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level2

	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:RARA-SLC9A3R1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RARA-SLC9A3R1
	FusionPDB ID: 72316
	FusionGDB2.0 ID: 72316
		Hgene	Tgene
	Gene symbol	RARA	SLC9A3R1
	Gene ID	5914	9368
	Gene name	retinoic acid receptor alpha	SLC9A3 regulator 1
	Synonyms	NR1B1\|RAR	EBP50\|NHERF\|NHERF-1\|NHERF1\|NPHLOP2
	Cytomap	17q21.2	17q25.1
	Type of gene	protein-coding	protein-coding
	Description	retinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2	Na(+)/H(+) exchange regulatory cofactor NHE-RF1Na+/H+ exchange regulatory co-factorezrin-radixin-moesin binding phosphoprotein-50regulatory cofactor of Na(+)/H(+) exchangersolute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory facto
	Modification date	20200327	20200313
	UniProtAcc	P10276	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000420042, ENST00000254066, ENST00000394081, ENST00000394086, ENST00000394089, ENST00000425707,	ENST00000262613, ENST00000413388,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	47 X 22 X 8=8272	9 X 12 X 6=648
	# samples	74	13
	** MAII score	log2(74/8272*10)=-3.48263900979862 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/648*10)=-2.31748218985617 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: RARA [Title/Abstract] AND SLC9A3R1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RARA(38508759)-SLC9A3R1(72758151), # samples:3
Anticipated loss of major functional domain due to fusion event.	RARA-SLC9A3R1 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. RARA-SLC9A3R1 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. RARA-SLC9A3R1 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. RARA-SLC9A3R1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RARA	GO:0007165	signal transduction	2825025
Hgene	RARA	GO:0030853	negative regulation of granulocyte differentiation	19917671
Hgene	RARA	GO:0032689	negative regulation of interferon-gamma production	18416830
Hgene	RARA	GO:0032720	negative regulation of tumor necrosis factor production	18416830
Hgene	RARA	GO:0032736	positive regulation of interleukin-13 production	18416830
Hgene	RARA	GO:0032753	positive regulation of interleukin-4 production	18416830
Hgene	RARA	GO:0032754	positive regulation of interleukin-5 production	18416830
Hgene	RARA	GO:0045630	positive regulation of T-helper 2 cell differentiation	18416830
Hgene	RARA	GO:0045892	negative regulation of transcription, DNA-templated	20080953
Hgene	RARA	GO:0045893	positive regulation of transcription, DNA-templated	18845237\|19850744\|20080953
Hgene	RARA	GO:0045944	positive regulation of transcription by RNA polymerase II	19850744\|21131358
Hgene	RARA	GO:0071300	cellular response to retinoic acid	19917671
Hgene	RARA	GO:0071391	cellular response to estrogen stimulus	20080953
Tgene	SLC9A3R1	GO:0008285	negative regulation of cell proliferation	20012548
Tgene	SLC9A3R1	GO:0070373	negative regulation of ERK1 and ERK2 cascade	20012548
Tgene	SLC9A3R1	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	20012548

Fusion gene breakpoints across RARA (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across SLC9A3R1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	UCS	TCGA-N8-A4PQ-01A	RARA	chr17	38508759	-	SLC9A3R1	chr17	72758151	+
ChimerDB4	UCS	TCGA-N8-A4PQ-01A	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+
ChimerDB4	UCS	TCGA-N8-A4PQ	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000254066

RARA

chr17

38508759

ENST00000262613

SLC9A3R1

chr17

72758151

2595

1262

440

1897

485

ENST00000394089

RARA

chr17

38508759

ENST00000262613

SLC9A3R1

chr17

72758151

2670

1337

515

1972

485

ENST00000425707

RARA

chr17

38508759

ENST00000262613

SLC9A3R1

chr17

72758151

2375

1042

511

1677

388

ENST00000394086

RARA

chr17

38508759

ENST00000262613

SLC9A3R1

chr17

72758151

2190

857

1492

496

ENST00000394081

RARA

chr17

38508759

ENST00000262613

SLC9A3R1

chr17

72758151

2467

1134

324

1769

481

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000254066	ENST00000262613	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+	0.019698305	0.9803017
ENST00000394089	ENST00000262613	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+	0.019228928	0.9807711
ENST00000425707	ENST00000262613	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+	0.019822814	0.98017716
ENST00000394086	ENST00000262613	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+	0.027318118	0.9726819
ENST00000394081	ENST00000262613	RARA	chr17	38508759	+	SLC9A3R1	chr17	72758151	+	0.021722449	0.97827756

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>72316_72316_1_RARA-SLC9A3R1_RARA_chr17_38508759_ENST00000254066_SLC9A3R1_chr17_72758151_ENST00000262613_length(amino acids)=485AA_BP=274
MWPLGMASNSSSCPTPGGGHLNGYPVPPYAFFFPPMLGGLSPPGALTTLQHQLPVSGYSTPSPATIETQSSSSEEIVPSPPSPPPLPRIY
KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKKEVPKPECS
ESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAAC
LDILRELRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDR
ETDEFFKKCRVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPSSTSSSDPILDF

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

>72316_72316_2_RARA-SLC9A3R1_RARA_chr17_38508759_ENST00000394081_SLC9A3R1_chr17_72758151_ENST00000262613_length(amino acids)=481AA_BP=270
MPSRGKMYESVEVGGPTPNPFLVVDFYNQNRACLLPEKGLPAPGPYSTPLRTPLWNGSNHSIETQSSSSEEIVPSPPSPPPLPRIYKPCF
VCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKKEVPKPECSESYT
LTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDIL
RELRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDE
FFKKCRVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPSSTSSSDPILDFNISL

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

>72316_72316_3_RARA-SLC9A3R1_RARA_chr17_38508759_ENST00000394086_SLC9A3R1_chr17_72758151_ENST00000262613_length(amino acids)=496AA_BP=285
MMSQTMTQAGVSFRHSVRAAQCHTRVPNTWPRATRPYASCRRSPRLRGRWPGSAGQGAGGRAPRAGWRAGDVTGSAIETQSSSSEEIVPS
PPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK
KKKEVPKPECSESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTI
ADQITLLKAACLDILRELRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAG
GDETKLLVVDRETDEFFKKCRVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPS

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

>72316_72316_4_RARA-SLC9A3R1_RARA_chr17_38508759_ENST00000394089_SLC9A3R1_chr17_72758151_ENST00000262613_length(amino acids)=485AA_BP=274
MWPLGMASNSSSCPTPGGGHLNGYPVPPYAFFFPPMLGGLSPPGALTTLQHQLPVSGYSTPSPATIETQSSSSEEIVPSPPSPPPLPRIY
KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKKEVPKPECS
ESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAAC
LDILRELRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDR
ETDEFFKKCRVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPSSTSSSDPILDF

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

>72316_72316_5_RARA-SLC9A3R1_RARA_chr17_38508759_ENST00000425707_SLC9A3R1_chr17_72758151_ENST00000262613_length(amino acids)=388AA_BP=177
MWPLGMASNSSSCPTPGGGHLNGYPVPPYAFFFPPMLGGLSPPGALTTLQHQLPVSGYSTPSPATVRNDRNKKKKEVPKPECSESYTLTP
EVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILREL
RPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFK
KCRVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPSSTSSSDPILDFNISLAMA

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:38508759/chr17:72758151)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
RARA P10276	.
FUNCTION: Receptor for retinoic acid (PubMed:19850744, PubMed:16417524, PubMed:20215566). Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes (PubMed:28167758). The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 (PubMed:28167758, PubMed:19398580). In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone deacetylation, chromatin condensation and transcriptional suppression (PubMed:16417524). On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation (PubMed:9267036, PubMed:19850744, PubMed:20215566). Formation of a complex with histone deacetylases might lead to inhibition of RARE DNA element binding and to transcriptional repression (PubMed:28167758). Transcriptional activation and RARE DNA element binding might be supported by the transcription factor KLF2 (PubMed:28167758). RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis (By similarity). Has a role in the survival of early spermatocytes at the beginning prophase of meiosis (By similarity). In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes (By similarity). In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Together with RXRA, positively regulates microRNA-10a expression, thereby inhibiting the GATA6/VCAM1 signaling response to pulsatile shear stress in vascular endothelial cells (PubMed:28167758). In association with HDAC3, HDAC5 and HDAC7 corepressors, plays a role in the repression of microRNA-10a and thereby promotes the inflammatory response (PubMed:28167758). {ECO:0000250\|UniProtKB:P11416, ECO:0000269\|PubMed:16417524, ECO:0000269\|PubMed:19398580, ECO:0000269\|PubMed:19850744, ECO:0000269\|PubMed:20215566, ECO:0000269\|PubMed:28167758, ECO:0000269\|PubMed:9267036}.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

88_153

269.0

463.0

DNA binding

Nuclear receptor

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

88_153

264.0

458.0

DNA binding

Nuclear receptor

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

88_153

269.0

463.0

DNA binding

Nuclear receptor

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

88_153

172.0

366.0

DNA binding

Nuclear receptor

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

154_182

269.0

463.0

Region

Note=Hinge

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

1_87

269.0

463.0

Region

Note=Modulating

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

154_182

264.0

458.0

Region

Note=Hinge

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

1_87

264.0

458.0

Region

Note=Modulating

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

154_182

269.0

463.0

Region

Note=Hinge

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

1_87

269.0

463.0

Region

Note=Modulating

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

1_87

172.0

366.0

Region

Note=Modulating

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

124_148

269.0

463.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

88_108

269.0

463.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

124_148

264.0

458.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

88_108

264.0

458.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

124_148

269.0

463.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

88_108

269.0

463.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

124_148

172.0

366.0

Zinc finger

NR C4-type

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

88_108

172.0

366.0

Zinc finger

NR C4-type

Tgene

SLC9A3R1

chr17:38508759

chr17:72758151

ENST00000262613

154_234

147.0

359.0

Domain

PDZ 2

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

183_417

269.0

463.0

Domain

NR LBD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

183_417

264.0

458.0

Domain

NR LBD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

183_417

269.0

463.0

Domain

NR LBD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

183_417

172.0

366.0

Domain

NR LBD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

408_416

269.0

463.0

Motif

9aaTAD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

408_416

264.0

458.0

Motif

9aaTAD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

408_416

269.0

463.0

Motif

9aaTAD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

408_416

172.0

366.0

Motif

9aaTAD

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000254066

404_419

269.0

463.0

Region

Note=Required for binding corepressor NCOR1

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394081

404_419

264.0

458.0

Region

Note=Required for binding corepressor NCOR1

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000394089

404_419

269.0

463.0

Region

Note=Required for binding corepressor NCOR1

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

154_182

172.0

366.0

Region

Note=Hinge

Hgene

RARA

chr17:38508759

chr17:72758151

ENST00000425707

404_419

172.0

366.0

Region

Note=Required for binding corepressor NCOR1

Tgene

SLC9A3R1

chr17:38508759

chr17:72758151

ENST00000262613

14_94

147.0

359.0

Domain

PDZ 1

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>1052_RARA_38508759_SLC9A3R1_72758151_1052_RARA_38508759_SLC9A3R1_72758151_ranked_0.pdb	RARA	38508759	38508759	ENST00000262613	SLC9A3R1	chr17	72758151	+	MMSQTMTQAGVSFRHSVRAAQCHTRVPNTWPRATRPYASCRRSPRLRGRWPGSAGQGAGGRAPRAGWRAGDVTGSAIETQSSSSEEIVPS PPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNK KKKEVPKPECSESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTI ADQITLLKAACLDILRELRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAG GDETKLLVVDRETDEFFKKCRVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPS	496

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

RARA_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
RARA
SLC9A3R1

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to RARA-SLC9A3R1

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to RARA-SLC9A3R1

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	RARA	C0023487	Acute Promyelocytic Leukemia	24	CTD_human;ORPHANET
Hgene	RARA	C0036341	Schizophrenia	3	PSYGENET
Hgene	RARA	C0006142	Malignant neoplasm of breast	1	CTD_human
Hgene	RARA	C0009363	Congenital ocular coloboma (disorder)	1	GENOMICS_ENGLAND
Hgene	RARA	C0010701	Phyllodes Tumor	1	CTD_human
Hgene	RARA	C0085183	Neoplasms, Second Primary	1	CTD_human
Hgene	RARA	C0086696	Neoplasms, Therapy-Associated	1	CTD_human
Hgene	RARA	C0149940	Sciatic Neuropathy	1	CTD_human
Hgene	RARA	C0154748	Lesion of Sciatic Nerve	1	CTD_human
Hgene	RARA	C0206650	Fibroadenoma	1	CTD_human
Hgene	RARA	C0242013	Sciatic Neuritis	1	CTD_human
Hgene	RARA	C0525045	Mood Disorders	1	PSYGENET
Hgene	RARA	C0600066	Malignant Cystosarcoma Phyllodes	1	CTD_human
Hgene	RARA	C0678222	Breast Carcinoma	1	CTD_human
Hgene	RARA	C0751924	Neuralgia-Neuritis, Sciatic Nerve	1	CTD_human
Hgene	RARA	C0751925	Sciatic Nerve Palsy	1	CTD_human
Hgene	RARA	C0877578	Treatment related secondary malignancy	1	CTD_human
Hgene	RARA	C1257931	Mammary Neoplasms, Human	1	CTD_human
Hgene	RARA	C1458155	Mammary Neoplasms	1	CTD_human
Hgene	RARA	C2239176	Liver carcinoma	1	CTD_human
Hgene	RARA	C4704874	Mammary Carcinoma, Human	1	CTD_human