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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:DDX10-AIPL1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: DDX10-AIPL1
	FusionPDB ID: 21874
	FusionGDB2.0 ID: 21874
		Hgene	Tgene
	Gene symbol	DDX10	AIPL1
	Gene ID	1662	23746
	Gene name	DEAD-box helicase 10	aryl hydrocarbon receptor interacting protein like 1
	Synonyms	Dbp4\|HRH-J8	AIPL2\|LCA4
	Cytomap	11q22.3	17p13.2
	Type of gene	protein-coding	protein-coding
	Description	probable ATP-dependent RNA helicase DDX10DDX10-NUP98 fusion protein type 2DEAD (Asp-Glu-Ala-Asp) box polypeptide 10DEAD box protein 10DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)	aryl-hydrocarbon-interacting protein-like 1
	Modification date	20200313	20200328
	UniProtAcc	Q13206	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000322536, ENST00000526794, ENST00000534221,	ENST00000250087, ENST00000570466, ENST00000571740, ENST00000574506, ENST00000575265, ENST00000576307, ENST00000576776, ENST00000381129,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 14 X 6=1176	2 X 2 X 2=8
	# samples	17	2
	** MAII score	log2(17/1176*10)=-2.79028140869866 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(2/8*10)=1.32192809488736
Context (manual curation of fusion genes in FusionPDB)	PubMed: DDX10 [Title/Abstract] AND AIPL1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	DDX10(108594189)-AIPL1(6331826), # samples:2
Anticipated loss of major functional domain due to fusion event.	DDX10-AIPL1 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. DDX10-AIPL1 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. DDX10-AIPL1 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. DDX10-AIPL1 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
Tgene	AIPL1	GO:0018343	protein farnesylation	14555765

Fusion gene breakpoints across DDX10 (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 AIPL1 (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	SARC	TCGA-DX-AB2P-01A	DDX10	chr11	108594189	+	AIPL1	chr17	6331826	-
ChimerDB4	SARC	TCGA-LI-A9QH-01A	DDX10	chr11	108594189	+	AIPL1	chr17	6331826	-

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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)

ENST00000322536

DDX10

chr11

108594189

ENST00000381129

AIPL1

chr17

6331826

4696

2094

2972

974

ENST00000526794

DDX10

chr11

108594189

ENST00000381129

AIPL1

chr17

6331826

4599

1997

2875

957

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
ENST00000322536	ENST00000381129	DDX10	chr11	108594189	+	AIPL1	chr17	6331826	-	0.001110931	0.998889
ENST00000526794	ENST00000381129	DDX10	chr11	108594189	+	AIPL1	chr17	6331826	-	0.001322687	0.9986773

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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

>21874_21874_1_DDX10-AIPL1_DDX10_chr11_108594189_ENST00000322536_AIPL1_chr17_6331826_ENST00000381129_length(amino acids)=974AA_BP=932
MSHAGSVSLALGVSCLGLIRAVAAAAAMGKTANSPGSGARPDPVRSFNRWKKKHSHRQNKKKQLRKQLKKPEWQVERESISRLMQNYEKI
NVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTREL
AYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENL
PKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEKAKYSTPATLEQNYIVCELQQKISVLYSFLRSHLKKKSIVFFSSCKEVQYLYRVF
CRLRPGVSILALHGRQQQMRRMEVYNEFVRKRAAVLFATDIAARGLDFPAVNWVLQFDCPEDANTYIHRAGRTARYKEDGEALLILLPSE
KAMVQQLLQKKVPVKEIKINPEKLIDVQKKLESILAQDQDLKERAQRCFVSYVRSVYLMKDKEVFDVSKLPIPEYALSLGLAVAPRVRFL
QKMQKQPTKELVRSQADKVIEPRAPSLTNDEVEEFRAYFNEKMSILQKGGKRLEGTEHRQDNDTGNEEQEEEEDDEEEMEEKLAKAKGSQ
APSLPNTSEAQKIKEVPTQFLDRDEEEEDADFLKVKRHNVFGLDLKDEKTLQHTGVYPILSRSLRQMAQGKDPTEWHVHTCGLANMFAYH
TLGYEDLDELQKEPQPLVFVIELLQVDAPSDYQRETWNLSNHEKMKAVPVLHGEGNRLFKLGRYEEASSKYQEAIICLRNLQTKEKPWEV
QWLKLEKMINTLILNYCQCLLKKEEYYEVLEHTSDILRHHPGIVKAYYVRARAHAEVWNEAEAKADLQKVLELEPSMQKAVRRELRLLEN

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

>21874_21874_2_DDX10-AIPL1_DDX10_chr11_108594189_ENST00000526794_AIPL1_chr17_6331826_ENST00000381129_length(amino acids)=957AA_BP=915
LIRAVAAAAAMGKTANSPGSGARPDPVRSFNRWKKKHSHRQNKKKQLRKQLKKPEWQVERESISRLMQNYEKINVNEITRFSDFPLSKKT
LKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDF
SAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSV
KDLARLSLKNPEYVWVHEKAKYSTPATLEQNYIVCELQQKISVLYSFLRSHLKKKSIVFFSSCKEVQYLYRVFCRLRPGVSILALHGRQQ
QMRRMEVYNEFVRKRAAVLFATDIAARGLDFPAVNWVLQFDCPEDANTYIHRAGRTARYKEDGEALLILLPSEKAMVQQLLQKKVPVKEI
KINPEKLIDVQKKLESILAQDQDLKERAQRCFVSYVRSVYLMKDKEVFDVSKLPIPEYALSLGLAVAPRVRFLQKMQKQPTKELVRSQAD
KVIEPRAPSLTNDEVEEFRAYFNEKMSILQKGGKRLEGTEHRQDNDTGNEEQEEEEDDEEEMEEKLAKAKGSQAPSLPNTSEAQKIKEVP
TQFLDRDEEEEDADFLKVKRHNVFGLDLKDEKTLQHTGVYPILSRSLRQMAQGKDPTEWHVHTCGLANMFAYHTLGYEDLDELQKEPQPL
VFVIELLQVDAPSDYQRETWNLSNHEKMKAVPVLHGEGNRLFKLGRYEEASSKYQEAIICLRNLQTKEKPWEVQWLKLEKMINTLILNYC
QCLLKKEEYYEVLEHTSDILRHHPGIVKAYYVRARAHAEVWNEAEAKADLQKVLELEPSMQKAVRRELRLLENRMAEKQEEERLRCRNML

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

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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/chr11:108594189/chr17:6331826)
- 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
DDX10 Q13206	.
FUNCTION: Putative ATP-dependent RNA helicase.	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

DDX10

chr11:108594189

chr17:6331826

ENST00000322536

100_274

655.0

876.0

Domain

Helicase ATP-binding

Hgene

DDX10

chr11:108594189

chr17:6331826

ENST00000322536

287_448

655.0

876.0

Domain

Helicase C-terminal

Hgene

DDX10

chr11:108594189

chr17:6331826

ENST00000322536

222_225

655.0

876.0

Motif

Note=DEAD box

Hgene

DDX10

chr11:108594189

chr17:6331826

ENST00000322536

69_97

655.0

876.0

Motif

Note=Q motif

Hgene

DDX10

chr11:108594189

chr17:6331826

ENST00000322536

113_120

655.0

876.0

Nucleotide binding

Note=ATP

Hgene

DDX10

chr11:108594189

chr17:6331826

ENST00000322536

89_91

655.0

876.0

Nucleotide binding

Note=ATP

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000250087

53_145

322.0

Domain

Note=PPIase FKBP-type

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576307

53_145

32.0

325.0

Domain

Note=PPIase FKBP-type

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000250087

178_211

322.0

Repeat

Note=TPR 1

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000250087

230_263

322.0

Repeat

Note=TPR 2

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000250087

264_297

322.0

Repeat

Note=TPR 3

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000381129

178_211

92.0

385.0

Repeat

Note=TPR 1

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000381129

230_263

92.0

385.0

Repeat

Note=TPR 2

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000381129

264_297

92.0

385.0

Repeat

Note=TPR 3

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000570466

178_211

70.0

363.0

Repeat

Note=TPR 1

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000570466

230_263

70.0

363.0

Repeat

Note=TPR 2

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000570466

264_297

70.0

363.0

Repeat

Note=TPR 3

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576307

178_211

32.0

325.0

Repeat

Note=TPR 1

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576307

230_263

32.0

325.0

Repeat

Note=TPR 2

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576307

264_297

32.0

325.0

Repeat

Note=TPR 3

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576776

178_211

92.0

361.0

Repeat

Note=TPR 1

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576776

230_263

92.0

361.0

Repeat

Note=TPR 2

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576776

264_297

92.0

361.0

Repeat

Note=TPR 3

- 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

AIPL1

chr11:108594189

chr17:6331826

ENST00000381129

53_145

92.0

385.0

Domain

Note=PPIase FKBP-type

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000570466

53_145

70.0

363.0

Domain

Note=PPIase FKBP-type

Tgene

AIPL1

chr11:108594189

chr17:6331826

ENST00000576776

53_145

92.0

361.0

Domain

Note=PPIase FKBP-type

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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 >>>1775_DDX10_108594189_AIPL1_6331826_ranked_0.pdb	DDX10	108594189	108594189	ENST00000381129	AIPL1	chr17	6331826	-	MSHAGSVSLALGVSCLGLIRAVAAAAAMGKTANSPGSGARPDPVRSFNRWKKKHSHRQNKKKQLRKQLKKPEWQVERESISRLMQNYEKI NVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTREL AYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENL PKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEKAKYSTPATLEQNYIVCELQQKISVLYSFLRSHLKKKSIVFFSSCKEVQYLYRVF CRLRPGVSILALHGRQQQMRRMEVYNEFVRKRAAVLFATDIAARGLDFPAVNWVLQFDCPEDANTYIHRAGRTARYKEDGEALLILLPSE KAMVQQLLQKKVPVKEIKINPEKLIDVQKKLESILAQDQDLKERAQRCFVSYVRSVYLMKDKEVFDVSKLPIPEYALSLGLAVAPRVRFL QKMQKQPTKELVRSQADKVIEPRAPSLTNDEVEEFRAYFNEKMSILQKGGKRLEGTEHRQDNDTGNEEQEEEEDDEEEMEEKLAKAKGSQ APSLPNTSEAQKIKEVPTQFLDRDEEEEDADFLKVKRHNVFGLDLKDEKTLQHTGVYPILSRSLRQMAQGKDPTEWHVHTCGLANMFAYH TLGYEDLDELQKEPQPLVFVIELLQVDAPSDYQRETWNLSNHEKMKAVPVLHGEGNRLFKLGRYEEASSKYQEAIICLRNLQTKEKPWEV QWLKLEKMINTLILNYCQCLLKKEEYYEVLEHTSDILRHHPGIVKAYYVRARAHAEVWNEAEAKADLQKVLELEPSMQKAVRRELRLLEN	974

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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.

DDX10_pLDDT.png

AIPL1_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
DDX10
AIPL1

- 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 DDX10-AIPL1

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 DDX10-AIPL1

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