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:NUP160-RBM6

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NUP160-RBM6
	FusionPDB ID: 60997
	FusionGDB2.0 ID: 60997
		Hgene	Tgene
	Gene symbol	NUP160	RBM6
	Gene ID	23279	10180
	Gene name	nucleoporin 160	RNA binding motif protein 6
	Synonyms	NPHS19	3G2\|DEF-3\|DEF3\|HLC-11\|NY-LU-12\|g16
	Cytomap	11p11.2	3p21.31
	Type of gene	protein-coding	protein-coding
	Description	nuclear pore complex protein Nup160160 kDa nucleoporinnucleoporin 160kDnucleoporin 160kDanucleoporin Nup160	RNA-binding protein 6RNA-binding protein DEF-3lung cancer antigen NY-LU-12lung cancer protooncogene 11
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000378460, ENST00000526870, ENST00000532747, ENST00000530326, ENST00000528071, ENST00000528501, ENST00000531016,	ENST00000421682, ENST00000422955, ENST00000441115, ENST00000266022, ENST00000442092, ENST00000443081, ENST00000539992,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 8 X 6=432	22 X 21 X 10=4620
	# samples	11	30
	** MAII score	log2(11/432*10)=-1.97352778863881 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(30/4620*10)=-3.94485844580754 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: NUP160 [Title/Abstract] AND RBM6 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NUP160(47869400)-RBM6(50114441), # samples:3
Anticipated loss of major functional domain due to fusion event.	NUP160-RBM6 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. NUP160-RBM6 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. NUP160-RBM6 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. NUP160-RBM6 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. NUP160-RBM6 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. NUP160-RBM6 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. NUP160-RBM6 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

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	NUP160	GO:0006406	mRNA export from nucleus	11684705

Fusion gene breakpoints across NUP160 (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 RBM6 (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	UCS	TCGA-N5-A4RA-01A	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+
ChimerDB4	UCS	TCGA-N5-A4RA	NUP160	chr11	47869399	-	RBM6	chr3	50114440	+
ChimerDB4	UCS	TCGA-N5-A4RA	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+

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)
ENST00000378460	NUP160	chr11	47869400	-	ENST00000443081	RBM6	chr3	50114441	+	602	361	47	376	109
ENST00000378460	NUP160	chr11	47869400	-	ENST00000539992	RBM6	chr3	50114441	+	602	361	47	376	109
ENST00000532747	NUP160	chr11	47869400	-	ENST00000266022	RBM6	chr3	50114441	+	467	224	12	239	75
ENST00000526870	NUP160	chr11	47869400	-	ENST00000443081	RBM6	chr3	50114441	+	690	449	135	464	109
ENST00000526870	NUP160	chr11	47869400	-	ENST00000539992	RBM6	chr3	50114441	+	690	449	135	464	109
ENST00000378460	NUP160	chr11	47869399	-	ENST00000443081	RBM6	chr3	50114440	+	602	361	47	376	109
ENST00000378460	NUP160	chr11	47869399	-	ENST00000539992	RBM6	chr3	50114440	+	602	361	47	376	109
ENST00000532747	NUP160	chr11	47869399	-	ENST00000266022	RBM6	chr3	50114440	+	467	224	12	239	75
ENST00000526870	NUP160	chr11	47869399	-	ENST00000443081	RBM6	chr3	50114440	+	690	449	135	464	109
ENST00000526870	NUP160	chr11	47869399	-	ENST00000539992	RBM6	chr3	50114440	+	690	449	135	464	109

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
ENST00000378460	ENST00000443081	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+	0.4950163	0.5049837
ENST00000378460	ENST00000539992	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+	0.4950163	0.5049837
ENST00000532747	ENST00000266022	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+	0.3077205	0.69227946
ENST00000526870	ENST00000443081	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+	0.5672988	0.43270117
ENST00000526870	ENST00000539992	NUP160	chr11	47869400	-	RBM6	chr3	50114441	+	0.5672988	0.43270117
ENST00000378460	ENST00000443081	NUP160	chr11	47869399	-	RBM6	chr3	50114440	+	0.4950163	0.5049837
ENST00000378460	ENST00000539992	NUP160	chr11	47869399	-	RBM6	chr3	50114440	+	0.4950163	0.5049837
ENST00000532747	ENST00000266022	NUP160	chr11	47869399	-	RBM6	chr3	50114440	+	0.3077205	0.69227946
ENST00000526870	ENST00000443081	NUP160	chr11	47869399	-	RBM6	chr3	50114440	+	0.5672988	0.43270117
ENST00000526870	ENST00000539992	NUP160	chr11	47869399	-	RBM6	chr3	50114440	+	0.5672988	0.43270117

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

>60997_60997_1_NUP160-RBM6_NUP160_chr11_47869399_ENST00000378460_RBM6_chr3_50114440_ENST00000443081_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_2_NUP160-RBM6_NUP160_chr11_47869399_ENST00000378460_RBM6_chr3_50114440_ENST00000539992_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_3_NUP160-RBM6_NUP160_chr11_47869399_ENST00000526870_RBM6_chr3_50114440_ENST00000443081_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_4_NUP160-RBM6_NUP160_chr11_47869399_ENST00000526870_RBM6_chr3_50114440_ENST00000539992_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_5_NUP160-RBM6_NUP160_chr11_47869399_ENST00000532747_RBM6_chr3_50114440_ENST00000266022_length(amino acids)=75AA_BP=

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

>60997_60997_6_NUP160-RBM6_NUP160_chr11_47869400_ENST00000378460_RBM6_chr3_50114441_ENST00000443081_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_7_NUP160-RBM6_NUP160_chr11_47869400_ENST00000378460_RBM6_chr3_50114441_ENST00000539992_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_8_NUP160-RBM6_NUP160_chr11_47869400_ENST00000526870_RBM6_chr3_50114441_ENST00000443081_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_9_NUP160-RBM6_NUP160_chr11_47869400_ENST00000526870_RBM6_chr3_50114441_ENST00000539992_length(amino acids)=109AA_BP=
MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE

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

>60997_60997_10_NUP160-RBM6_NUP160_chr11_47869400_ENST00000532747_RBM6_chr3_50114441_ENST00000266022_length(amino acids)=75AA_BP=

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

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/chr11:47869400/chr3:50114441)
- 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

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000422955

826_829

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000422955

892_895

560.0

602.0

Compositional bias

Note=Poly-Pro

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000422955

915_921

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000442092

826_829

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000442092

892_895

560.0

602.0

Compositional bias

Note=Poly-Pro

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000442092

915_921

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000422955

826_829

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000422955

892_895

560.0

602.0

Compositional bias

Note=Poly-Pro

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000422955

915_921

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000442092

826_829

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000442092

892_895

560.0

602.0

Compositional bias

Note=Poly-Pro

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000442092

915_921

560.0

602.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000422955

1051_1097

560.0

602.0

Domain

G-patch

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000442092

1051_1097

560.0

602.0

Domain

G-patch

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000422955

1051_1097

560.0

602.0

Domain

G-patch

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000442092

1051_1097

560.0

602.0

Domain

G-patch

- 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

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000266022

826_829

1082.0

1124.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000266022

892_895

1082.0

1124.0

Compositional bias

Note=Poly-Pro

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000266022

915_921

1082.0

1124.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000266022

826_829

1082.0

1124.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000266022

892_895

1082.0

1124.0

Compositional bias

Note=Poly-Pro

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000266022

915_921

1082.0

1124.0

Compositional bias

Note=Poly-Glu

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000266022

1051_1097

1082.0

1124.0

Domain

G-patch

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000266022

456_536

1082.0

1124.0

Domain

RRM

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000422955

456_536

560.0

602.0

Domain

RRM

Tgene

RBM6

chr11:47869399

chr3:50114440

ENST00000442092

456_536

560.0

602.0

Domain

RRM

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000266022

1051_1097

1082.0

1124.0

Domain

G-patch

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000266022

456_536

1082.0

1124.0

Domain

RRM

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000422955

456_536

560.0

602.0

Domain

RRM

Tgene

RBM6

chr11:47869400

chr3:50114441

ENST00000442092

456_536

560.0

602.0

Domain

RRM

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 >>>34_NUP160_47869400_RBM6_50114441_ranked_0.pdb	NUP160	47869399	47869400	ENST00000539992	RBM6	chr3	50114441	+	MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSGAERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVE	109

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.

NUP160_pLDDT.png

RBM6_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
NUP160
RBM6

- 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

Top

Related Drugs to NUP160-RBM6

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to NUP160-RBM6

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