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Fusion Protein:CFTR-SEC23IP

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CFTR-SEC23IP
	FusionPDB ID: 16156
	FusionGDB2.0 ID: 16156
		Hgene	Tgene
	Gene symbol	CFTR	SEC23IP
	Gene ID	1080	11196
	Gene name	CF transmembrane conductance regulator	SEC23 interacting protein
	Synonyms	ABC35\|ABCC7\|CF\|CFTR/MRP\|MRP7\|TNR-CFTR\|dJ760C5.1	MSTP053\|P125\|P125A
	Cytomap	7q31.2	10q26.11-q26.12
	Type of gene	protein-coding	protein-coding
	Description	cystic fibrosis transmembrane conductance regulatorcAMP-dependent chloride channelchannel conductance-controlling ATPasecystic fibrosis transmembrane conductance regulatingcystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-f	SEC23-interacting protein
	Modification date	20200329	20200313
	UniProtAcc	P13569 Main function of 5'-partner protein: FUNCTION: Epithelial ion channel that plays an important role in the regulation of epithelial ion and water transport and fluid homeostasis (PubMed:26823428). Mediates the transport of chloride ions across the cell membrane (PubMed:10792060, PubMed:11524016, PubMed:11707463, PubMed:12519745, PubMed:15010471, PubMed:12588899, PubMed:17036051, PubMed:19398555, PubMed:19621064, PubMed:22178883, PubMed:25330774, PubMed:1712898, PubMed:8910473, PubMed:9804160, PubMed:12529365, PubMed:17182731, PubMed:26846474, PubMed:28087700). Channel activity is coupled to ATP hydrolysis (PubMed:8910473). The ion channel is also permeable to HCO(3-); selectivity depends on the extracellular chloride concentration (PubMed:15010471, PubMed:19019741). Exerts its function also by modulating the activity of other ion channels and transporters (PubMed:12403779, PubMed:22178883, PubMed:22121115, PubMed:27941075). Plays an important role in airway fluid homeostasis (PubMed:16645176, PubMed:19621064, PubMed:26823428). Contributes to the regulation of the pH and the ion content of the airway surface fluid layer and thereby plays an important role in defense against pathogens (PubMed:14668433, PubMed:16645176, PubMed:26823428). Modulates the activity of the epithelial sodium channel (ENaC) complex, in part by regulating the cell surface expression of the ENaC complex (PubMed:17434346, PubMed:27941075, PubMed:17182731). Inhibits the activity of the ENaC channel containing subunits SCNN1A, SCNN1B and SCNN1G (PubMed:17182731). Inhibits the activity of the ENaC channel containing subunits SCNN1D, SCNN1B and SCNN1G, but not of the ENaC channel containing subunits SCNN1A, SCNN1B and SCNN1G (PubMed:27941075). May regulate bicarbonate secretion and salvage in epithelial cells by regulating the transporter SLC4A7 (PubMed:12403779). Can inhibit the chloride channel activity of ANO1 (PubMed:22178883). Plays a role in the chloride and bicarbonate homeostasis during sperm epididymal maturation and capacitation (PubMed:19923167, PubMed:27714810). {ECO:0000269\|PubMed:10792060, ECO:0000269\|PubMed:11524016, ECO:0000269\|PubMed:11707463, ECO:0000269\|PubMed:12403779, ECO:0000269\|PubMed:12519745, ECO:0000269\|PubMed:12529365, ECO:0000269\|PubMed:12588899, ECO:0000269\|PubMed:14668433, ECO:0000269\|PubMed:15010471, ECO:0000269\|PubMed:16645176, ECO:0000269\|PubMed:17036051, ECO:0000269\|PubMed:1712898, ECO:0000269\|PubMed:17182731, ECO:0000269\|PubMed:19019741, ECO:0000269\|PubMed:19398555, ECO:0000269\|PubMed:19621064, ECO:0000269\|PubMed:22178883, ECO:0000269\|PubMed:25330774, ECO:0000269\|PubMed:26627831, ECO:0000269\|PubMed:26823428, ECO:0000269\|PubMed:26846474, ECO:0000269\|PubMed:27714810, ECO:0000269\|PubMed:27941075, ECO:0000269\|PubMed:28087700, ECO:0000269\|PubMed:8910473, ECO:0000269\|PubMed:9804160, ECO:0000305\|PubMed:19923167}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000003084, ENST00000454343, ENST00000608965,	ENST00000475542, ENST00000369075, ENST00000543134,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 5 X 3=90	7 X 9 X 4=252
	# samples	6	7
	** MAII score	log2(6/90*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/252*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CFTR [Title/Abstract] AND SEC23IP [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CFTR [Title/Abstract] AND SEC23IP [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CFTR(117199709)-SEC23IP(121685548), # samples:1
Anticipated loss of major functional domain due to fusion event.	CFTR-SEC23IP 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. CFTR-SEC23IP 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. CFTR-SEC23IP 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. CFTR-SEC23IP 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	CFTR	GO:0015701	bicarbonate transport	15010471\|19019741
Hgene	CFTR	GO:0034976	response to endoplasmic reticulum stress	21884936\|28067262
Hgene	CFTR	GO:1902476	chloride transmembrane transport	11524016\|11707463\|19019741
Hgene	CFTR	GO:1902943	positive regulation of voltage-gated chloride channel activity	22006324
Hgene	CFTR	GO:1904322	cellular response to forskolin	15010471\|19621064

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:117199709/chr10:121685548)
- 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.

Retention analysis results 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, are available here.

Fusion gene breakpoints across CFTR (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 SEC23IP (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 Amino Acid Sequences

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)

ENST00000003084

CFTR

chr7

117199709

ENST00000369075

SEC23IP

chr10

121685548

4179

1716

2597

836

ENST00000003084

CFTR

chr7

117199709

ENST00000543134

SEC23IP

chr10

121685548

2767

1716

2597

836

ENST00000454343

CFTR

chr7

117199709

ENST00000369075

SEC23IP

chr10

121685548

3996

1533

2414

775

ENST00000454343

CFTR

chr7

117199709

ENST00000543134

SEC23IP

chr10

121685548

2584

1533

2414

775

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
ENST00000003084	ENST00000369075	CFTR	chr7	117199709	+	SEC23IP	chr10	121685548	+	0.000426627	0.9995734
ENST00000003084	ENST00000543134	CFTR	chr7	117199709	+	SEC23IP	chr10	121685548	+	0.000857176	0.99914277
ENST00000454343	ENST00000369075	CFTR	chr7	117199709	+	SEC23IP	chr10	121685548	+	0.000571279	0.9994287
ENST00000454343	ENST00000543134	CFTR	chr7	117199709	+	SEC23IP	chr10	121685548	+	0.001195157	0.9988048

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for CFTR-SEC23IP

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
CFTR	chr7	117199709	SEC23IP	chr10	121685548	1533	482	RYRSVIKACQLEEKKAASEKKAVAAT
CFTR	chr7	117199709	SEC23IP	chr10	121685548	1716	543	RYRSVIKACQLEEKKAASEKKAVAAT

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Potential FusionNeoAntigen Information of CFTR-SEC23IP in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA I

FusionNeoAntigen peptide

Binding score

Immunogenic score

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of CFTR-SEC23IP in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of CFTR-SEC23IP

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CFTR-SEC23IP

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele

PDB ID

File name

BPseq

Docking score

Glide score

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Vaccine Design for the FusionNeoAntigens of CFTR-SEC23IP

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide sequence

FusionNeoAntigen RNA sequence

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of CFTR-SEC23IP

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type

Fusion gene

Hchr

Hbp

Henst

Tchr

Tbp

Tenst

Sample

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Potential target of CAR-T therapy development for CFTR-SEC23IP

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000003084

123_146

528

1481.0

Transmembrane

Helical%3B Name%3D2

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000003084

196_216

528

1481.0

Transmembrane

Helical%3B Name%3D3

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000003084

223_243

528

1481.0

Transmembrane

Helical%3B Name%3D4

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000003084

299_319

528

1481.0

Transmembrane

Helical%3B Name%3D5

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000003084

340_358

528

1481.0

Transmembrane

Helical%3B Name%3D6

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000003084

78_98

528

1481.0

Transmembrane

Helical%3B Name%3D1

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000454343

123_146

467

1420.0

Transmembrane

Helical%3B Name%3D2

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000454343

196_216

467

1420.0

Transmembrane

Helical%3B Name%3D3

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000454343

223_243

467

1420.0

Transmembrane

Helical%3B Name%3D4

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000454343

299_319

467

1420.0

Transmembrane

Helical%3B Name%3D5

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000454343

340_358

467

1420.0

Transmembrane

Helical%3B Name%3D6

Hgene

CFTR

chr7:117199709

chr10:121685548

ENST00000454343

78_98

467

1420.0

Transmembrane

Helical%3B Name%3D1

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to CFTR-SEC23IP

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 CFTR-SEC23IP

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

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)