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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:FOCAD-ELAVL2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FOCAD-ELAVL2
	FusionPDB ID: 30995
	FusionGDB2.0 ID: 42450
		Hgene	Tgene
	Gene symbol	FOCAD	ELAVL2
	Gene ID	54914	1993
	Gene name	focadhesin	ELAV like RNA binding protein 2
	Synonyms	KIAA1797	HEL-N1\|HELN1\|HUB
	Cytomap	9p21.3	9p21.3
	Type of gene	protein-coding	protein-coding
	Description	focadhesin	ELAV-like protein 2ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)ELAV like neuron-specific RNA binding protein 2ELAV-like neuronal protein 1 isoform Hel-N2hu-antigen Bnervous system-specific RNA-binding protein Hel-N1
	Modification date	20200313	20200313
	UniProtAcc	Q5VW36	Q12926
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000338382, ENST00000380249, ENST00000605086, ENST00000604828,	ENST00000223951, ENST00000380110, ENST00000380117, ENST00000397312, ENST00000462649, ENST00000544538,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 12 X 11=2112	4 X 3 X 4=48
	# samples	17	5
	** MAII score	log2(17/2112*10)=-3.63500318322075 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/48*10)=0.0588936890535686 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: FOCAD [Title/Abstract] AND ELAVL2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FOCAD(20823114)-ELAVL2(23762247), # samples:2
Anticipated loss of major functional domain due to fusion event.	FOCAD-ELAVL2 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. FOCAD-ELAVL2 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 FOCAD (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 ELAVL2 (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	LUSC	TCGA-63-A5MM-01A	FOCAD	chr9	20823114	+	ELAVL2	chr9	23762247	-
ChimerDB4	LUSC	TCGA-63-A5MM	FOCAD	chr9	20823114	+	ELAVL2	chr9	23762247	-
ChimerDB4	LUSC	TCGA-63-A5MM	FOCAD	chr9	20823114	+	ELAVL2	chr9	23765097	-

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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)
ENST00000380249	FOCAD	chr9	20823114	+	ENST00000380110	ELAVL2	chr9	23762247	-	5835	2284	232	3381	1049
ENST00000338382	FOCAD	chr9	20823114	+	ENST00000380110	ELAVL2	chr9	23762247	-	5471	1920	0	3017	1005
ENST00000605086	FOCAD	chr9	20823114	+	ENST00000380110	ELAVL2	chr9	23762247	-	3941	390	99	1487	462

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
ENST00000380249	ENST00000380110	FOCAD	chr9	20823114	+	ELAVL2	chr9	23762247	-	0.000105984	0.999894
ENST00000338382	ENST00000380110	FOCAD	chr9	20823114	+	ELAVL2	chr9	23762247	-	5.46E-05	0.9999454
ENST00000605086	ENST00000380110	FOCAD	chr9	20823114	+	ELAVL2	chr9	23762247	-	0.000111465	0.99988854

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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

>30995_30995_1_FOCAD-ELAVL2_FOCAD_chr9_20823114_ENST00000338382_ELAVL2_chr9_23762247_ENST00000380110_length(amino acids)=1005AA_BP=640
MSDDIRKRFEFPNSLIQSQAVGHLIAAVLKENGFSEKIHQSTNQTPALNLLWEKCCSDNVVVRTACCEGLVALVAQDHAEFSYVLNGILN
LIPSTRNTHGLIKAIMHLLQMQALKEGQGGEKNIQSIYTIRNHPHPLITVLEHRPDCWPVFLQQLTAFFQQCPERLEVSCIQIMAPFLWY
LYCEPSQLQEYAKLRLALLKVLLQPQVLCDKDQPSILEQQILQLCCDIVPCLQVKDLIQTTEAMMFIEEVCLSLLRHPVFWKIQLTQMSL
QLLCVSEVSLKITGECSSSIHLLEHSVELLKEDFPVELVIIGIALLLLQTPASQQKPILNLALKLLSVTEDQKIPKSSLLLVMPILQILS
STALEDCISVDEEGPSRQQLALNLLEMIQQECYRDDHQKLSYKLVCPVTSMYGTIFTAWRILEVMTDSSAASDWLASVESLLPITAVIPA
PAFLLLAHLLVEDKGQNLHQILKVTTELAQADSSQVPNLIPVLMFKLGRPLEPILYNDILYTLPKLGVHKVCIGQILRIIQLLGTTPRLR
AVTLRLLTSLWEKQDRVYPELQRFMAVSDVPSLSVGKEVQWEKLIAKAASIRDICKQRPYQHGADMLAAISQVLNECTKPDQATPAALVL
QGLHALCQAEQVIAAMETQLSNGPTCNNTANGPTTINNNCSSPVDSGNTEDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKI
TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGIS
RGVGFIRFDKRIEAEEAIKGLNGQKPPGATEPITVKFANNPSQKTNQAILSQLYQSPNRRYPGPLAQQAQRFRLDNLLNMAYGVKSRFSP
MTIDGMTSLAGINIPGHPGTGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGD

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

>30995_30995_2_FOCAD-ELAVL2_FOCAD_chr9_20823114_ENST00000380249_ELAVL2_chr9_23762247_ENST00000380110_length(amino acids)=1049AA_BP=684
MFLFGHLCSSLQLTPFLIDHQGNFHPHRLAVENEAAHIHVREAKMSDDIRKRFEFPNSLIQSQAVGHLIAAVLKENGFSEKIHQSTNQTP
ALNLLWEKCCSDNVVVRTACCEGLVALVAQDHAEFSYVLNGILNLIPSTRNTHGLIKAIMHLLQMQALKEGQGGEKNIQSIYTIRNHPHP
LITVLEHRPDCWPVFLQQLTAFFQQCPERLEVSCIQIMAPFLWYLYCEPSQLQEYAKLRLALLKVLLQPQVLCDKDQPSILEQQILQLCC
DIVPCLQVKDLIQTTEAMMFIEEVCLSLLRHPVFWKIQLTQMSLQLLCVSEVSLKITGECSSSIHLLEHSVELLKEDFPVELVIIGIALL
LLQTPASQQKPILNLALKLLSVTEDQKIPKSSLLLVMPILQILSSTALEDCISVDEEGPSRQQLALNLLEMIQQECYRDDHQKLSYKLVC
PVTSMYGTIFTAWRILEVMTDSSAASDWLASVESLLPITAVIPAPAFLLLAHLLVEDKGQNLHQILKVTTELAQADSSQVPNLIPVLMFK
LGRPLEPILYNDILYTLPKLGVHKVCIGQILRIIQLLGTTPRLRAVTLRLLTSLWEKQDRVYPELQRFMAVSDVPSLSVGKEVQWEKLIA
KAASIRDICKQRPYQHGADMLAAISQVLNECTKPDQATPAALVLQGLHALCQAEQVIAAMETQLSNGPTCNNTANGPTTINNNCSSPVDS
GNTEDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS
IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGLNGQKPPGATEPITVKFANNPSQKTN
QAILSQLYQSPNRRYPGPLAQQAQRFRLDNLLNMAYGVKSRFSPMTIDGMTSLAGINIPGHPGTGWCIFVYNLAPDADESILWQMFGPFG

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

>30995_30995_3_FOCAD-ELAVL2_FOCAD_chr9_20823114_ENST00000605086_ELAVL2_chr9_23762247_ENST00000380110_length(amino acids)=462AA_BP=97
MRLLTSLWEKQDRVYPELQRFMAVSDVPSLSVGKEVQWEKLIAKAASIRDICKQRPYQHGADMLAAISQVLNECTKPDQATPAALVLQGL
HALCQAEQVIAAMETQLSNGPTCNNTANGPTTINNNCSSPVDSGNTEDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQ
SLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGISRGV
GFIRFDKRIEAEEAIKGLNGQKPPGATEPITVKFANNPSQKTNQAILSQLYQSPNRRYPGPLAQQAQRFRLDNLLNMAYGVKSRFSPMTI
DGMTSLAGINIPGHPGTGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVL

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

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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/chr9:20823114/chr9:23762247)
- 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
FOCAD Q5VW36	ELAVL2 Q12926
FUNCTION: Potential tumor suppressor in gliomas. {ECO:0000250, ECO:0000269\|PubMed:22427331}.	FUNCTION: RNA-binding protein that binds to the 3' untranslated region (3'UTR) of target mRNAs (By similarity). Seems to recognize a GAAA motif (By similarity). Can bind to its own 3'UTR, the FOS 3'UTR and the ID 3'UTR (By similarity). {ECO:0000250\|UniProtKB:Q60899}.

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

FOCAD

chr9:20823114

chr9:23762247

ENST00000338382

404_424

640.0

1802.0

Transmembrane

Helical

Hgene

FOCAD

chr9:20823114

chr9:23762247

ENST00000338382

441_461

640.0

1802.0

Transmembrane

Helical

Hgene

FOCAD

chr9:20823114

chr9:23762247

ENST00000380249

404_424

640.0

1802.0

Transmembrane

Helical

Hgene

FOCAD

chr9:20823114

chr9:23762247

ENST00000380249

441_461

640.0

1802.0

Transmembrane

Helical

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000223951

125_205

347.0

Domain

RRM 2

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000223951

276_354

347.0

Domain

RRM 3

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000223951

39_117

347.0

Domain

RRM 1

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000380117

125_205

360.0

Domain

RRM 2

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000380117

276_354

360.0

Domain

RRM 3

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000380117

39_117

360.0

Domain

RRM 1

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000397312

125_205

360.0

Domain

RRM 2

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000397312

276_354

360.0

Domain

RRM 3

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000397312

39_117

360.0

Domain

RRM 1

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000544538

125_205

360.0

Domain

RRM 2

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000544538

276_354

360.0

Domain

RRM 3

Tgene

ELAVL2

chr9:20823114

chr9:23762247

ENST00000544538

39_117

360.0

Domain

RRM 1

- 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

FOCAD

chr9:20823114

chr9:23762247

ENST00000338382

1036_1056

640.0

1802.0

Transmembrane

Helical

Hgene

FOCAD

chr9:20823114

chr9:23762247

ENST00000380249

1036_1056

640.0

1802.0

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 >>>1829_FOCAD_20823114_ELAVL2_23762247_ranked_0.pdb	FOCAD	20823114	20823114	ENST00000380110	ELAVL2	chr9	23762247	-	MFLFGHLCSSLQLTPFLIDHQGNFHPHRLAVENEAAHIHVREAKMSDDIRKRFEFPNSLIQSQAVGHLIAAVLKENGFSEKIHQSTNQTP ALNLLWEKCCSDNVVVRTACCEGLVALVAQDHAEFSYVLNGILNLIPSTRNTHGLIKAIMHLLQMQALKEGQGGEKNIQSIYTIRNHPHP LITVLEHRPDCWPVFLQQLTAFFQQCPERLEVSCIQIMAPFLWYLYCEPSQLQEYAKLRLALLKVLLQPQVLCDKDQPSILEQQILQLCC DIVPCLQVKDLIQTTEAMMFIEEVCLSLLRHPVFWKIQLTQMSLQLLCVSEVSLKITGECSSSIHLLEHSVELLKEDFPVELVIIGIALL LLQTPASQQKPILNLALKLLSVTEDQKIPKSSLLLVMPILQILSSTALEDCISVDEEGPSRQQLALNLLEMIQQECYRDDHQKLSYKLVC PVTSMYGTIFTAWRILEVMTDSSAASDWLASVESLLPITAVIPAPAFLLLAHLLVEDKGQNLHQILKVTTELAQADSSQVPNLIPVLMFK LGRPLEPILYNDILYTLPKLGVHKVCIGQILRIIQLLGTTPRLRAVTLRLLTSLWEKQDRVYPELQRFMAVSDVPSLSVGKEVQWEKLIA KAASIRDICKQRPYQHGADMLAAISQVLNECTKPDQATPAALVLQGLHALCQAEQVIAAMETQLSNGPTCNNTANGPTTINNNCSSPVDS GNTEDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGLNGQKPPGATEPITVKFANNPSQKTN QAILSQLYQSPNRRYPGPLAQQAQRFRLDNLLNMAYGVKSRFSPMTIDGMTSLAGINIPGHPGTGWCIFVYNLAPDADESILWQMFGPFG	1049

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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.

FOCAD_pLDDT.png

ELAVL2_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
FOCAD
ELAVL2

- 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 FOCAD-ELAVL2

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 FOCAD-ELAVL2

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