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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:TADA1-CADM3

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TADA1-CADM3
	FusionPDB ID: 88684
	FusionGDB2.0 ID: 88684
		Hgene	Tgene
	Gene symbol	TADA1	CADM3
	Gene ID	117143	57863
	Gene name	transcriptional adaptor 1	cell adhesion molecule 3
	Synonyms	ADA1\|HFI1\|STAF42\|TADA1L\|hADA1	BIgR\|IGSF4B\|NECL1\|Necl-1\|TSLL1\|synCAM3
	Cytomap	1q24.1	1q23.2
	Type of gene	protein-coding	protein-coding
	Description	transcriptional adapter 1SPT3-associated factor 42 (STAF42)transcriptional adapter 1-like proteintranscriptional adaptor 1 (HFI1 homolog, yeast)	cell adhesion molecule 3TSLC1-like 1brain immunoglobulin receptordendritic cell nectin-like protein 1 short isoformimmunoglobulin superfamily member 4Bsynaptic cell adhesion molecule 3
	Modification date	20200313	20200313
	UniProtAcc	.	Q8N126
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000367874, ENST00000467021,	ENST00000497636, ENST00000368124, ENST00000368125,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 3 X 2=12	3 X 4 X 3=36
	# samples	3	4
	** MAII score	log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(4/36*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: TADA1 [Title/Abstract] AND CADM3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TADA1(166838682)-CADM3(159169541), # samples:3
Anticipated loss of major functional domain due to fusion event.	TADA1-CADM3 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. TADA1-CADM3 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
Hgene	TADA1	GO:0043966	histone H3 acetylation	11564863

Fusion gene breakpoints across TADA1 (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 CADM3 (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	LUAD	TCGA-05-4432-01A	TADA1	chr1	166838681	-	CADM3	chr1	159169540	+
ChimerDB4	LUAD	TCGA-05-4432-01A	TADA1	chr1	166838682	-	CADM3	chr1	159169541	+
ChimerDB4	LUAD	TCGA-05-4432	TADA1	chr1	166838681	-	CADM3	chr1	159169540	+

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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)
ENST00000367874	TADA1	chr1	166838682	-	ENST00000368124	CADM3	chr1	159169541	+	1661	326	1538	822	238
ENST00000367874	TADA1	chr1	166838682	-	ENST00000368125	CADM3	chr1	159169541	+	2962	326	1538	822	238
ENST00000367874	TADA1	chr1	166838681	-	ENST00000368124	CADM3	chr1	159169540	+	1661	326	1538	822	238
ENST00000367874	TADA1	chr1	166838681	-	ENST00000368125	CADM3	chr1	159169540	+	2962	326	1538	822	238

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
ENST00000367874	ENST00000368124	TADA1	chr1	166838682	-	CADM3	chr1	159169541	+	0.005172269	0.9948277
ENST00000367874	ENST00000368125	TADA1	chr1	166838682	-	CADM3	chr1	159169541	+	0.007749539	0.9922504
ENST00000367874	ENST00000368124	TADA1	chr1	166838681	-	CADM3	chr1	159169540	+	0.005172269	0.9948277
ENST00000367874	ENST00000368125	TADA1	chr1	166838681	-	CADM3	chr1	159169540	+	0.007749539	0.9922504

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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

>88684_88684_1_TADA1-CADM3_TADA1_chr1_166838681_ENST00000367874_CADM3_chr1_159169540_ENST00000368124_length(amino acids)=238AA_BP=
MLSNAMGGVVAVQQSRVLGKSEGPLRGGSRGSSGPRAVPLPLLLEQGGAATLCYLQGQFLWKGPGFVHFRGEWGESPPPSFLSKSTLPCR
DPRPPQVTVLGPCMAACCLQATSPQDSRTHHFPIAMEERCQGGTCLPVRSAQVCGYQRKSHSQPLPTTIPFLGSWRSLGSCSVVEAERRA

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

>88684_88684_2_TADA1-CADM3_TADA1_chr1_166838681_ENST00000367874_CADM3_chr1_159169540_ENST00000368125_length(amino acids)=238AA_BP=
MLSNAMGGVVAVQQSRVLGKSEGPLRGGSRGSSGPRAVPLPLLLEQGGAATLCYLQGQFLWKGPGFVHFRGEWGESPPPSFLSKSTLPCR
DPRPPQVTVLGPCMAACCLQATSPQDSRTHHFPIAMEERCQGGTCLPVRSAQVCGYQRKSHSQPLPTTIPFLGSWRSLGSCSVVEAERRA

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

>88684_88684_3_TADA1-CADM3_TADA1_chr1_166838682_ENST00000367874_CADM3_chr1_159169541_ENST00000368124_length(amino acids)=238AA_BP=
MLSNAMGGVVAVQQSRVLGKSEGPLRGGSRGSSGPRAVPLPLLLEQGGAATLCYLQGQFLWKGPGFVHFRGEWGESPPPSFLSKSTLPCR
DPRPPQVTVLGPCMAACCLQATSPQDSRTHHFPIAMEERCQGGTCLPVRSAQVCGYQRKSHSQPLPTTIPFLGSWRSLGSCSVVEAERRA

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

>88684_88684_4_TADA1-CADM3_TADA1_chr1_166838682_ENST00000367874_CADM3_chr1_159169541_ENST00000368125_length(amino acids)=238AA_BP=
MLSNAMGGVVAVQQSRVLGKSEGPLRGGSRGSSGPRAVPLPLLLEQGGAATLCYLQGQFLWKGPGFVHFRGEWGESPPPSFLSKSTLPCR
DPRPPQVTVLGPCMAACCLQATSPQDSRTHHFPIAMEERCQGGTCLPVRSAQVCGYQRKSHSQPLPTTIPFLGSWRSLGSCSVVEAERRA

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

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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/chr1:166838682/chr1:159169541)
- 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
.	CADM3 Q8N126
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: Involved in the cell-cell adhesion. Has both calcium-independent homophilic cell-cell adhesion activity and calcium-independent heterophilic cell-cell adhesion activity with IGSF4, NECTIN1 and NECTIN3. Interaction with EPB41L1 may regulate structure or function of cell-cell junctions (By similarity). {ECO:0000250}.

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

CADM3

chr1:166838681

chr1:159169540

ENST00000368124

352_398

351.3333333333333

433.0

Topological domain

Cytoplasmic

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368125

352_398

317.3333333333333

399.0

Topological domain

Cytoplasmic

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368124

352_398

351.3333333333333

433.0

Topological domain

Cytoplasmic

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368125

352_398

317.3333333333333

399.0

Topological domain

Cytoplasmic

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368125

331_351

317.3333333333333

399.0

Transmembrane

Helical

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368125

331_351

317.3333333333333

399.0

Transmembrane

Helical

- 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

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368124

130_228

351.3333333333333

433.0

Domain

Note=Ig-like C2-type 1

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368124

233_315

351.3333333333333

433.0

Domain

Note=Ig-like C2-type 2

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368124

25_126

351.3333333333333

433.0

Domain

Note=Ig-like V-type

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368125

130_228

317.3333333333333

399.0

Domain

Note=Ig-like C2-type 1

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368125

233_315

317.3333333333333

399.0

Domain

Note=Ig-like C2-type 2

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368125

25_126

317.3333333333333

399.0

Domain

Note=Ig-like V-type

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368124

130_228

351.3333333333333

433.0

Domain

Note=Ig-like C2-type 1

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368124

233_315

351.3333333333333

433.0

Domain

Note=Ig-like C2-type 2

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368124

25_126

351.3333333333333

433.0

Domain

Note=Ig-like V-type

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368125

130_228

317.3333333333333

399.0

Domain

Note=Ig-like C2-type 1

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368125

233_315

317.3333333333333

399.0

Domain

Note=Ig-like C2-type 2

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368125

25_126

317.3333333333333

399.0

Domain

Note=Ig-like V-type

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368124

25_330

351.3333333333333

433.0

Topological domain

Extracellular

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368125

25_330

317.3333333333333

399.0

Topological domain

Extracellular

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368124

25_330

351.3333333333333

433.0

Topological domain

Extracellular

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368125

25_330

317.3333333333333

399.0

Topological domain

Extracellular

Tgene

CADM3

chr1:166838681

chr1:159169540

ENST00000368124

331_351

351.3333333333333

433.0

Transmembrane

Helical

Tgene

CADM3

chr1:166838682

chr1:159169541

ENST00000368124

331_351

351.3333333333333

433.0

Transmembrane

Helical

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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 >>>376_TADA1_166838681_CADM3_159169540_ranked_0.pdb	TADA1	166838681	166838681	ENST00000368125	CADM3	chr1	159169540	+	MLSNAMGGVVAVQQSRVLGKSEGPLRGGSRGSSGPRAVPLPLLLEQGGAATLCYLQGQFLWKGPGFVHFRGEWGESPPPSFLSKSTLPCR DPRPPQVTVLGPCMAACCLQATSPQDSRTHHFPIAMEERCQGGTCLPVRSAQVCGYQRKSHSQPLPTTIPFLGSWRSLGSCSVVEAERRA	238

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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.

TADA1_pLDDT.png

CADM3_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
TADA1
CADM3

- 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

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Related Drugs to TADA1-CADM3

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 TADA1-CADM3

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