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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:EIF4ENIF1-C22orf24

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: EIF4ENIF1-C22orf24
	FusionPDB ID: 25995
	FusionGDB2.0 ID: 25995
		Hgene	Tgene
	Gene symbol	EIF4ENIF1	C22orf24
	Gene ID	56478	25775
	Gene name	eukaryotic translation initiation factor 4E nuclear import factor 1	chromosome 22 open reading frame 24
	Synonyms	4E-T\|Clast4	HSN44A4A
	Cytomap	22q12.2	22q12.3
	Type of gene	protein-coding	protein-coding
	Description	eukaryotic translation initiation factor 4E transporter2610509L04Rik4E-transportereIF4E transporter	uncharacterized protein C22orf24
	Modification date	20200327	20200320
	UniProtAcc	Q9NRA8	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000330125, ENST00000344710, ENST00000397523, ENST00000397525, ENST00000382180, ENST00000441289,	ENST00000486651, ENST00000248984, ENST00000543051,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 5 X 5=125	3 X 3 X 3=27
	# samples	6	4
	** MAII score	log2(6/125*10)=-1.05889368905357 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/27*10)=0.567040592723894 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: EIF4ENIF1 [Title/Abstract] AND C22orf24 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	EIF4ENIF1(31867830)-C22orf24(32330435), # samples:3
Anticipated loss of major functional domain due to fusion event.	EIF4ENIF1-C22orf24 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. EIF4ENIF1-C22orf24 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. EIF4ENIF1-C22orf24 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. EIF4ENIF1-C22orf24 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 EIF4ENIF1 (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 C22orf24 (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	PRAD	TCGA-XK-AAIV-01A	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-
ChimerDB4	PRAD	TCGA-XK-AAIV	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-

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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)
ENST00000344710	EIF4ENIF1	chr22	31867830	-	ENST00000248984	C22orf24	chr22	32330435	-	1257	328	428	0	143
ENST00000344710	EIF4ENIF1	chr22	31867830	-	ENST00000543051	C22orf24	chr22	32330435	-	767	328	312	659	115
ENST00000397525	EIF4ENIF1	chr22	31867830	-	ENST00000248984	C22orf24	chr22	32330435	-	1323	394	494	0	165
ENST00000397525	EIF4ENIF1	chr22	31867830	-	ENST00000543051	C22orf24	chr22	32330435	-	833	394	378	725	115
ENST00000330125	EIF4ENIF1	chr22	31867830	-	ENST00000248984	C22orf24	chr22	32330435	-	1174	245	229	576	115
ENST00000330125	EIF4ENIF1	chr22	31867830	-	ENST00000543051	C22orf24	chr22	32330435	-	684	245	229	576	115
ENST00000397523	EIF4ENIF1	chr22	31867830	-	ENST00000248984	C22orf24	chr22	32330435	-	1126	197	181	528	115
ENST00000397523	EIF4ENIF1	chr22	31867830	-	ENST00000543051	C22orf24	chr22	32330435	-	636	197	181	528	115

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
ENST00000344710	ENST00000248984	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.35368124	0.64631873
ENST00000344710	ENST00000543051	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.27252516	0.72747487
ENST00000397525	ENST00000248984	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.1630451	0.8369549
ENST00000397525	ENST00000543051	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.11046454	0.8895355
ENST00000330125	ENST00000248984	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.24847125	0.7515288
ENST00000330125	ENST00000543051	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.12369048	0.8763095
ENST00000397523	ENST00000248984	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.36708385	0.63291615
ENST00000397523	ENST00000543051	EIF4ENIF1	chr22	31867830	-	C22orf24	chr22	32330435	-	0.119861364	0.8801386

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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

>25995_25995_1_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000330125_C22orf24_chr22_32330435_ENST00000248984_length(amino acids)=115AA_BP=5
MKNMTGFSINLTSFGRIPWPHAGVGTCPSPQSWISPFLQSHREHHYAKTSSHSQPSPQSLALCLAYSRCSINICQMTECISLASGCHQAL

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

>25995_25995_2_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000330125_C22orf24_chr22_32330435_ENST00000543051_length(amino acids)=115AA_BP=5
MKNMTGFSINLTSFGRIPWPHAGVGTCPSPQSWISPFLQSHREHHYAKTSSHSQPSPQSLALCLAYSRCSINICQMTECISLASGCHQAL

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

>25995_25995_3_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000344710_C22orf24_chr22_32330435_ENST00000248984_length(amino acids)=143AA_BP=1
MKKGRNPALWARAGAHSSVRPRDPSKRSQVDTETCHIFQKGMKASVWNGGVLLYPRVLLLYSDGGIWRQEASSGQGKHLHFLFHPYFSYP

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

>25995_25995_4_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000344710_C22orf24_chr22_32330435_ENST00000543051_length(amino acids)=115AA_BP=5
MKNMTGFSINLTSFGRIPWPHAGVGTCPSPQSWISPFLQSHREHHYAKTSSHSQPSPQSLALCLAYSRCSINICQMTECISLASGCHQAL

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

>25995_25995_5_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000397523_C22orf24_chr22_32330435_ENST00000248984_length(amino acids)=115AA_BP=5
MKNMTGFSINLTSFGRIPWPHAGVGTCPSPQSWISPFLQSHREHHYAKTSSHSQPSPQSLALCLAYSRCSINICQMTECISLASGCHQAL

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

>25995_25995_6_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000397523_C22orf24_chr22_32330435_ENST00000543051_length(amino acids)=115AA_BP=5
MKNMTGFSINLTSFGRIPWPHAGVGTCPSPQSWISPFLQSHREHHYAKTSSHSQPSPQSLALCLAYSRCSINICQMTECISLASGCHQAL

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

>25995_25995_7_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000397525_C22orf24_chr22_32330435_ENST00000248984_length(amino acids)=165AA_BP=1
MKKGRNPALWARAGAHSSVRPRDPSKRSQVDTETCHIFQKGMKASVWNGGVLLYPRVLLLYSDGGIWRQEASSGQGKHLHFLFHPYFSYP

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

>25995_25995_8_EIF4ENIF1-C22orf24_EIF4ENIF1_chr22_31867830_ENST00000397525_C22orf24_chr22_32330435_ENST00000543051_length(amino acids)=115AA_BP=5
MKNMTGFSINLTSFGRIPWPHAGVGTCPSPQSWISPFLQSHREHHYAKTSSHSQPSPQSLALCLAYSRCSINICQMTECISLASGCHQAL

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

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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/chr22:31867830/chr22:32330435)
- 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
EIF4ENIF1 Q9NRA8	.
FUNCTION: EIF4E-binding protein that regulates translation and stability of mRNAs in processing bodies (P-bodies) (PubMed:16157702, PubMed:24335285, PubMed:27342281, PubMed:32354837). Plays a key role in P-bodies to coordinate the storage of translationally inactive mRNAs in the cytoplasm and prevent their degradation (PubMed:24335285, PubMed:32354837). Acts as a binding platform for multiple RNA-binding proteins: promotes deadenylation of mRNAs via its interaction with the CCR4-NOT complex, and blocks decapping via interaction with eIF4E (EIF4E and EIF4E2), thereby protecting deadenylated and repressed mRNAs from degradation (PubMed:27342281, PubMed:32354837). Component of a multiprotein complex that sequesters and represses translation of proneurogenic factors during neurogenesis (By similarity). Promotes miRNA-mediated translational repression (PubMed:24335285, PubMed:27342281, PubMed:28487484). Required for the formation of P-bodies (PubMed:16157702, PubMed:22966201, PubMed:27342281, PubMed:32354837). Involved in mRNA translational repression mediated by the miRNA effector TNRC6B by protecting TNRC6B-targeted mRNAs from decapping and subsequent decay (PubMed:32354837). Also acts as a nucleoplasmic shuttling protein, which mediates the nuclear import of EIF4E and DDX6 by a piggy-back mechanism (PubMed:10856257, PubMed:28216671). {ECO:0000250\|UniProtKB:Q9EST3, ECO:0000269\|PubMed:10856257, ECO:0000269\|PubMed:16157702, ECO:0000269\|PubMed:22966201, ECO:0000269\|PubMed:24335285, ECO:0000269\|PubMed:27342281, ECO:0000269\|PubMed:28216671, ECO:0000269\|PubMed:28487484, ECO:0000269\|PubMed:32354837}.	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

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

1_24

56.666666666666664

986.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

1_24

56.666666666666664

812.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

1_24

56.666666666666664

986.0

Region

Disordered

- 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

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

148_210

56.666666666666664

986.0

Compositional bias

Note=Arg-rich

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

148_210

56.666666666666664

812.0

Compositional bias

Note=Arg-rich

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

148_210

56.666666666666664

986.0

Compositional bias

Note=Arg-rich

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

195_211

56.666666666666664

986.0

Motif

Nuclear localization signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

438_447

56.666666666666664

986.0

Motif

Nuclear export signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

613_638

56.666666666666664

986.0

Motif

Nuclear export signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

195_211

56.666666666666664

812.0

Motif

Nuclear localization signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

438_447

56.666666666666664

812.0

Motif

Nuclear export signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

613_638

56.666666666666664

812.0

Motif

Nuclear export signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

195_211

56.666666666666664

986.0

Motif

Nuclear localization signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

438_447

56.666666666666664

986.0

Motif

Nuclear export signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

613_638

56.666666666666664

986.0

Motif

Nuclear export signal

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

664_693

56.666666666666664

986.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

707_803

56.666666666666664

986.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000330125

922_953

56.666666666666664

986.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

664_693

56.666666666666664

812.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

707_803

56.666666666666664

812.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000344710

922_953

56.666666666666664

812.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

664_693

56.666666666666664

986.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

707_803

56.666666666666664

986.0

Region

Disordered

Hgene

EIF4ENIF1

chr22:31867830

chr22:32330435

ENST00000397525

922_953

56.666666666666664

986.0

Region

Disordered

Tgene

C22orf24

chr22:31867830

chr22:32330435

ENST00000248984

27_47

50.333333333333336

161.0

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 >>>163_EIF4ENIF1_31867830_C22orf24_32330435_ranked_0.pdb	EIF4ENIF1	31867830	31867830	ENST00000543051	C22orf24	chr22	32330435	-	MKKGRNPALWARAGAHSSVRPRDPSKRSQVDTETCHIFQKGMKASVWNGGVLLYPRVLLLYSDGGIWRQEASSGQGKHLHFLFHPYFSYP	165

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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.

EIF4ENIF1_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
EIF4ENIF1
C22orf24

- 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
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000330125	-	3	19	131_161	56.666666666666664	986.0	CSDE1
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000344710	-	3	17	131_161	56.666666666666664	812.0	CSDE1
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000397525	-	3	19	131_161	56.666666666666664	986.0	CSDE1
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000330125	-	3	19	219_240	56.666666666666664	986.0	DDX6
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000344710	-	3	17	219_240	56.666666666666664	812.0	DDX6
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000397525	-	3	19	219_240	56.666666666666664	986.0	DDX6
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000330125	-	3	19	448_490	56.666666666666664	986.0	LSM14A
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000330125	-	3	19	940_985	56.666666666666664	986.0	LSM14A
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000344710	-	3	17	448_490	56.666666666666664	812.0	LSM14A
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000344710	-	3	17	940_985	56.666666666666664	812.0	LSM14A
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000397525	-	3	19	448_490	56.666666666666664	986.0	LSM14A
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000397525	-	3	19	940_985	56.666666666666664	986.0	LSM14A
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000330125	-	3	19	695_713	56.666666666666664	986.0	PATL1
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000344710	-	3	17	695_713	56.666666666666664	812.0	PATL1
Hgene	EIF4ENIF1	chr22:31867830	chr22:32330435	ENST00000397525	-	3	19	695_713	56.666666666666664	986.0	PATL1

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Related Drugs to EIF4ENIF1-C22orf24

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 EIF4ENIF1-C22orf24

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