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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:SS18-SSX4

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SS18-SSX4
FusionPDB ID: 86685
FusionGDB2.0 ID: 86685
HgeneTgene
Gene symbol

SS18

SSX4

Gene ID

6760

6759

Gene nameSS18 subunit of BAF chromatin remodeling complexSSX family member 4
SynonymsSSXT|SYTCT5.4
Cytomap

18q11.2

Xp11.23

Type of geneprotein-codingprotein-coding
Descriptionprotein SSXTSS18, nBAF chromatin remodeling complex subunitsynovial sarcoma translocated to X chromosome proteinsynovial sarcoma translocation, chromosome 18synovial sarcoma, translocated to X chromosomeprotein SSX4cancer/testis antigen 5.4synovial sarcoma, X breakpoint 4
Modification date2020032920200313
UniProtAcc

O75177

O60224

Ensembl transtripts involved in fusion geneENST idsENST00000269137, ENST00000415083, 
ENST00000539849, ENST00000542420, 
ENST00000542743, ENST00000545952, 
ENST00000585241, 		ENST00000375517, 
ENST00000376886, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 33 X 8=63361 X 4 X 2=8
# samples 382
** MAII scorelog2(38/6336*10)=-4.05950101174866
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: SS18 [Title/Abstract] AND SSX4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SS18(23612363)-SSX4(48248786), # samples:2
Anticipated loss of major functional domain due to fusion event.SS18-SSX4 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.
SS18-SSX4 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.
SS18-SSX4 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.
SS18-SSX4 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.
SS18-SSX4 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
SS18-SSX4 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted 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
HgeneSS18

GO:0045944

positive regulation of transcription by RNA polymerase II

15919756


check buttonFusion gene breakpoints across SS18 (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 SSX4 (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
ChimerKB3..SS18chr18

23596216

-SSX4chrX

48244002

+
ChimerKB3..SS18chr18

23596216

-SSX4chrX

48248787

+
ChimerKB3..SS18chr18

23596216

-SSX4chrX

48251310

+
ChimerKB3..SS18chr18

23612362

-SSX4chrX

48244002

+
ChimerKB3..SS18chr18

23612362

-SSX4chrX

48248787

+
ChimerKB3..SS18chr18

23612362

-SSX4chrX

48251310

+
ChiTaRS5.0N/AAF114234SS18chr18

23612363

-SSX4chrX

48248786

+
ChiTaRS5.0N/AAF257500SS18chr18

23612363

-SSX4chrX

48248786

+


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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)
ENST00000415083SS18chr1823612362-ENST00000376886SSX4chrX48244002+23761286561783575
ENST00000415083SS18chr1823612362-ENST00000375517SSX4chrX48244002+17451286561678540
ENST00000269137SS18chr1823612362-ENST00000376886SSX4chrX48244002+255914691611966601
ENST00000269137SS18chr1823612362-ENST00000375517SSX4chrX48244002+192814691611861566
ENST00000545952SS18chr1823612362-ENST00000376886SSX4chrX48244002+237412843031781492
ENST00000545952SS18chr1823612362-ENST00000375517SSX4chrX48244002+174312843031676457
ENST00000415083SS18chr1823612362-ENST00000376886SSX4chrX48248787+21151286561522488
ENST00000269137SS18chr1823612362-ENST00000376886SSX4chrX48248787+229814691611705514
ENST00000545952SS18chr1823612362-ENST00000376886SSX4chrX48248787+211312843031520405
ENST00000415083SS18chr1823612362-ENST00000375517SSX4chrX48251310+14841286561417453
ENST00000542743SS18chr1823612362-ENST00000376886SSX4chrX48251310+202413313501462370
ENST00000269137SS18chr1823612362-ENST00000375517SSX4chrX48251310+166714691611600479
ENST00000545952SS18chr1823612362-ENST00000375517SSX4chrX48251310+148212843031415370
ENST00000415083SS18chr1823612363-ENST00000376886SSX4chrX48248786+21151286561522488
ENST00000269137SS18chr1823612363-ENST00000376886SSX4chrX48248786+229814691611705514
ENST00000545952SS18chr1823612363-ENST00000376886SSX4chrX48248786+211312843031520405

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
ENST00000415083ENST00000376886SS18chr1823612363-SSX4chrX48248786+0.0023628670.99763715
ENST00000269137ENST00000376886SS18chr1823612363-SSX4chrX48248786+0.0027843790.9972156
ENST00000545952ENST00000376886SS18chr1823612363-SSX4chrX48248786+0.0010668810.99893314

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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

>86685_86685_1_SS18-SSX4_SS18_chr18_23612362_ENST00000269137_SSX4_chrX_48244002_ENST00000375517_length(amino acids)=566AA_BP=436
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLADSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQ
CIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQM
NGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQ
QYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQD
AYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEW
EKMKSSEKIVYVYMKLNYEVMTKLGFKVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKDPKGGNMPGPTDCVRES

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>86685_86685_2_SS18-SSX4_SS18_chr18_23612362_ENST00000269137_SSX4_chrX_48244002_ENST00000376886_length(amino acids)=601AA_BP=435
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLADSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQ
CIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQM
NGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQ
QYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQD
AYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEW
EKMKSSEKIVYVYMKLNYEVMTKLGFKVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKIMPKKPAEEENGLKEVP

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

>86685_86685_3_SS18-SSX4_SS18_chr18_23612362_ENST00000269137_SSX4_chrX_48248787_ENST00000376886_length(amino acids)=514AA_BP=436
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLADSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQ
CIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQM
NGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQ
QYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQD
AYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLK

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

>86685_86685_4_SS18-SSX4_SS18_chr18_23612362_ENST00000269137_SSX4_chrX_48251310_ENST00000375517_length(amino acids)=479AA_BP=436
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLADSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQ
CIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQM
NGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQ
QYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQD
AYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQDPKGGNMPGPTDCV

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

>86685_86685_5_SS18-SSX4_SS18_chr18_23612362_ENST00000415083_SSX4_chrX_48244002_ENST00000375517_length(amino acids)=540AA_BP=410
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGM
NQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMT
MSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDY
YGDQYSHGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG
QQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKIVYVYMKLNYEVMTKLGF
KVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTSNSPRGYDTCP

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

>86685_86685_6_SS18-SSX4_SS18_chr18_23612362_ENST00000415083_SSX4_chrX_48244002_ENST00000376886_length(amino acids)=575AA_BP=409
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGM
NQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMT
MSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDY
YGDQYSHGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG
QQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKIVYVYMKLNYEVMTKLGF
KVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPGNPSTLEKINK

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

>86685_86685_7_SS18-SSX4_SS18_chr18_23612362_ENST00000415083_SSX4_chrX_48248787_ENST00000376886_length(amino acids)=488AA_BP=410
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGM
NQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMT
MSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDY
YGDQYSHGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG
QQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPGNPSTLEK

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

>86685_86685_8_SS18-SSX4_SS18_chr18_23612362_ENST00000415083_SSX4_chrX_48251310_ENST00000375517_length(amino acids)=453AA_BP=410
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGM
NQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMT
MSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDY
YGDQYSHGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG
QQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTSNSPRGYD

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

>86685_86685_9_SS18-SSX4_SS18_chr18_23612362_ENST00000542743_SSX4_chrX_48251310_ENST00000376886_length(amino acids)=370AA_BP=327
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQ
LNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPM
GMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYP
GQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTS

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

>86685_86685_10_SS18-SSX4_SS18_chr18_23612362_ENST00000545952_SSX4_chrX_48244002_ENST00000375517_length(amino acids)=457AA_BP=327
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQ
LNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPM
GMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYP
GQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKIVYVYMKLNYE
VMTKLGFKVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTSNSP

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

>86685_86685_11_SS18-SSX4_SS18_chr18_23612362_ENST00000545952_SSX4_chrX_48244002_ENST00000376886_length(amino acids)=492AA_BP=326
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQ
LNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPM
GMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYP
GQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKIVYVYMKLNYE
VMTKLGFKVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPGNPS

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

>86685_86685_12_SS18-SSX4_SS18_chr18_23612362_ENST00000545952_SSX4_chrX_48248787_ENST00000376886_length(amino acids)=405AA_BP=327
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQ
LNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPM
GMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYP
GQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPG

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

>86685_86685_13_SS18-SSX4_SS18_chr18_23612362_ENST00000545952_SSX4_chrX_48251310_ENST00000375517_length(amino acids)=370AA_BP=327
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQ
LNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPM
GMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYP
GQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTS

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>86685_86685_14_SS18-SSX4_SS18_chr18_23612363_ENST00000269137_SSX4_chrX_48248786_ENST00000376886_length(amino acids)=514AA_BP=436
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLADSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQ
CIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQM
NGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQ
QYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQD
AYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLK

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

>86685_86685_15_SS18-SSX4_SS18_chr18_23612363_ENST00000415083_SSX4_chrX_48248786_ENST00000376886_length(amino acids)=488AA_BP=410
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGM
NQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMT
MSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDY
YGDQYSHGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG
QQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPGNPSTLEK

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

>86685_86685_16_SS18-SSX4_SS18_chr18_23612363_ENST00000545952_SSX4_chrX_48248786_ENST00000376886_length(amino acids)=405AA_BP=327
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQ
LNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPM
GMMGQVNQGNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQDAYQGPPPQQGYPPQQQQYP
GQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPG

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

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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/chr18:23612363/chrX:48248786)
- 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
SS18

O75177

SSX4

O60224

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Could act as a modulator of transcription.

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
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-91095_99379.0388.0Compositional biasNote=Poly-Pro
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-101195_99410.0419.0Compositional biasNote=Poly-Pro
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910374_377379.0388.0MotifSH2-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-91050_53379.0388.0MotifSH2-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011374_377410.0419.0MotifSH2-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011392_401410.0419.0MotifSH3-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-101150_53410.0419.0MotifSH2-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-9102_186379.0388.0RegionNote=Transcriptional activation
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910344_369379.0388.0RegionNote=2 X 13 AA imperfect tandem repeats
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-10112_186410.0419.0RegionNote=Transcriptional activation
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011344_369410.0419.0RegionNote=2 X 13 AA imperfect tandem repeats
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910344_356379.0388.0RepeatNote=1
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910357_369379.0388.0RepeatNote=2
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011344_356410.0419.0RepeatNote=1
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011357_369410.0419.0RepeatNote=2

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910175_418379.0388.0Compositional biasNote=Gln-rich
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011175_418410.0419.0Compositional biasNote=Gln-rich
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910392_401379.0388.0MotifSH3-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000269137-910413_416379.0388.0MotifSH2-binding
HgeneSS18chr18:23612363chrX:48248786ENST00000415083-1011413_416410.0419.0MotifSH2-binding
TgeneSSX4chr18:23612363chrX:48248786ENST000003768864820_83110.0337.3333333333333DomainKRAB-related


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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 (123) >>>123.pdbFusion protein BP residue: 327
CIF file (123) >>>123.cif		SS18chr1823612362-SSX4chrX48251310+
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSH
NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNM
PSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQ
GPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPP
YRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQ
DAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQ
GQQYGGYRPTQPGPPQPPQQRPYGYDQDPKGGNMPGPTDCVRESSWWFMK
370
3D view using mol* of 123 (AA BP:327)
PDB file (168) >>>168.pdbFusion protein BP residue: 327
CIF file (168) >>>168.cif		SS18chr1823612362-SSX4chrX48248787+
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSH
NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNM
PSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQ
GPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPP
YRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQ
DAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQ
GQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLKEVPEASGPQ
NDGKQLCPPGNPSTLEKINKTSGPKRGKHAWTHRLRERKQLVVYEEISDP
405
3D view using mol* of 168 (AA BP:327)
PDB file (223) >>>223.pdbFusion protein BP residue: 410
CIF file (223) >>>223.cif		SS18chr1823612362-SSX4chrX48251310+
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQY
QQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPR
SHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSM
NMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQP
NQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQI
PPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGHNDYGY
QQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQ
QYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQP
PQQRPYGYDQDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTSNSPRGYD
453
3D view using mol* of 223 (AA BP:410)
PDB file (229) >>>229.pdbFusion protein BP residue: 327
CIF file (229) >>>229.cif		SS18chr1823612362-SSX4chrX48244002+
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSH
NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNM
PSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQ
GPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPP
YRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQ
DAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQ
GQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKI
VYVYMKLNYEVMTKLGFKVTLPPFMRSKRAADFHGNDFGNDRNHRNQVER
PQMTFGSLQRIFPKDPKGGNMPGPTDCVRESSWWFMKRSATLRKMTSNSP
457
3D view using mol* of 229 (AA BP:327)
PDB file (262) >>>262.pdbFusion protein BP residue: 436
CIF file (262) >>>262.cif		SS18chr1823612362-SSX4chrX48251310+
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLA
DSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGK
TSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS
GPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQL
NMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPR
PNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNH
MMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPD
GNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGP
QYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQDPKGGNMPGPTDCV
479
3D view using mol* of 262 (AA BP:436)
PDB file (281) >>>281.pdbFusion protein BP residue: 410
CIF file (281) >>>281.cif		SS18chr1823612362-SSX4chrX48248787+
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQY
QQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPR
SHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSM
NMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQP
NQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQI
PPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGHNDYGY
QQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQ
QYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQP
PQQRPYGYDQIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPGNPSTLEK
488
3D view using mol* of 281 (AA BP:410)
PDB file (285) >>>285.pdbFusion protein BP residue: 326
CIF file (285) >>>285.cif		SS18chr1823612362-SSX4chrX48244002+
MLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSH
NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNM
PSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQPNQ
GPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQIPP
YRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGNSQYGQQQ
DAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQ
GQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKI
VYVYMKLNYEVMTKLGFKVTLPPFMRSKRAADFHGNDFGNDRNHRNQVER
PQMTFGSLQRIFPKIMPKKPAEEENGLKEVPEASGPQNDGKQLCPPGNPS
492
3D view using mol* of 285 (AA BP:326)
PDB file (325) >>>325.pdbFusion protein BP residue: 436
CIF file (325) >>>325.cif		SS18chr1823612362-SSX4chrX48248787+
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLA
DSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGK
TSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS
GPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQL
NMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPR
PNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNH
MMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPD
GNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGP
QYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQIMPKKPAEEENGLK
EVPEASGPQNDGKQLCPPGNPSTLEKINKTSGPKRGKHAWTHRLRERKQL
514
3D view using mol* of 325 (AA BP:436)
PDB file (374) >>>374.pdbFusion protein BP residue: 410
CIF file (374) >>>374.cif		SS18chr1823612362-SSX4chrX48244002+
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQY
QQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPR
SHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSM
NMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQP
NQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQI
PPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGHNDYGY
QQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQ
QYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQP
PQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKIVYVYMKLNYEVMTKLGF
KVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKDPK
540
3D view using mol* of 374 (AA BP:410)
PDB file (416) >>>416.pdbFusion protein BP residue: 436
CIF file (416) >>>416.cif		SS18chr1823612362-SSX4chrX48244002+
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLA
DSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGK
TSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS
GPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQL
NMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPR
PNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNH
MMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPD
GNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGP
QYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEW
EKMKSSEKIVYVYMKLNYEVMTKLGFKVTLPPFMRSKRAADFHGNDFGND
RNHRNQVERPQMTFGSLQRIFPKDPKGGNMPGPTDCVRESSWWFMKRSAT
566
3D view using mol* of 416 (AA BP:436)
PDB file (437) >>>437.pdbFusion protein BP residue: 409
CIF file (437) >>>437.cif		SS18chr1823612362-SSX4chrX48244002+
MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQY
QQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPR
SHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSM
NMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMSMQP
NQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNHMMGQRQI
PPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGHNDYGY
QQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQ
QYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQP
PQQRPYGYDQAFDDIAKYFSKKEWEKMKSSEKIVYVYMKLNYEVMTKLGF
KVTLPPFMRSKRAADFHGNDFGNDRNHRNQVERPQMTFGSLQRIFPKIMP
KKPAEEENGLKEVPEASGPQNDGKQLCPPGNPSTLEKINKTSGPKRGKHA
575
3D view using mol* of 437 (AA BP:409)
PDB file (475) >>>475.pdbFusion protein BP residue: 435
CIF file (475) >>>475.cif		SS18chr1823612362-SSX4chrX48244002+
MARVPPSGLPRRPSAWPRSIPPPRIPEVVQPERPASLPQFAVHPERSGLA
DSGDGGNMSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGK
TSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS
GPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQL
NMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMTMSQGQPMGNYGPR
PNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGNH
MMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPD
GNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGP
QYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQAFDDIAKYFSKKEW
EKMKSSEKIVYVYMKLNYEVMTKLGFKVTLPPFMRSKRAADFHGNDFGND
RNHRNQVERPQMTFGSLQRIFPKIMPKKPAEEENGLKEVPEASGPQNDGK
QLCPPGNPSTLEKINKTSGPKRGKHAWTHRLRERKQLVVYEEISDPEEDD
601
3D view using mol* of 475 (AA BP:435)


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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.
SS18_pLDDT.png
all structure
all structure
SSX4_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.
SS18_SSX4_123_PAE.png (AA BP:327)
all structure
SS18_SSX4_123_pLDDT.png (AA BP:327)
all structure
SS18_SSX4_123_pLDDT_and_active_sites.png (AA BP:327)
all structure
SS18_SSX4_123_violinplot.png (AA BP:327)
all structure
SS18_SSX4_168_PAE.png (AA BP:327)
all structure
SS18_SSX4_168_pLDDT.png (AA BP:327)
all structure
SS18_SSX4_168_pLDDT_and_active_sites.png (AA BP:327)
all structure
SS18_SSX4_168_violinplot.png (AA BP:327)
all structure
SS18_SSX4_223_PAE.png (AA BP:410)
all structure
SS18_SSX4_223_pLDDT.png (AA BP:410)
all structure
SS18_SSX4_223_pLDDT_and_active_sites.png (AA BP:410)
all structure
SS18_SSX4_223_violinplot.png (AA BP:410)
all structure
SS18_SSX4_229_PAE.png (AA BP:327)
all structure
SS18_SSX4_229_pLDDT.png (AA BP:327)
all structure
SS18_SSX4_229_pLDDT_and_active_sites.png (AA BP:327)
all structure
SS18_SSX4_229_violinplot.png (AA BP:327)
all structure
SS18_SSX4_262_PAE.png (AA BP:436)
all structure
SS18_SSX4_262_pLDDT.png (AA BP:436)
all structure
SS18_SSX4_262_pLDDT_and_active_sites.png (AA BP:436)
all structure
SS18_SSX4_262_violinplot.png (AA BP:436)
all structure
SS18_SSX4_281_pLDDT.png (AA BP:410)
all structure
SS18_SSX4_281_pLDDT_and_active_sites.png (AA BP:410)
all structure
SS18_SSX4_281_violinplot.png (AA BP:410)
all structure
SS18_SSX4_285_pLDDT.png (AA BP:326)
all structure
SS18_SSX4_285_pLDDT_and_active_sites.png (AA BP:326)
all structure
SS18_SSX4_285_violinplot.png (AA BP:326)
all structure
SS18_SSX4_325_pLDDT.png (AA BP:436)
all structure
SS18_SSX4_325_pLDDT_and_active_sites.png (AA BP:436)
all structure
SS18_SSX4_325_violinplot.png (AA BP:436)
all structure
SS18_SSX4_374_pLDDT.png (AA BP:410)
all structure
SS18_SSX4_374_pLDDT_and_active_sites.png (AA BP:410)
all structure
SS18_SSX4_374_violinplot.png (AA BP:410)
all structure
SS18_SSX4_416_pLDDT.png (AA BP:436)
all structure
SS18_SSX4_416_pLDDT_and_active_sites.png (AA BP:436)
all structure
SS18_SSX4_416_violinplot.png (AA BP:436)
all structure
SS18_SSX4_437_pLDDT.png (AA BP:409)
all structure
SS18_SSX4_437_pLDDT_and_active_sites.png (AA BP:409)
all structure
SS18_SSX4_437_violinplot.png (AA BP:409)
all structure
SS18_SSX4_475_pLDDT.png (AA BP:435)
all structure
SS18_SSX4_475_pLDDT_and_active_sites.png (AA BP:435)
all structure
SS18_SSX4_475_violinplot.png (AA BP:435)
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
SS18_SSX4_123.png
all structure
SS18_SSX4_168.png
all structure
SS18_SSX4_223.png
all structure
SS18_SSX4_229.png
all structure
SS18_SSX4_262.png
all structure
SS18_SSX4_281.png
all structure
SS18_SSX4_285.png
all structure
SS18_SSX4_325.png
all structure
SS18_SSX4_374.png
all structure
SS18_SSX4_416.png
all structure
SS18_SSX4_437.png
all structure
SS18_SSX4_475.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
1230.33890.2790.3430.8570.3810.5620.3780.7110.5321.15Chain A: 141,142,143,144
1680.32180.2153.0870.8370.4570.7870.0930.9960.0930.637Chain A: 33,34,35,36,37,38
2230.999881.011200.9980.5190.7441.0651.0250.9741.0520.696Chain A: 22,25,26,28,29,32,33,35,36,39,51,54,58,61
,424,427,428,429,431,432,435,438,439
2291.0823421.151990.2410.5240.7110.9521.40.6632.1131.527Chain A: 1,2,3,6,7,9,10,12,13,14,16,17,19,20,320,3
21,322,323,325,328,329,331,350,353,354,356,357,358
,360,361,364,365,416,417,418,419,421,422,424,425,4
26,427,428,429,430,431,432,434,435,436,450,452,453
,455,456,457
2620.954760.985222.950.6480.6910.9911.0560.7641.3830.858Chain A: 82,85,86,89,92,93,96,99,101,104,108,111,1
15,447,450,453,454,455,457,458,461,465
2811.0181381.096480.5430.6780.6120.8161.0350.6481.5971.183Chain A: 5,6,7,8,9,11,12,13,14,15,16,17,20,21,23,2
4,27,49,51,52,53,54,55,56,57,58,59,60,63,64,464,46
7,468
2851.1551811.238551.8870.450.7791.0442.4770.5184.7850.719Chain A: 1,2,4,5,6,8,9,322,323,325,328,329,331,332
,350,351,353,354,355,356,357,360,361,364,405,408,4
09,411,412,413,414,415
3250.835590.857218.4910.720.6110.7920.7460.711.0511.03Chain A: 65,66,68,69,71,72,73,77,78,109,112,113,11
6,117,120,121
3740.934548551.05032545.060.66320.43220.40220.35330.45730.77250.9652Chain A: 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
20,21,22,23,24,25,27,28,29,30,31,32,33,34,35,36,37
,38,39,40,41,42,43,44,46,47,48,49,50,51,52,53,54,5
5,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,
72,73,74,75,76,77,78,400,401,402,403,404,405,406,4
07,408,409,410,411,412,413,414,416,417,418,419,420
,421,422,423,424,426,427,428,429,430,431,432,433,4
34,435,436,437,438,439,440,441,442,443,444,445,446
,447,448,450,451,452,453,454,455,456,457,458,459,4
60,461,462,465,466,480,481,482,483,484,485,486,487
,488,489,490,491,492,493,494,495,496,497,498,499,5
00,501,502,503,504,505,506,507,508,509,510,511,512
,513,514,515,516,517,518,519,520,521,522,523,524,5
25,526,527,528,529,530,531,532,533,534,535,536,537
,538,539,540
4160.963440.93261.740.380.9361.3992.9290.7763.7770.628Chain A: 460,463,464,467,468,471,481,512,514,517,5
36,539,540,543,544
4371.0561291.121366.6670.5640.6870.9141.3910.711.9580.793Chain A: 35,39,44,47,48,51,54,55,58,430,433,434,43
7,488,491,492,495,496,497,498,499,500,501
4751.09251131.1832227.0660.56540.68510.87991.89050.51493.67140.7784Chain A: 434,456,459,460,462,463,514,517,518,521,5
22,523,524,525,526,527,528

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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
223ZINC000000057255DB00310Chlorthalidone-6.63185-6.63325
223ZINC000000020253DB00310Chlorthalidone-6.46611-6.46751
223ZINC000000509440DB00842Oxazepam-6.45659-6.45659
223ZINC000000006157DB00751Epinastine-4.76565-6.40975
223ZINC000001547851DB11868Etiracetam-6.40559-6.40559
223ZINC000008143864DB09134Ioversol-6.37744-6.37744
223ZINC000000896634DB00231Temazepam-6.37103-6.37103
223ZINC000000085733DB00181Baclofen-6.29964-6.29964
223ZINC000000007782DB06201Rufinamide-6.26332-6.26332
223ZINC000000020220DB00537Ciprofloxacin-6.12308-6.22288
223ZINC000000121541DB00643Mebendazole-5.53118-6.21388
223ZINC000028973446DB00628Clorazepic acid-6.20329-6.20329
223ZINC000000006427DB00829Diazepam-6.18983-6.18983
223ZINC000000896731DB00744Zileuton-6.15026-6.16886
223ZINC000019632917DB00475Chlordiazepoxide-6.11138-6.15928
223ZINC000001482184DB00853Temozolomide-6.15248-6.15408
223ZINC000000001899DB00299Penciclovir-6.11976-6.11976
223ZINC000084441937DB00759Tetracycline-5.97564-6.11524
223ZINC000001999441DB04861Nebivolol-6.0585-6.0783
223ZINC000008035395DB09134Ioversol-6.07282-6.07282

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group
ZINC000000057255DB00310ChlorthalidoneSmall moleculeNS(=O)(=O)C1=C(Cl)C=CC(=C1)C1(O)NC(=O)C2=CC=CC=C12Approved
ZINC000008143864DB09134IoversolSmall moleculeOCCN(C(=O)CO)C1=C(I)C(C(=O)NCC(O)CO)=C(I)C(C(=O)NCC(O)CO)=C1IApproved
ZINC000000085733DB00181BaclofenSmall moleculeNCC(CC(O)=O)C1=CC=C(Cl)C=C1Approved
ZINC000000007782DB06201RufinamideSmall moleculeNC(=O)C1=CN(CC2=C(F)C=CC=C2F)N=N1Approved
ZINC000000020220DB00537CiprofloxacinSmall moleculeOC(=O)C1=CN(C2CC2)C2=CC(N3CCNCC3)=C(F)C=C2C1=OApproved|Investigational
ZINC000000121541DB00643MebendazoleSmall moleculeCOC(=O)NC1=NC2=C(N1)C=C(C=C2)C(=O)C1=CC=CC=C1Approved|Vet_approved
ZINC000028973446DB00628Clorazepic acidSmall moleculeOC(=O)C1N=C(C2=CC=CC=C2)C2=C(NC1=O)C=CC(Cl)=C2Approved|Illicit
ZINC000000006427DB00829DiazepamSmall moleculeCN1C2=C(C=C(Cl)C=C2)C(=NCC1=O)C1=CC=CC=C1Approved|Illicit|Investigational|Vet_approved
ZINC000000896731DB00744ZileutonSmall moleculeCC(N(O)C(N)=O)C1=CC2=CC=CC=C2S1Approved|Investigational|Withdrawn
ZINC000019632917DB00475ChlordiazepoxideSmall moleculeCNC1=NC2=C(C=C(Cl)C=C2)C(C2=CC=CC=C2)=[N+]([O-])C1Approved|Illicit|Investigational
ZINC000001482184DB00853TemozolomideSmall moleculeCN1N=NC2=C(N=CN2C1=O)C(N)=OApproved|Investigational
ZINC000000001899DB00299PenciclovirSmall moleculeNC1=NC(=O)C2=C(N1)N(CCC(CO)CO)C=N2Approved
ZINC000084441937DB00759TetracyclineSmall molecule[H][C@@]12C[C@@]3([H])C(=C(O)[C@]1(O)C(=O)C(C(N)=O)=C(O)[C@H]2N(C)C)C(=O)C1=C(O)C=CC=C1[C@@]3(C)OApproved|Vet_approved

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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
ZINC000000057255338.7659.032531.7580.001243.761234.49553.501911.03247.7510.165259.13800
ZINC000000020253338.7655.817531.4750243.204234.86453.406910.35647.7510.189259.23300
ZINC000000509440286.7173.437510.92324.832130.585284.06271.444859.77125.29.187389.41500
ZINC000000006157249.3154.842470.72692.01978.033300.6750820.853228.106310000
ZINC000000006157249.3153.771466.45387.1778.72300.5640823.493228.486310000
ZINC000001547851170.2113.554386.861254.133132.72800627.87225.59.606259.07500
ZINC000008143864807.1165.478759.618304.239335.9096.136113.3331427.748818.29.2111031
ZINC000000896634300.7443.437532.5397.28798.824265.01571.404911.44315.79.157396.4600
ZINC000000085733213.6633.613420.9180.54149.736119.12871.506697.141339.549248.77600
ZINC000000007782238.1964.498437.53839.302165.455174.30158.479721.091259.71376.02800
ZINC000000020220331.3468.67578.412299.833178.53968.48731.5531017.371168.925248.3301
ZINC000000020220331.3468.111575.511298.04176.66769.24631.5581012.813168.79248.64801
ZINC000000121541295.2976.562576.16198.468169.387308.3060957.18158.911383.64100
ZINC000000121541295.2972.873577.03396.773172.83307.430959.022038.668388.18700
ZINC000000121541295.29710.919575.19998.469170.072306.6580956.419158.861383.46100
ZINC000028973446314.7279.396534.8491.861174.43287.10671.453912.79503.59.55378.06300
ZINC000000006427284.7444.728520.923120.03161.526267.93971.426890.968049.194310000
ZINC000000896731236.2883.773444.59884.301131.134195.10534.058746.48133.78.644378.1800
ZINC000000896731236.2885.297450.81685.528135.414201.88127.993746.81233.78.57376.55600
ZINC000019632917299.7594.645553.04137.02264.707279.78871.524941.819138.565310000
ZINC000019632917299.7595.502549.003118.96574.766283.8271.453935.577138.408310000
ZINC000001482184194.1523.411379.12887.887235.05156.190597.216279.649251.42500
ZINC000000001899253.2610.065488.204144.44279.88563.8780807.08858.98.591242.53601
ZINC000084441937444.447.923627.272219.71287.581119.98101207.68538.259.493121.61712
ZINC000084441937444.444.721623.745218.485285.56119.69901199.7538.259.391121.78812
ZINC000084441937444.448.559624.636216.229288.829119.57701207.75538.259.339121.38112
ZINC000084441937444.447.965648.626222.257306.467119.90201232.21238.259.32118.38912
ZINC000001999441405.4414.722712.226273.48884.211260.77493.7531256.14736.49.229395.14300
ZINC000001999441405.4410.513723.645269.65591.189269.03293.7681265.84436.49.27394.03900
ZINC000008035395807.11612.861789.663274.386383.30110.854121.1231453.819818.29.4271031


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity
ZINC000000057255NS(=O)(=O)c1cc([C@@]2(O)NC(=O)c3ccccc32)ccc1Cl0.1281419780.345401829
ZINC000000020253NS(=O)(=O)c1cc([C@]2(O)NC(=O)c3ccccc32)ccc1Cl0.1281419780.345401829
ZINC000000509440O=C1Nc2ccc(Cl)cc2C(c2ccccc2)=N[C@@H]1O0.1835012410.419564566
ZINC000000006157NC1=NC[C@@H]2c3ccccc3Cc3ccccc3N120.1494885010.300300567
ZINC000001547851CC[C@@H](C(N)=O)N1CCCC1=O0.1573358610.410047131
ZINC000008143864O=C(NC[C@H](O)CO)c1c(I)c(C(=O)NC[C@H](O)CO)c(I)c(N(CCO)C(=O)CO)c1I0.0517806690.23149478
ZINC000000896634CN1C(=O)[C@@H](O)N=C(c2ccccc2)c2cc(Cl)ccc210.1813563480.322163665
ZINC000000085733NC[C@@H](CC(=O)O)c1ccc(Cl)cc10.2512033360.372196692
ZINC000000007782NC(=O)c1cn(Cc2c(F)cccc2F)nn10.2771451560.235759804
ZINC000000020220O=C(O)c1cn(C2CC2)c2cc(N3CCNCC3)c(F)cc2c1=O0.2310316290.323908212
ZINC000000121541COC(=O)/N=c1[nH]c2ccc(C(=O)c3ccccc3)cc2[nH]10.2096963420.592445172
ZINC000028973446O=C(O)[C@H]1N=C(c2ccccc2)c2cc(Cl)ccc2NC1=O0.1681911380.395189961
ZINC000000006427CN1C(=O)CN=C(c2ccccc2)c2cc(Cl)ccc210.3260706180.290159579
ZINC000000896731C[C@H](c1cc2ccccc2s1)N(O)C(N)=O0.1363358820.223511692
ZINC000019632917CNC1=Nc2ccc(Cl)cc2C(c2ccccc2)=[N+]([O-])C10.1473206730.447326601
ZINC000001482184Cn1nnc2c(C(N)=O)ncn2c1=O0.1608864090.261932701
ZINC000000001899Nc1nc2c(ncn2CCC(CO)CO)c(=O)[nH]10.149437740.469025203
ZINC000084441937CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C(=O)c4c(O)cccc4[C@@](C)(O)[C@H]3C[C@@H]120.0311261360.341399693
ZINC000001999441O[C@@H](CNC[C@@H](O)[C@@H]1CCc2cc(F)ccc2O1)[C@H]1CCc2cc(F)ccc2O10.0555500820.198725964
ZINC000008035395O=C(NC[C@@H](O)CO)c1c(I)c(C(=O)NC[C@@H](O)CO)c(I)c(N(CCO)C(=O)CO)c1I0.0517806690.23149478


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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
SS18SMARCA2, SMARCB1, EP300, MLLT10, GRB2, Bcl7b, SMARCD1, RBM14, YWHAG, ELAVL1, CUL3, CST11, ATF2, TLE1, SMARCA5, HDAC1, HDAC2, EED, SUZ12, EZH2, SS18, NFKBID, DPF3, DPF2, SMARCE1, ARID1B, ARID1A, PHF10, SMARCC2, SMARCC1, GLTSCR1, SMARCD3, SMARCD2, SMARCA4, ARID2, DPF1, ACTL6A, ACTL6B, BCL7A, BCL7C, BCL7B, BRD9, CDKN1A, NEFM, RAB5C, SYNCRIP, Wash, FUS, DDIT3, FLI1, nsp13ab, BRD3, NR3C1, SS18L1, BRD7, PBRM1, ACTC1, STK11IP, DDX58, UBQLN2, PTPRR, T, ELF5, ERG, ETV4, FOS, GATA2, GCM1, HNF4A, IRF1, IRF4, KLF3, KLF5, LHX2, MYOD1, PAX7, SOX17, SOX2, SP7,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SS18all structure
SSX4all 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


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Related Drugs to SS18-SSX4


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 SS18-SSX4


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID
SS18SSX4Pancreatic AdenocarcinomaMyCancerGenome
SS18SSX4Breast Invasive Ductal CarcinomaMyCancerGenome
SS18SSX4Esophagogastric CarcinomaMyCancerGenome
SS18SSX4Invasive Breast CarcinomaMyCancerGenome
SS18SSX4Papillary Renal Cell CarcinomaMyCancerGenome

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSS18C0039101synovial sarcoma2CTD_human;ORPHANET