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Center for Computational Systems Medicine level3
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Potential Active Site Information

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Potentially Interacting Small Molecules through Virtual Screening

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Biochemical Features of Small Molecules with ADME

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Drug Toxicity Information

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PAX3-NCOA1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PAX3-NCOA1
FusionPDB ID: 62942
FusionGDB2.0 ID: 62942
HgeneTgene
Gene symbol

PAX3

NCOA1

Gene ID

5077

8648

Gene namepaired box 3nuclear receptor coactivator 1
SynonymsCDHS|HUP2|WS1|WS3F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74
Cytomap

2q36.1

2p23.3

Type of geneprotein-codingprotein-coding
Descriptionpaired box protein Pax-3paired box homeotic gene 3paired domain gene 3paired domain gene HuP2transcriptional factor PAX3nuclear receptor coactivator 1Hin-2 proteinclass E basic helix-loop-helix protein 74renal carcinoma antigen NY-REN-52steroid receptor coactivator-1
Modification date2020031320200313
UniProtAcc

PAXBP1

Q15788

Ensembl transtripts involved in fusion geneENST idsENST00000336840, ENST00000344493, 
ENST00000350526, ENST00000392069, 
ENST00000392070, ENST00000409551, 
ENST00000464706, ENST00000258387, 
ENST00000409828, 		ENST00000288599, 
ENST00000348332, ENST00000395856, 
ENST00000405141, ENST00000407230, 
ENST00000469850, ENST00000538539, 
ENST00000406961, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 10 X 5=35011 X 13 X 7=1001
# samples 813
** MAII scorelog2(8/350*10)=-2.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/1001*10)=-2.94485844580754
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 NCOA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PAX3(223163334)-NCOA1(24949456), # samples:1
PAX3(223085940)-NCOA1(24949456), # samples:1
Anticipated loss of major functional domain due to fusion event.PAX3-NCOA1 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-NCOA1 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-NCOA1 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-NCOA1 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePAX3

GO:0045893

positive regulation of transcription, DNA-templated

11863357

HgenePAX3

GO:0045944

positive regulation of transcription by RNA polymerase II

11863357

TgeneNCOA1

GO:0000435

positive regulation of transcription from RNA polymerase II promoter by galactose

10207113

TgeneNCOA1

GO:0006351

transcription, DNA-templated

9223431

TgeneNCOA1

GO:0045893

positive regulation of transcription, DNA-templated

11891224|15367689

TgeneNCOA1

GO:0045944

positive regulation of transcription by RNA polymerase II

15919756


check buttonFusion 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.
all structure

check buttonFusion gene breakpoints across NCOA1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4rhabdomyosarcomaAY633656PAX3chr2

223163334

NCOA1chr2

24949456
ChimerKB3..PAX3chr2

222871578

-NCOA1chr2

24802959

+
ChimerKB3..PAX3chr2

223085940

-NCOA1chr2

24949457

+
ChimerKB3..PAX3chr2

223163334

-NCOA1chr2

24949456

+
ChiTaRS5.0N/AAY633656PAX3chr2

223085940

-NCOA1chr2

24949456

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000392069PAX3chr2223085940-ENST00000406961NCOA1chr224949457+536213243663050894
ENST00000344493PAX3chr2223085940-ENST00000406961NCOA1chr224949457+537713393813065894
ENST00000350526PAX3chr2223085940-ENST00000406961NCOA1chr224949457+513310951372821894
ENST00000336840PAX3chr2223085940-ENST00000406961NCOA1chr224949457+537713393813065894
ENST00000392070PAX3chr2223085940-ENST00000406961NCOA1chr224949457+537713393813065894
ENST00000409551PAX3chr2223085940-ENST00000406961NCOA1chr224949457+527312352802961893
ENST00000392069PAX3chr2223085940-ENST00000406961NCOA1chr224949456+536213243663050894
ENST00000344493PAX3chr2223085940-ENST00000406961NCOA1chr224949456+537713393813065894
ENST00000350526PAX3chr2223085940-ENST00000406961NCOA1chr224949456+513310951372821894
ENST00000336840PAX3chr2223085940-ENST00000406961NCOA1chr224949456+537713393813065894
ENST00000392070PAX3chr2223085940-ENST00000406961NCOA1chr224949456+537713393813065894
ENST00000409551PAX3chr2223085940-ENST00000406961NCOA1chr224949456+527312352802961893

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000392069ENST00000406961PAX3chr2223085940-NCOA1chr224949456+0.0027725760.9972274
ENST00000344493ENST00000406961PAX3chr2223085940-NCOA1chr224949456+0.0026936140.99730635
ENST00000350526ENST00000406961PAX3chr2223085940-NCOA1chr224949456+0.0025721140.9974279
ENST00000336840ENST00000406961PAX3chr2223085940-NCOA1chr224949456+0.0026936140.99730635
ENST00000392070ENST00000406961PAX3chr2223085940-NCOA1chr224949456+0.0026936140.99730635
ENST00000409551ENST00000406961PAX3chr2223085940-NCOA1chr224949456+0.0025810340.997419

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Fusion Amino Acid Sequences


check button 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

>62942_62942_1_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000336840_NCOA1_chr2_24949456_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_2_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000336840_NCOA1_chr2_24949457_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_3_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000344493_NCOA1_chr2_24949456_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_4_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000344493_NCOA1_chr2_24949457_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_5_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000350526_NCOA1_chr2_24949456_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_6_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000350526_NCOA1_chr2_24949457_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_7_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000392069_NCOA1_chr2_24949456_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_8_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000392069_NCOA1_chr2_24949457_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_9_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000392070_NCOA1_chr2_24949456_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_10_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000392070_NCOA1_chr2_24949457_ENST00000406961_length(amino acids)=894AA_BP=319
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEES
EKKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR
RARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQ
CISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVG
INMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNP
GTPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSL
LQQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIN

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

>62942_62942_11_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000409551_NCOA1_chr2_24949456_ENST00000406961_length(amino acids)=893AA_BP=318
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEESE
KKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR
ARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQC
ISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSSP
SPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVGI
NMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNPG
TPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLL
QQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIND

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

>62942_62942_12_PAX3-NCOA1_PAX3_chr2_223085940_ENST00000409551_NCOA1_chr2_24949457_ENST00000406961_length(amino acids)=893AA_BP=318
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRY
QETGSIRPGAIGGSKPKVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSVSSISRILRSKFGKGEEEEADLERKEAEESE
KKAKHSIDGILSERASAPQSDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR
ARWRKQAGANQLMAFNHLIPGGFPPTAMPTLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTAINQSKSEDQC
ISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETELAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSSP
SPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPPAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVGI
NMRSGMQQQITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSSGLPVQMGNPRLPQGAPQQFPYPPNYGTNPG
TPPASTSPFSQLAANPEASLANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPSLSPGSSMVPMPIPPPQSSLL
QQTPPASGYQSPDMKAWQQGAIGNNNVFSQAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGMNTVCPEQIND

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

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:223163334/chr2:24949456)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PAX3

PAXBP1

NCOA1

Q15788

917FUNCTION: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3. {ECO:0000269|PubMed:10449719, ECO:0000269|PubMed:12954634, ECO:0000269|PubMed:7481822, ECO:0000269|PubMed:9223281, ECO:0000269|PubMed:9223431, ECO:0000269|PubMed:9296499, ECO:0000269|PubMed:9427757}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePAX3chr2:223085940chr2:24949456ENST00000336840-69219_278319.3333333333333408.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000336840-6934_161319.3333333333333408.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000344493-68219_278319.3333333333333404.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000344493-6834_161319.3333333333333404.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000350526-68219_278319.3333333333333480.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000350526-6834_161319.3333333333333480.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000392069-610219_278319.3333333333333506.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000392069-61034_161319.3333333333333506.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000392070-69219_278319.3333333333333485.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000392070-6934_161319.3333333333333485.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000409551-69219_278318.3333333333333484.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000409551-6934_161318.3333333333333484.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000336840-69113_161319.3333333333333408.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000336840-6937_93319.3333333333333408.0RegionPAI subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000344493-68113_161319.3333333333333404.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000344493-6837_93319.3333333333333404.0RegionPAI subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000350526-68113_161319.3333333333333480.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000350526-6837_93319.3333333333333480.0RegionPAI subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000392069-610113_161319.3333333333333506.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000392069-61037_93319.3333333333333506.0RegionPAI subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000392070-69113_161319.3333333333333485.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000392070-6937_93319.3333333333333485.0RegionPAI subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000409551-69113_161318.3333333333333484.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000409551-6937_93318.3333333333333484.0RegionPAI subdomain
TgeneNCOA1chr2:223085940chr2:24949456ENST0000028859911221053_1138866.33333333333342199.3333333333335Compositional biasNote=Gln-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST0000034833211211053_1138866.33333333333341442.0Compositional biasNote=Gln-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST0000039585611211053_1138866.33333333333341441.0Compositional biasNote=Gln-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST0000040514114251053_1138866.33333333333342183.6666666666665Compositional biasNote=Gln-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST0000040696113231053_1138866.33333333333341442.0Compositional biasNote=Gln-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST0000053853912231053_1138866.33333333333341422.6666666666667Compositional biasNote=Gln-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST0000028859911221435_1439866.33333333333342199.3333333333335MotifNote=LXXLL motif 7
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122913_917866.33333333333342199.3333333333335MotifNote=LXXLL motif 6
TgeneNCOA1chr2:223085940chr2:24949456ENST0000034833211211435_1439866.33333333333341442.0MotifNote=LXXLL motif 7
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121913_917866.33333333333341442.0MotifNote=LXXLL motif 6
TgeneNCOA1chr2:223085940chr2:24949456ENST0000039585611211435_1439866.33333333333341441.0MotifNote=LXXLL motif 7
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121913_917866.33333333333341441.0MotifNote=LXXLL motif 6
TgeneNCOA1chr2:223085940chr2:24949456ENST0000040514114251435_1439866.33333333333342183.6666666666665MotifNote=LXXLL motif 7
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425913_917866.33333333333342183.6666666666665MotifNote=LXXLL motif 6
TgeneNCOA1chr2:223085940chr2:24949456ENST0000040696113231435_1439866.33333333333341442.0MotifNote=LXXLL motif 7
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323913_917866.33333333333341442.0MotifNote=LXXLL motif 6
TgeneNCOA1chr2:223085940chr2:24949456ENST0000053853912231435_1439866.33333333333341422.6666666666667MotifNote=LXXLL motif 7
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223913_917866.33333333333341422.6666666666667MotifNote=LXXLL motif 6

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePAX3chr2:223085940chr2:24949456ENST00000258387-15219_2780207.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000258387-1534_1610207.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000409828-14219_2780216.0DNA bindingHomeobox
HgenePAX3chr2:223085940chr2:24949456ENST00000409828-1434_1610216.0DNA bindingPaired
HgenePAX3chr2:223085940chr2:24949456ENST00000258387-15113_1610207.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000258387-1537_930207.0RegionPAI subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000409828-14113_1610216.0RegionRED subdomain
HgenePAX3chr2:223085940chr2:24949456ENST00000409828-1437_930216.0RegionPAI subdomain
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122389_682866.33333333333342199.3333333333335Compositional biasNote=Ser-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121389_682866.33333333333341442.0Compositional biasNote=Ser-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121389_682866.33333333333341441.0Compositional biasNote=Ser-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425389_682866.33333333333342183.6666666666665Compositional biasNote=Ser-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323389_682866.33333333333341442.0Compositional biasNote=Ser-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223389_682866.33333333333341422.6666666666667Compositional biasNote=Ser-rich
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122109_180866.33333333333342199.3333333333335DomainPAS
TgeneNCOA1chr2:223085940chr2:24949456ENST00000288599112223_80866.33333333333342199.3333333333335DomainbHLH
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121109_180866.33333333333341442.0DomainPAS
TgeneNCOA1chr2:223085940chr2:24949456ENST00000348332112123_80866.33333333333341442.0DomainbHLH
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121109_180866.33333333333341441.0DomainPAS
TgeneNCOA1chr2:223085940chr2:24949456ENST00000395856112123_80866.33333333333341441.0DomainbHLH
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425109_180866.33333333333342183.6666666666665DomainPAS
TgeneNCOA1chr2:223085940chr2:24949456ENST00000405141142523_80866.33333333333342183.6666666666665DomainbHLH
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323109_180866.33333333333341442.0DomainPAS
TgeneNCOA1chr2:223085940chr2:24949456ENST00000406961132323_80866.33333333333341442.0DomainbHLH
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223109_180866.33333333333341422.6666666666667DomainPAS
TgeneNCOA1chr2:223085940chr2:24949456ENST00000538539122323_80866.33333333333341422.6666666666667DomainbHLH
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122112_116866.33333333333342199.3333333333335MotifNote=LXXLL motif 2
TgeneNCOA1chr2:223085940chr2:24949456ENST00000288599112246_50866.33333333333342199.3333333333335MotifNote=LXXLL motif 1
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122633_637866.33333333333342199.3333333333335MotifNote=LXXLL motif 3
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122690_694866.33333333333342199.3333333333335MotifNote=LXXLL motif 4
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122749_753866.33333333333342199.3333333333335MotifNote=LXXLL motif 5
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121112_116866.33333333333341442.0MotifNote=LXXLL motif 2
TgeneNCOA1chr2:223085940chr2:24949456ENST00000348332112146_50866.33333333333341442.0MotifNote=LXXLL motif 1
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121633_637866.33333333333341442.0MotifNote=LXXLL motif 3
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121690_694866.33333333333341442.0MotifNote=LXXLL motif 4
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121749_753866.33333333333341442.0MotifNote=LXXLL motif 5
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121112_116866.33333333333341441.0MotifNote=LXXLL motif 2
TgeneNCOA1chr2:223085940chr2:24949456ENST00000395856112146_50866.33333333333341441.0MotifNote=LXXLL motif 1
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121633_637866.33333333333341441.0MotifNote=LXXLL motif 3
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121690_694866.33333333333341441.0MotifNote=LXXLL motif 4
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121749_753866.33333333333341441.0MotifNote=LXXLL motif 5
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425112_116866.33333333333342183.6666666666665MotifNote=LXXLL motif 2
TgeneNCOA1chr2:223085940chr2:24949456ENST00000405141142546_50866.33333333333342183.6666666666665MotifNote=LXXLL motif 1
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425633_637866.33333333333342183.6666666666665MotifNote=LXXLL motif 3
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425690_694866.33333333333342183.6666666666665MotifNote=LXXLL motif 4
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425749_753866.33333333333342183.6666666666665MotifNote=LXXLL motif 5
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323112_116866.33333333333341442.0MotifNote=LXXLL motif 2
TgeneNCOA1chr2:223085940chr2:24949456ENST00000406961132346_50866.33333333333341442.0MotifNote=LXXLL motif 1
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323633_637866.33333333333341442.0MotifNote=LXXLL motif 3
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323690_694866.33333333333341442.0MotifNote=LXXLL motif 4
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323749_753866.33333333333341442.0MotifNote=LXXLL motif 5
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223112_116866.33333333333341422.6666666666667MotifNote=LXXLL motif 2
TgeneNCOA1chr2:223085940chr2:24949456ENST00000538539122346_50866.33333333333341422.6666666666667MotifNote=LXXLL motif 1
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223633_637866.33333333333341422.6666666666667MotifNote=LXXLL motif 3
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223690_694866.33333333333341422.6666666666667MotifNote=LXXLL motif 4
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223749_753866.33333333333341422.6666666666667MotifNote=LXXLL motif 5


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Fusion Protein Structures

check button 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)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file (701) >>>701.pdbFusion protein BP residue: 318
CIF file (701) >>>701.cif		PAX3chr2223085940-NCOA1chr224949457+
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRP
LPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGA
IGGSKPKVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPSV
SSISRILRSKFGKGEEEEADLERKEAEESEKKAKHSIDGILSERASAPQS
DEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREE
LAQRAKLTEARVQVWFSNRRARWRKQAGANQLMAFNHLIPGGFPPTAMPT
LPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVTA
INQSKSEDQCISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETEL
AELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSSP
SPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRPP
AAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVGINMRSGMQQQI
TPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPSS
GLPVQMGNPRLPQGAPQQFPYPPNYGTNPGTPPASTSPFSQLAANPEASL
ANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAPS
LSPGSSMVPMPIPPPQSSLLQQTPPASGYQSPDMKAWQQGAIGNNNVFSQ
AVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPGM
NTVCPEQINDPALRHTGLYCNQLSSTDLLKTEADGTQQVQQVQVFADVQC
893
3D view using mol* of 701 (AA BP:318)
PDB file (702) >>>702.pdbFusion protein BP residue: 319
CIF file (702) >>>702.cif		PAX3chr2223085940-NCOA1chr224949457+
MTTLAGAVPRMMRPGPGQNYPRSGFPLEVSTPLGQGRVNQLGGVFINGRP
LPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGA
IGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLKDAVCDRNTVPS
VSSISRILRSKFGKGEEEEADLERKEAEESEKKAKHSIDGILSERASAPQ
SDEGSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTRE
ELAQRAKLTEARVQVWFSNRRARWRKQAGANQLMAFNHLIPGGFPPTAMP
TLPTYQLSETSYQPTSIPQGLPELELEAIDNQFGQPGTGDQIPWTNNTVT
AINQSKSEDQCISSQLDELLCPPTTVEGRNDEKALLEQLVSFLSGKDETE
LAELDRALGIDKLVQGGGLDVLSERFPPQQATPPLIMEERPNLYSQPYSS
PSPTANLPSPFQGMVRQKPSLGTMPVQVTPPRGAFSPGMGMQPRQTLNRP
PAAPNQLRLQLQQRLQGQQQLIHQNRQAILNQFAATAPVGINMRSGMQQQ
ITPQPPLNAQMLAQRQRELYSQQHRQRQLIQQQRAMLMRQQSFGNNLPPS
SGLPVQMGNPRLPQGAPQQFPYPPNYGTNPGTPPASTSPFSQLAANPEAS
LANRNSMVSRGMTGNIGGQFGTGINPQMQQNVFQYPGAGMVPQGEANFAP
SLSPGSSMVPMPIPPPQSSLLQQTPPASGYQSPDMKAWQQGAIGNNNVFS
QAVQNQPTPAQPGVYNNMSITVSMAGGNTNVQNMNPMMAQMQMSSLQMPG
MNTVCPEQINDPALRHTGLYCNQLSSTDLLKTEADGTQQVQQVQVFADVQ
894
3D view using mol* of 702 (AA BP:319)


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pLDDT score distribution

check button 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
all structure
all structure
NCOA1_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
PAX3_NCOA1_701_pLDDT.png (AA BP:318)
all structure
PAX3_NCOA1_701_pLDDT_and_active_sites.png (AA BP:318)
all structure
PAX3_NCOA1_701_violinplot.png (AA BP:318)
all structure
PAX3_NCOA1_702_pLDDT.png (AA BP:319)
all structure
PAX3_NCOA1_702_pLDDT_and_active_sites.png (AA BP:319)
all structure
PAX3_NCOA1_702_violinplot.png (AA BP:319)
all structure


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Ramachandran Plot of Fusion Protein Structure


check button 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_NCOA1_701.png
all structure
PAX3_NCOA1_702.png
all structure

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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Fusion AA seq ID in FusionPDBSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
7010.9952691.023884.5970.5790.6750.8890.6790.9870.6880.56Chain A: 27,29,31,39,43,44,45,46,47,48,49,50,51,52
,55,56,76,77,78,79,82,85,86,88,89,92,93,95,97,98,9
9,100,101,102,104,105,214,215,216,217,218,219,220,
221,222,223,224
7021.0051901.035491.8620.5610.6830.940.8390.9650.870.536Chain A: 26,27,29,31,39,43,44,45,46,47,48,49,50,51
,52,54,55,56,58,75,76,77,78,79,82,84,85,86,88,89,9
2,93,98,99,101,220

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Potentially Interacting Small Molecules through Virtual Screening


check button The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.
Fusion AA seq ID in FusionPDBZINC IDDrugBank IDDrug nameDocking scoreGlide gscore

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group

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Biochemical Features of Small Molecules


check button ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)
ZINC IDmol_MWdipoleSASAFOSAFISAPISAWPSAvolumedonorHBaccptHBIPHuman Oral AbsorptionPercent Human Oral AbsorptionRule Of FiveRule Of Three


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors
PAX3IPO13, 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,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PAX3all structure
NCOA1all structure


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122781_988866.33333333333342199.3333333333335CREBBP
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121781_988866.33333333333341442.0CREBBP
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121781_988866.33333333333341441.0CREBBP
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425781_988866.33333333333342183.6666666666665CREBBP
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323781_988866.33333333333341442.0CREBBP
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223781_988866.33333333333341422.6666666666667CREBBP
TgeneNCOA1chr2:223085940chr2:24949456ENST000002885991122361_567866.33333333333342199.3333333333335STAT3
TgeneNCOA1chr2:223085940chr2:24949456ENST000003483321121361_567866.33333333333341442.0STAT3
TgeneNCOA1chr2:223085940chr2:24949456ENST000003958561121361_567866.33333333333341441.0STAT3
TgeneNCOA1chr2:223085940chr2:24949456ENST000004051411425361_567866.33333333333342183.6666666666665STAT3
TgeneNCOA1chr2:223085940chr2:24949456ENST000004069611323361_567866.33333333333341442.0STAT3
TgeneNCOA1chr2:223085940chr2:24949456ENST000005385391223361_567866.33333333333341422.6666666666667STAT3


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Related Drugs to PAX3-NCOA1


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

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Related Diseases to PAX3-NCOA1


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

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePAX3C1847800Waardenburg Syndrome Type 133CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgenePAX3C0079661Klein's Syndrome16CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgenePAX3C3266898Waardenburg Syndrome12CLINGEN;CTD_human;GENOMICS_ENGLAND
HgenePAX3C1852510Craniofacial deafness hand syndrome5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgenePAX3C0038219Status Dysraphicus4CTD_human
HgenePAX3C0080178Spina Bifida4CTD_human
HgenePAX3C0266508Rachischisis4CTD_human
HgenePAX3C0011999Diastematomyelia3CTD_human
HgenePAX3C0027794Neural Tube Defects3CTD_human
HgenePAX3C0027806Neurenteric Cyst3CTD_human
HgenePAX3C0080218Tethered Cord Syndrome3CTD_human
HgenePAX3C0152234Iniencephaly3CTD_human
HgenePAX3C0152426Craniorachischisis3CTD_human
HgenePAX3C0266453Exencephaly3CTD_human
HgenePAX3C0344479Spinal Cord Myelodysplasia3CTD_human
HgenePAX3C0599973Waardenburg Anophthalmia Syndrome3ORPHANET
HgenePAX3C0702169Acrania3CTD_human
HgenePAX3C0206655Alveolar rhabdomyosarcoma2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgenePAX3C0011052Prelingual Deafness1CTD_human
HgenePAX3C0011053Deafness1CTD_human
HgenePAX3C0018566Congenital Hand Deformities1CTD_human
HgenePAX3C0086395Hearing Loss, Extreme1CTD_human
HgenePAX3C0205944Sarcoma, Epithelioid1CTD_human
HgenePAX3C0205945Sarcoma, Spindle Cell1CTD_human
HgenePAX3C0265541Cranioschisis1CTD_human
HgenePAX3C0376634Craniofacial Abnormalities1CTD_human
HgenePAX3C0497552Congenital neurologic anomalies1CTD_human
HgenePAX3C0581883Complete Hearing Loss1CTD_human
HgenePAX3C0751068Deafness, Acquired1CTD_human
HgenePAX3C1261473Sarcoma1CTD_human
HgenePAX3C1710096Sinonasal undifferentiated carcinoma1CTD_human
HgenePAX3C3665473Bilateral Deafness1CTD_human
HgenePAX3C4082305Deaf Mutism1CTD_human
TgeneNCOA1C0006142Malignant neoplasm of breast1CTD_human
TgeneNCOA1C0014175Endometriosis1CTD_human
TgeneNCOA1C0024668Mammary Neoplasms, Experimental1CTD_human
TgeneNCOA1C0027627Neoplasm Metastasis1CTD_human
TgeneNCOA1C0033578Prostatic Neoplasms1CTD_human
TgeneNCOA1C0269102Endometrioma1CTD_human
TgeneNCOA1C0376358Malignant neoplasm of prostate1CTD_human
TgeneNCOA1C0678222Breast Carcinoma1CTD_human
TgeneNCOA1C1257931Mammary Neoplasms, Human1CTD_human
TgeneNCOA1C1458155Mammary Neoplasms1CTD_human
TgeneNCOA1C4704874Mammary Carcinoma, Human1CTD_human