UTHEALTH HOME ABOUT SBMI A-Z WEBMAIL INSIDE THE UNIVERSITY

Home

Download

Statistics

Examples

Help

Contact

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:RANBP9-TXNDC5

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RANBP9-TXNDC5
	FusionPDB ID: 72099
	FusionGDB2.0 ID: 72099
		Hgene	Tgene
	Gene symbol	RANBP9	TXNDC5
	Gene ID	10048	81567
	Gene name	RAN binding protein 9	thioredoxin domain containing 5
	Synonyms	BPM-L\|BPM90\|RANBPM\|RanBP7	ENDOPDI\|ERP46\|HCC-2\|HCC2\|PDIA15\|STRF8\|UNQ364
	Cytomap	6p23	6p24.3
	Type of gene	protein-coding	protein-coding
	Description	ran-binding protein 9Ran Binding Protein in the Microtubule organizing centernovel centrosomal protein RanBPMran binding protein, centrosomalran-binding protein M	thioredoxin domain-containing protein 5ER protein 46endoplasmic reticulum protein ERp46endoplasmic reticulum resident protein 46endothelial protein disulphide isomeraseepididymis secretory sperm binding proteinprotein disulfide isomerase family A, m
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000011619, ENST00000469916, ENST00000539980,	ENST00000473453, ENST00000379757, ENST00000539054,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 8 X 6=672	3 X 1 X 3=9
	# samples	10	3
	** MAII score	log2(10/672*10)=-2.74846123300404 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/9*10)=1.73696559416621 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: RANBP9 [Title/Abstract] AND TXNDC5 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RANBP9(13697017)-TXNDC5(7904956), # samples:3
Anticipated loss of major functional domain due to fusion event.	RANBP9-TXNDC5 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. RANBP9-TXNDC5 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. RANBP9-TXNDC5 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. RANBP9-TXNDC5 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

Fusion gene breakpoints across RANBP9 (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 TXNDC5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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	LGG	TCGA-HT-7604-01A	RANBP9	chr6	13697017	-	TXNDC5	chr6	7904956	-
ChimerDB4	LGG	TCGA-HT-7604	RANBP9	chr6	13697017	-	TXNDC5	chr6	7904956	-

Top

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)
ENST00000011619	RANBP9	chr6	13697017	-	ENST00000539054	TXNDC5	chr6	7904956	-	3672	742	59	1777	572
ENST00000011619	RANBP9	chr6	13697017	-	ENST00000379757	TXNDC5	chr6	7904956	-	3405	742	59	1777	572

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
ENST00000011619	ENST00000539054	RANBP9	chr6	13697017	-	TXNDC5	chr6	7904956	-	0.002515447	0.99748456
ENST00000011619	ENST00000379757	RANBP9	chr6	13697017	-	TXNDC5	chr6	7904956	-	0.00444561	0.9955544

Top

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

>72099_72099_1_RANBP9-TXNDC5_RANBP9_chr6_13697017_ENST00000011619_TXNDC5_chr6_7904956_ENST00000379757_length(amino acids)=572AA_BP=347
MSGQPPPPPPQQQQQQQQLSPPPPAALAPVSGVVLPAPPAVSAGSSPAGSPGGGAGGEGLGAAAAALLLHPPPPPPPATAAPPPPPPPPP
PPASAAAPASGPPAPPGLAAGPGPAGGAPTPALVAGSSAAAPFPHGDSALNEQEKELQRRLKRLYPAVDEQETPLPRSWSPKDKFSYIGL
SQNNLRVHYKGHGKTPKDAASVRATHPIPAACGIYYFEVKIVSKGRDGCGHCQRLQPTWNDLGDKYNSMEDAKVYVAKVDCTAHSDVCSA
QGVRGYPTLKLFKPGQEAVKYQGPRDFQTLENWMLQTLNEEPVTPEPEVEPPSAPELKQGLYELSASNFELHVAQGDHFIKFFAPWCGHC
KALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQRTETGATETVTPSEA
PVLAAEPEADKGTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLL

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

>72099_72099_2_RANBP9-TXNDC5_RANBP9_chr6_13697017_ENST00000011619_TXNDC5_chr6_7904956_ENST00000539054_length(amino acids)=572AA_BP=347
MSGQPPPPPPQQQQQQQQLSPPPPAALAPVSGVVLPAPPAVSAGSSPAGSPGGGAGGEGLGAAAAALLLHPPPPPPPATAAPPPPPPPPP
PPASAAAPASGPPAPPGLAAGPGPAGGAPTPALVAGSSAAAPFPHGDSALNEQEKELQRRLKRLYPAVDEQETPLPRSWSPKDKFSYIGL
SQNNLRVHYKGHGKTPKDAASVRATHPIPAACGIYYFEVKIVSKGRDGCGHCQRLQPTWNDLGDKYNSMEDAKVYVAKVDCTAHSDVCSA
QGVRGYPTLKLFKPGQEAVKYQGPRDFQTLENWMLQTLNEEPVTPEPEVEPPSAPELKQGLYELSASNFELHVAQGDHFIKFFAPWCGHC
KALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQRTETGATETVTPSEA
PVLAAEPEADKGTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLL

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

Top

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/chr6:13697017/chr6:7904956)
- 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
.	.
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.	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

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

11_18

227.66666666666666

730.0

Compositional bias

Note=Poly-Gln

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

21_24

227.66666666666666

730.0

Compositional bias

Note=Poly-Pro

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

25_131

227.66666666666666

730.0

Compositional bias

Note=Ala-rich

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

5_10

227.66666666666666

730.0

Compositional bias

Note=Poly-Pro

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

62_66

227.66666666666666

730.0

Compositional bias

Note=Poly-Ala

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

71_77

227.66666666666666

730.0

Compositional bias

Note=Poly-Pro

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

82_92

227.66666666666666

730.0

Compositional bias

Note=Poly-Pro

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000379757

170_295

87.66666666666667

433.0

Domain

Thioredoxin 2

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000379757

304_429

87.66666666666667

433.0

Domain

Thioredoxin 3

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000473453

170_295

325.0

Domain

Thioredoxin 2

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000473453

304_429

325.0

Domain

Thioredoxin 3

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000473453

36_169

325.0

Domain

Thioredoxin 1

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000379757

429_432

87.66666666666667

433.0

Motif

Prevents secretion from ER

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000473453

429_432

325.0

Motif

Prevents secretion from ER

- 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

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

147_334

227.66666666666666

730.0

Domain

B30.2/SPRY

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

365_397

227.66666666666666

730.0

Domain

LisH

Hgene

RANBP9

chr6:13697017

chr6:7904956

ENST00000011619

403_460

227.66666666666666

730.0

Domain

CTLH

Tgene

TXNDC5

chr6:13697017

chr6:7904956

ENST00000379757

36_169

87.66666666666667

433.0

Domain

Thioredoxin 1

Top

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 >>>1228_RANBP9_13697017_TXNDC5_7904956_1228_RANBP9_13697017_TXNDC5_7904956_ranked_0.pdb	RANBP9	13697017	13697017	ENST00000379757	TXNDC5	chr6	7904956	-	MSGQPPPPPPQQQQQQQQLSPPPPAALAPVSGVVLPAPPAVSAGSSPAGSPGGGAGGEGLGAAAAALLLHPPPPPPPATAAPPPPPPPPP PPASAAAPASGPPAPPGLAAGPGPAGGAPTPALVAGSSAAAPFPHGDSALNEQEKELQRRLKRLYPAVDEQETPLPRSWSPKDKFSYIGL SQNNLRVHYKGHGKTPKDAASVRATHPIPAACGIYYFEVKIVSKGRDGCGHCQRLQPTWNDLGDKYNSMEDAKVYVAKVDCTAHSDVCSA QGVRGYPTLKLFKPGQEAVKYQGPRDFQTLENWMLQTLNEEPVTPEPEVEPPSAPELKQGLYELSASNFELHVAQGDHFIKFFAPWCGHC KALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQRTETGATETVTPSEA PVLAAEPEADKGTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLL	572

Top

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.

RANBP9_pLDDT.png

TXNDC5_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.

Top

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

Top

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
RANBP9
TXNDC5

- 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
Hgene	RANBP9	chr6:13697017	chr6:7904956	ENST00000011619	-	2	14	401_407	227.66666666666666	730.0	CALB1
Hgene	RANBP9	chr6:13697017	chr6:7904956	ENST00000011619	-	2	14	615_729	227.66666666666666	730.0	FMR1

Top

Related Drugs to RANBP9-TXNDC5

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to RANBP9-TXNDC5

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