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level3

	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
	Potential Active Site Information
	Potentially Interacting Small Molecules through Virtual Screening
	Biochemical Features of Small Molecules with ADME
	Drug Toxicity Information
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PAX3-FOXO1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PAX3-FOXO1
	FusionPDB ID: 62939
	FusionGDB2.0 ID: 62939
		Hgene	Tgene
	Gene symbol	PAX3	FOXO1
	Gene ID	5077	2308
	Gene name	paired box 3	forkhead box O1
	Synonyms	CDHS\|HUP2\|WS1\|WS3	FKH1\|FKHR\|FOXO1A
	Cytomap	2q36.1	13q14.11
	Type of gene	protein-coding	protein-coding
	Description	paired box protein Pax-3paired box homeotic gene 3paired domain gene 3paired domain gene HuP2transcriptional factor PAX3	forkhead box protein O1forkhead box protein O1Aforkhead, Drosophila, homolog of, in rhabdomyosarcoma
	Modification date	20200313	20200322
	UniProtAcc	PAXBP1	Q12778
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000336840, ENST00000344493, ENST00000350526, ENST00000392069, ENST00000392070, ENST00000409551, ENST00000464706, ENST00000258387, ENST00000409828,	ENST00000473775, ENST00000379561,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 10 X 5=350	11 X 11 X 7=847
	# samples	8	14
	** MAII score	log2(8/350*10)=-2.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/847*10)=-2.59693514238723 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PAX3 [Title/Abstract] AND FOXO1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PAX3(223084859)-FOXO1(41135000), # samples:4 FOXO1(41239718)-PAX3(223066911), # samples:3
Anticipated loss of major functional domain due to fusion event.	PAX3-FOXO1 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. PAX3-FOXO1 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. PAX3-FOXO1 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. PAX3-FOXO1 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. FOXO1-PAX3 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. FOXO1-PAX3 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	PAX3	GO:0045893	positive regulation of transcription, DNA-templated	11863357
Hgene	PAX3	GO:0045944	positive regulation of transcription by RNA polymerase II	11863357
Tgene	FOXO1	GO:0009267	cellular response to starvation	20543840
Tgene	FOXO1	GO:0032873	negative regulation of stress-activated MAPK cascade	19696738
Tgene	FOXO1	GO:0043066	negative regulation of apoptotic process	10871843
Tgene	FOXO1	GO:0045893	positive regulation of transcription, DNA-templated	7862145\|10871843\|12228231
Tgene	FOXO1	GO:0045944	positive regulation of transcription by RNA polymerase II	10871843\|12228231
Tgene	FOXO1	GO:0071455	cellular response to hyperoxia	20543840

Fusion gene breakpoints across PAX3 (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 FOXO1 (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
ChimerKB3	.	.	PAX3	chr2	223084858	-	FOXO1	chr13	41134997	-
ChimerKB3	.	.	PAX3	chr2	223163334	-	FOXO1	chr13	41133662	-
ChimerKB4	.	.	PAX3	chr2	223084858	-	FOXO1	chr13	41134997	-
ChiTaRS5.0	N/A	BC008826	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-
ChiTaRS5.0	N/A	EU446645	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-
ChiTaRS5.0	N/A	U02308	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-
ChiTaRS5.0	N/A	U02368	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-

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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)
ENST00000392069	PAX3	chr2	223084858	-	ENST00000379561	FOXO1	chr13	41134997	-	6259	1539	366	2876	836
ENST00000344493	PAX3	chr2	223084858	-	ENST00000379561	FOXO1	chr13	41134997	-	6274	1554	381	2891	836
ENST00000350526	PAX3	chr2	223084858	-	ENST00000379561	FOXO1	chr13	41134997	-	6030	1310	137	2647	836
ENST00000336840	PAX3	chr2	223084858	-	ENST00000379561	FOXO1	chr13	41134997	-	6274	1554	381	2891	836
ENST00000392070	PAX3	chr2	223084858	-	ENST00000379561	FOXO1	chr13	41134997	-	6274	1554	381	2891	836
ENST00000409551	PAX3	chr2	223084858	-	ENST00000379561	FOXO1	chr13	41134997	-	6170	1450	280	2787	835
ENST00000392069	PAX3	chr2	223084859	-	ENST00000379561	FOXO1	chr13	41135000	-	6259	1539	366	2876	836
ENST00000344493	PAX3	chr2	223084859	-	ENST00000379561	FOXO1	chr13	41135000	-	6274	1554	381	2891	836
ENST00000350526	PAX3	chr2	223084859	-	ENST00000379561	FOXO1	chr13	41135000	-	6030	1310	137	2647	836
ENST00000336840	PAX3	chr2	223084859	-	ENST00000379561	FOXO1	chr13	41135000	-	6274	1554	381	2891	836
ENST00000392070	PAX3	chr2	223084859	-	ENST00000379561	FOXO1	chr13	41135000	-	6274	1554	381	2891	836
ENST00000409551	PAX3	chr2	223084859	-	ENST00000379561	FOXO1	chr13	41135000	-	6170	1450	280	2787	835

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
ENST00000392069	ENST00000379561	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-	0.000723874	0.9992761
ENST00000344493	ENST00000379561	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-	0.000715586	0.99928445
ENST00000350526	ENST00000379561	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-	0.000650102	0.9993499
ENST00000336840	ENST00000379561	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-	0.000715586	0.99928445
ENST00000392070	ENST00000379561	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-	0.000715586	0.99928445
ENST00000409551	ENST00000379561	PAX3	chr2	223084859	-	FOXO1	chr13	41135000	-	0.000865039	0.99913496

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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

>62939_62939_1_PAX3-FOXO1_PAX3_chr2_223084858_ENST00000336840_FOXO1_chr13_41134997_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_2_PAX3-FOXO1_PAX3_chr2_223084858_ENST00000344493_FOXO1_chr13_41134997_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_3_PAX3-FOXO1_PAX3_chr2_223084858_ENST00000350526_FOXO1_chr13_41134997_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_4_PAX3-FOXO1_PAX3_chr2_223084858_ENST00000392069_FOXO1_chr13_41134997_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_5_PAX3-FOXO1_PAX3_chr2_223084858_ENST00000392070_FOXO1_chr13_41134997_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_6_PAX3-FOXO1_PAX3_chr2_223084858_ENST00000409551_FOXO1_chr13_41134997_ENST00000379561_length(amino acids)=835AA_BP=389
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEESE
KKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR
ARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTRH
GFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSRA
AKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTLP
SLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSYG
GMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPLP
HTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLDF

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

>62939_62939_7_PAX3-FOXO1_PAX3_chr2_223084859_ENST00000336840_FOXO1_chr13_41135000_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_8_PAX3-FOXO1_PAX3_chr2_223084859_ENST00000344493_FOXO1_chr13_41135000_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_9_PAX3-FOXO1_PAX3_chr2_223084859_ENST00000350526_FOXO1_chr13_41135000_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_10_PAX3-FOXO1_PAX3_chr2_223084859_ENST00000392069_FOXO1_chr13_41135000_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_11_PAX3-FOXO1_PAX3_chr2_223084859_ENST00000392070_FOXO1_chr13_41135000_ENST00000379561_length(amino acids)=836AA_BP=390
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTR
HGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR
AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTL
PSLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSY
GGMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPL
PHTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLD

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

>62939_62939_12_PAX3-FOXO1_PAX3_chr2_223084859_ENST00000409551_FOXO1_chr13_41135000_ENST00000379561_length(amino acids)=835AA_BP=389
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEESE
KKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR
ARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSSSAYCLPSTRH
GFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLHSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSRA
AKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSNASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTLP
SLSEISNPENMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPNYQKYTYGQSSMSPLPQMPIQTLQDNKSSYG
GMSQYNCAPGLLKELLTSDSPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPSSHTHPGHAQQTSAVNGRPLP
HTVSTMPHTSGMNRLTQVKTPVQVPLPHPMQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRNDLMDGDTLDF

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

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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/chr2:223084859/chr13:41135000)
- 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
PAX3 PAXBP1	FOXO1 Q12778
917	FUNCTION: Transcription factor that is the main target of insulin signaling and regulates metabolic homeostasis in response to oxidative stress (PubMed:10358076, PubMed:12228231, PubMed:15220471, PubMed:15890677, PubMed:18356527, PubMed:19221179, PubMed:20543840, PubMed:21245099). Binds to the insulin response element (IRE) with consensus sequence 5'-TT[G/A]TTTTG-3' and the related Daf-16 family binding element (DBE) with consensus sequence 5'-TT[G/A]TTTAC-3' (PubMed:10358076). Activity suppressed by insulin (PubMed:10358076). Main regulator of redox balance and osteoblast numbers and controls bone mass (By similarity). Orchestrates the endocrine function of the skeleton in regulating glucose metabolism (By similarity). Also acts as a key regulator of chondrogenic commitment of skeletal progenitor cells in response to lipid availability: when lipids levels are low, translocates to the nucleus and promotes expression of SOX9, which induces chondrogenic commitment and suppresses fatty acid oxidation (By similarity). Acts synergistically with ATF4 to suppress osteocalcin/BGLAP activity, increasing glucose levels and triggering glucose intolerance and insulin insensitivity (By similarity). Also suppresses the transcriptional activity of RUNX2, an upstream activator of osteocalcin/BGLAP (By similarity). In hepatocytes, promotes gluconeogenesis by acting together with PPARGC1A and CEBPA to activate the expression of genes such as IGFBP1, G6PC1 and PCK1 (By similarity). Important regulator of cell death acting downstream of CDK1, PKB/AKT1 and STK4/MST1 (PubMed:18356527, PubMed:19221179). Promotes neural cell death (PubMed:18356527). Mediates insulin action on adipose tissue (By similarity). Regulates the expression of adipogenic genes such as PPARG during preadipocyte differentiation and, adipocyte size and adipose tissue-specific gene expression in response to excessive calorie intake (By similarity). Regulates the transcriptional activity of GADD45A and repair of nitric oxide-damaged DNA in beta-cells (By similarity). Required for the autophagic cell death induction in response to starvation or oxidative stress in a transcription-independent manner (PubMed:20543840). Mediates the function of MLIP in cardiomyocytes hypertrophy and cardiac remodeling (By similarity). Regulates endothelial cell (EC) viability and apoptosis in a PPIA/CYPA-dependent manner via transcription of CCL2 and BCL2L11 which are involved in EC chemotaxis and apoptosis (PubMed:31063815). {ECO:0000250\|UniProtKB:A4L7N3, ECO:0000250\|UniProtKB:G3V7R4, ECO:0000250\|UniProtKB:Q9R1E0, ECO:0000269\|PubMed:10358076, ECO:0000269\|PubMed:12228231, ECO:0000269\|PubMed:15220471, ECO:0000269\|PubMed:15890677, ECO:0000269\|PubMed:18356527, ECO:0000269\|PubMed:19221179, ECO:0000269\|PubMed:20543840, ECO:0000269\|PubMed:21245099, ECO:0000269\|PubMed:31063815}.

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

PAX3

chr2:223084859

chr13:41135000

ENST00000336840

219_278

391.0

408.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000336840

34_161

391.0

408.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000344493

219_278

391.0

404.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000344493

34_161

391.0

404.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000350526

219_278

391.0

480.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000350526

34_161

391.0

480.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392069

219_278

391.0

506.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392069

34_161

391.0

506.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392070

219_278

391.0

485.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392070

34_161

391.0

485.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409551

219_278

390.0

484.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409551

34_161

390.0

484.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000336840

113_161

391.0

408.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000336840

37_93

391.0

408.0

Region

PAI subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000344493

113_161

391.0

404.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000344493

37_93

391.0

404.0

Region

PAI subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000350526

113_161

391.0

480.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000350526

37_93

391.0

480.0

Region

PAI subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392069

113_161

391.0

506.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392069

37_93

391.0

506.0

Region

PAI subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392070

113_161

391.0

485.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000392070

37_93

391.0

485.0

Region

PAI subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409551

113_161

390.0

484.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409551

37_93

390.0

484.0

Region

PAI subdomain

Tgene

FOXO1

chr2:223084859

chr13:41135000

ENST00000379561

211_218

210.0

1440.3333333333333

Region

Note=DNA-binding

Tgene

FOXO1

chr2:223084859

chr13:41135000

ENST00000379561

234_237

210.0

1440.3333333333333

Region

Note=DNA-binding

- 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

PAX3

chr2:223084859

chr13:41135000

ENST00000258387

219_278

207.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000258387

34_161

207.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409828

219_278

216.0

DNA binding

Homeobox

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409828

34_161

216.0

DNA binding

Paired

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000258387

113_161

207.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000258387

37_93

207.0

Region

PAI subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409828

113_161

216.0

Region

RED subdomain

Hgene

PAX3

chr2:223084859

chr13:41135000

ENST00000409828

37_93

216.0

Region

PAI subdomain

Tgene

FOXO1

chr2:223084859

chr13:41135000

ENST00000379561

120_130

210.0

1440.3333333333333

Compositional bias

Note=Poly-Pro

Tgene

FOXO1

chr2:223084859

chr13:41135000

ENST00000379561

152_155

210.0

1440.3333333333333

Compositional bias

Note=Poly-Ser

Tgene

FOXO1

chr2:223084859

chr13:41135000

ENST00000379561

91_102

210.0

1440.3333333333333

Compositional bias

Note=Poly-Ala

Tgene

FOXO1

chr2:223084859

chr13:41135000

ENST00000379561

159_235

210.0

1440.3333333333333

DNA binding

Fork-head

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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 (670) >>>670.pdbFusion protein BP residue: 389 CIF file (670) >>>670.cif	PAX3	chr2	223084858	-	FOXO1	chr13	41134997	-	MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRP LPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGA IGGSKPKVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSV SSISRILRSKFGKGEEEEADLERKEAEESEKKAKHSIDGILSERASAPQS DEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREE LAQRAKLTEARVQVWFSNRRARWRKQAGANQLMAFNHLIPGGFPPTAMPT LPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDSS SAYCLPSTRHGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSLH SKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSRA AKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSSN ASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTLPSLSEISNPEN MENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSPN YQKYTYGQSSMSPLPQMPIQTLQDNKSSYGGMSQYNCAPGLLKELLTSDS PPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNPS SHTHPGHAQQTSAVNGRPLPHTVSTMPHTSGMNRLTQVKTPVQVPLPHPM QMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIRN	835
3D view using mol* of 670 (AA BP:389)


PDB file (671) >>>671.pdbFusion protein BP residue: 390 CIF file (671) >>>671.cif	PAX3	chr2	223084858	-	FOXO1	chr13	41134997	-	MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRP LPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGA IGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPS VSSISRILRSKFGKGEEEEADLERKEAEESEKKAKHSIDGILSERASAPQ SDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTRE ELAQRAKLTEARVQVWFSNRRARWRKQAGANQLMAFNHLIPGGFPPTAMP TLPTYQLSETSYQPTSIPQAVSDPSSTVHRPQPLPPSTVHQSTIPSNPDS SSAYCLPSTRHGFSSYTDSFVPPSGPSNPMNPTIGNGLSPQNSIRHNLSL HSKFIRVQNEGTGKSSWWMLNPEGGKSGKSPRRRAASMDNNSKFAKSRSR AAKKKASLQSGQEGAGDSPGSQFSKWPASPGSHSNDDFDNWSTFRPRTSS NASTISGRLSPIMTEQDDLGEGDVHSMVYPPSAAKMASTLPSLSEISNPE NMENLLDNLNLLSSPTSLTVSTQSSPGTMMQQTPCYSFAPPNTSLNSPSP NYQKYTYGQSSMSPLPQMPIQTLQDNKSSYGGMSQYNCAPGLLKELLTSD SPPHNDIMTPVDPGVAQPNSRVLGQNVMMGPNSVMSTYGSQASHNKMMNP SSHTHPGHAQQTSAVNGRPLPHTVSTMPHTSGMNRLTQVKTPVQVPLPHP MQMSALGGYSSVSSCNGYGRMGLLHQEKLPSDLDGMFIERLDCDMESIIR	836
3D view using mol* of 671 (AA BP:390)

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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.

PAX3_pLDDT.png

FOXO1_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.

PAX3_FOXO1_670_pLDDT.png (AA BP:389)

PAX3_FOXO1_670_pLDDT_and_active_sites.png (AA BP:389)

PAX3_FOXO1_670_violinplot.png (AA BP:389)

PAX3_FOXO1_671_pLDDT.png (AA BP:390)

PAX3_FOXO1_671_pLDDT_and_active_sites.png (AA BP:390)

PAX3_FOXO1_671_violinplot.png (AA BP:390)

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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

PAX3_FOXO1_670.png

PAX3_FOXO1_671.png

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Potential Active Site Information

The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.

Fusion AA seq ID in FusionPDB	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
670	0.984	278	1.016	990.584	0.667	0.655	0.845	0.514	0.974	0.528	0.747	Chain A: 26,27,28,29,31,39,40,43,44,45,46,49,50,51 ,52,55,56,57,60,61,76,77,78,79,82,85,86,89,90,92,9 3,94,95,96,97,98,99,100,101,102,209,210,211,212,21 3,214,215,216,217,218,219,220,221,222
671	0.992	139	1.062	314.188	0.684	0.593	0.827	0.659	0.716	0.92	1.179	Chain A: 57,60,61,63,64,69,84,87,88,90,91,92,93,94 ,95,96,209,210,211,212,213,214,215,216,217,218,219 ,220

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Potentially Interacting Small Molecules through Virtual Screening

The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.

Fusion AA seq ID in FusionPDB

ZINC ID

DrugBank ID

Drug name

Docking score

Glide gscore

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Drug information from DrugBank of the top 20 interacting small molecules.

ZINC ID

DrugBank ID

Drug name

Drug type

SMILES

Drug group

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Biochemical Features of Small Molecules

ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)

ZINC ID

mol_MW

dipole

SASA

FOSA

FISA

PISA

WPSA

volume

donorHB

accptHB

Human Oral Absorption

Percent Human Oral Absorption

Rule Of Five

Rule Of Three

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Drug Toxicity Information

Toxicity information of individual drugs using eToxPred

ZINC ID

Smile

Surface Accessibility

Toxicity

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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
PAX3	IPO13, SOX10, DAXX, MSX1, MEOX1, MEOX2, TBP, PSMD4, Rad23b, RAD23B, HDAC10, TRIM28, HDAC1, POU3F2, TAF1, PCTP, SPIN1, SKAP1, FOXE1, FZR1, NELL2, EGLN3, KRTAP8-1, KRTAP6-2, KIF20A, CIC, FOXO1, IGLC1, COL1A1, NTPCR, HBB, COL1A2, COL3A1, FITM2, MPL, S100A2, FBLN5,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PAX3
FOXO1

- 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 PAX3-FOXO1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene	Tgene	Drug	Source	PMID
PAX3	FOXO1	Histone Deacetylase Inhibitor (Hdaci)	PubMed	30459282

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Related Diseases to PAX3-FOXO1

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene	Tgene	Disease	Source	PMID
PAX3	FOXO1	Rhabdomyosarcoma (Rms)	PubMed	30459282
PAX3	FOXO1	Alveolar Rhabdomyosarcoma	MyCancerGenome
PAX3	FOXO1	Colon Adenocarcinoma	MyCancerGenome
PAX3	FOXO1	Breast Invasive Ductal Carcinoma	MyCancerGenome
PAX3	FOXO1	Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma	MyCancerGenome
PAX3	FOXO1	Endometrial Clear Cell Adenocarcinoma	MyCancerGenome

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	PAX3	C1847800	Waardenburg Syndrome Type 1	33	CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
Hgene	PAX3	C0079661	Klein's Syndrome	16	CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Hgene	PAX3	C3266898	Waardenburg Syndrome	12	CLINGEN;CTD_human;GENOMICS_ENGLAND
Hgene	PAX3	C1852510	Craniofacial deafness hand syndrome	5	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Hgene	PAX3	C0038219	Status Dysraphicus	4	CTD_human
Hgene	PAX3	C0080178	Spina Bifida	4	CTD_human
Hgene	PAX3	C0266508	Rachischisis	4	CTD_human
Hgene	PAX3	C0011999	Diastematomyelia	3	CTD_human
Hgene	PAX3	C0027794	Neural Tube Defects	3	CTD_human
Hgene	PAX3	C0027806	Neurenteric Cyst	3	CTD_human
Hgene	PAX3	C0080218	Tethered Cord Syndrome	3	CTD_human
Hgene	PAX3	C0152234	Iniencephaly	3	CTD_human
Hgene	PAX3	C0152426	Craniorachischisis	3	CTD_human
Hgene	PAX3	C0266453	Exencephaly	3	CTD_human
Hgene	PAX3	C0344479	Spinal Cord Myelodysplasia	3	CTD_human
Hgene	PAX3	C0599973	Waardenburg Anophthalmia Syndrome	3	ORPHANET
Hgene	PAX3	C0702169	Acrania	3	CTD_human
Hgene	PAX3	C0206655	Alveolar rhabdomyosarcoma	2	CTD_human;GENOMICS_ENGLAND;ORPHANET
Hgene	PAX3	C0011052	Prelingual Deafness	1	CTD_human
Hgene	PAX3	C0011053	Deafness	1	CTD_human
Hgene	PAX3	C0018566	Congenital Hand Deformities	1	CTD_human
Hgene	PAX3	C0086395	Hearing Loss, Extreme	1	CTD_human
Hgene	PAX3	C0205944	Sarcoma, Epithelioid	1	CTD_human
Hgene	PAX3	C0205945	Sarcoma, Spindle Cell	1	CTD_human
Hgene	PAX3	C0265541	Cranioschisis	1	CTD_human
Hgene	PAX3	C0376634	Craniofacial Abnormalities	1	CTD_human
Hgene	PAX3	C0497552	Congenital neurologic anomalies	1	CTD_human
Hgene	PAX3	C0581883	Complete Hearing Loss	1	CTD_human
Hgene	PAX3	C0751068	Deafness, Acquired	1	CTD_human
Hgene	PAX3	C1261473	Sarcoma	1	CTD_human
Hgene	PAX3	C1710096	Sinonasal undifferentiated carcinoma	1	CTD_human
Hgene	PAX3	C3665473	Bilateral Deafness	1	CTD_human
Hgene	PAX3	C4082305	Deaf Mutism	1	CTD_human
Tgene	FOXO1	C0020542	Pulmonary Hypertension	1	CTD_human
Tgene	FOXO1	C0022578	Keratoconus	1	CTD_human
Tgene	FOXO1	C0023467	Leukemia, Myelocytic, Acute	1	CTD_human
Tgene	FOXO1	C0026998	Acute Myeloid Leukemia, M1	1	CTD_human
Tgene	FOXO1	C0033578	Prostatic Neoplasms	1	CTD_human
Tgene	FOXO1	C0206655	Alveolar rhabdomyosarcoma	1	CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	FOXO1	C0376358	Malignant neoplasm of prostate	1	CTD_human
Tgene	FOXO1	C1879321	Acute Myeloid Leukemia (AML-M2)	1	CTD_human