_chr22_40717094_ENST00000454349_length(amino acids)=311AA_BP=136
MGRGPGPPLPERGAGRRARPGSGCERPPAPRPRAPRAAPPRAWLAGGRACGRPPRRAPMDGPAIITQVTNPKEDEGRLPGAGEKASQCNV
SLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTA
LHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVGPALNLFGGSTGLGQWSSSAGGSSGADLAGASL

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:37988702/chr22:40717094)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
CTDSPL Q05D32	.
FUNCTION: Probable phosphatase. {ECO:0000250}.	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.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000301923

1150_1220

854.0

1030.0

Compositional bias

Note=Gln-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000402203

1150_1220

854.0

1030.0

Compositional bias

Note=Gln-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000301923

1648_1720

854.0

1030.0

Domain

Note=RRM

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000335727

1648_1720

1548.0

1724.0

Domain

Note=RRM

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000402203

1648_1720

854.0

1030.0

Domain

Note=RRM

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000301923

1472_1490

854.0

1030.0

Region

Note=PABPC1-interacting motif-2 (PAM2)

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000402203

1472_1490

854.0

1030.0

Region

Note=PABPC1-interacting motif-2 (PAM2)

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

CTDSPL

chr3:37988702

chr22:40717094

ENST00000273179

102_260

78.0

277.0

Domain

FCP1 homology

Hgene

CTDSPL

chr3:37988702

chr22:40717094

ENST00000443503

102_260

78.0

266.0

Domain

FCP1 homology

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000301923

1_39

854.0

1030.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000335727

1_39

1548.0

1724.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000402203

1_39

854.0

1030.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000454349

1_39

1658.0

1834.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000301923

825_880

854.0

1030.0

Compositional bias

Note=Pro-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000335727

1150_1220

1548.0

1724.0

Compositional bias

Note=Gln-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000335727

825_880

1548.0

1724.0

Compositional bias

Note=Pro-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000402203

825_880

854.0

1030.0

Compositional bias

Note=Pro-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000454349

1150_1220

1658.0

1834.0

Compositional bias

Note=Gln-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000454349

825_880

1658.0

1834.0

Compositional bias

Note=Pro-rich

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000454349

1648_1720

1658.0

1834.0

Domain

Note=RRM

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000335727

1472_1490

1548.0

1724.0

Region

Note=PABPC1-interacting motif-2 (PAM2)

Tgene

TNRC6B

chr3:37988702

chr22:40717094

ENST00000454349

1472_1490

1658.0

1834.0

Region

Note=PABPC1-interacting motif-2 (PAM2)

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Fusion Protein Structures

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)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>565_CTDSPL_37988702_TNRC6B_40717094_ranked_0.pdb	CTDSPL	37988702	37988702	ENST00000335727	TNRC6B	chr22	40717094	+	MGRGPGPPLPERGAGRRARPGSGCERPPAPRPRAPRAAPPRAWLAGGRACGRPPRRAPMDGPAIITQVTNPKEDEGRLPGAGEKASQCNV SLKKQRSRSILSSFFCCFRDYNVEAPPPSSPSVLPPLVEENGGLQKIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTA LHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVGPALNLFGGSTGLGQWSSSAGGSSGADLAGASL	311

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pLDDT score distribution

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.

CTDSPL_pLDDT.png

TNRC6B_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

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

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
CTDSPL
TNRC6B

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Tgene	TNRC6B	chr3:37988702	chr22:40717094	ENST00000301923		21	24	1_994	854.0	1030.0	argonaute proteins
Tgene	TNRC6B	chr3:37988702	chr22:40717094	ENST00000335727		18	21	1_994	1548.0	1724.0	argonaute proteins
Tgene	TNRC6B	chr3:37988702	chr22:40717094	ENST00000402203		21	24	1_994	854.0	1030.0	argonaute proteins
Tgene	TNRC6B	chr3:37988702	chr22:40717094	ENST00000454349		20	23	1_994	1658.0	1834.0	argonaute proteins

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Related Drugs to CTDSPL-TNRC6B

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to CTDSPL-TNRC6B

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source