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	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:MSI2-SLC39A11

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MSI2-SLC39A11
	FusionPDB ID: 55331
	FusionGDB2.0 ID: 55331
		Hgene	Tgene
	Gene symbol	MSI2	SLC39A11
	Gene ID	124540	201266
	Gene name	musashi RNA binding protein 2	solute carrier family 39 member 11
	Synonyms	MSI2H	C17orf26\|ZIP-11\|ZIP11
	Cytomap	17q22	17q24.3-q25.1
	Type of gene	protein-coding	protein-coding
	Description	RNA-binding protein Musashi homolog 2musashi homolog 2musashi-2	zinc transporter ZIP11Zrt- and Irt-like protein 11solute carrier family 39 (metal ion transporter), member 11
	Modification date	20200313	20200313
	UniProtAcc	Q96DH6	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000284073, ENST00000322684, ENST00000416426, ENST00000442934, ENST00000579180, ENST00000579505,	ENST00000579732, ENST00000579988, ENST00000255559, ENST00000542342,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	40 X 16 X 16=10240	24 X 14 X 9=3024
	# samples	45	29
	** MAII score	log2(45/10240*10)=-4.50814690367033 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(29/3024*10)=-3.38233333420614 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: MSI2 [Title/Abstract] AND SLC39A11 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MSI2(55339553)-SLC39A11(71027853), # samples:3
Anticipated loss of major functional domain due to fusion event.	MSI2-SLC39A11 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. MSI2-SLC39A11 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 MSI2 (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 SLC39A11 (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	BRCA	TCGA-AN-A0FW-01A	MSI2	chr17	55339553	-	SLC39A11	chr17	71027853	-
ChimerDB4	BRCA	TCGA-AN-A0FW-01A	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-
ChimerDB4	BRCA	TCGA-AN-A0FW	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-

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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)
ENST00000416426	MSI2	chr17	55339553	+	ENST00000255559	SLC39A11	chr17	71027853	-	2877	381	93	1241	382
ENST00000416426	MSI2	chr17	55339553	+	ENST00000542342	SLC39A11	chr17	71027853	-	2897	381	93	1262	389
ENST00000284073	MSI2	chr17	55339553	+	ENST00000255559	SLC39A11	chr17	71027853	-	3017	521	179	1381	400
ENST00000284073	MSI2	chr17	55339553	+	ENST00000542342	SLC39A11	chr17	71027853	-	3037	521	179	1402	407
ENST00000322684	MSI2	chr17	55339553	+	ENST00000255559	SLC39A11	chr17	71027853	-	2831	335	35	1195	386
ENST00000322684	MSI2	chr17	55339553	+	ENST00000542342	SLC39A11	chr17	71027853	-	2851	335	35	1216	393

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
ENST00000416426	ENST00000255559	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-	0.003694717	0.99630535
ENST00000416426	ENST00000542342	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-	0.005200877	0.99479914
ENST00000284073	ENST00000255559	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-	0.003417048	0.9965829
ENST00000284073	ENST00000542342	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-	0.00418955	0.9958105
ENST00000322684	ENST00000255559	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-	0.001956762	0.9980432
ENST00000322684	ENST00000542342	MSI2	chr17	55339553	+	SLC39A11	chr17	71027853	-	0.002002292	0.9979977

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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

>55331_55331_1_MSI2-SLC39A11_MSI2_chr17_55339553_ENST00000284073_SLC39A11_chr17_71027853_ENST00000255559_length(amino acids)=400AA_BP=114
MGVGGRGGSDMEANGSQGTSGSANDSQHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLG
QPHHELDSKTIDPKVAFPRRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALN
FGSTLMKKKSDPEGPALLFPESELSIRIDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHNVPEGLAV
GVGFGAIEKTASATFESARNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYALAFAAGAM

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

>55331_55331_2_MSI2-SLC39A11_MSI2_chr17_55339553_ENST00000284073_SLC39A11_chr17_71027853_ENST00000542342_length(amino acids)=407AA_BP=114
MGVGGRGGSDMEANGSQGTSGSANDSQHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLG
QPHHELDSKTIDPKVAFPRRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALN
FGSTLMKKKSDPEGPALLFPESELSIRIGRAGLLSDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHN
VPEGLAVGVGFGAIEKTASATFESARNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYAL

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

>55331_55331_3_MSI2-SLC39A11_MSI2_chr17_55339553_ENST00000322684_SLC39A11_chr17_71027853_ENST00000255559_length(amino acids)=386AA_BP=100
MADLTSVLTSVMFSPSSKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPK
VAFPRRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALNFGSTLMKKKSDPEG
PALLFPESELSIRIDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHNVPEGLAVGVGFGAIEKTASAT
FESARNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYALAFAAGAMVYVVMDDIIPEAQI

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

>55331_55331_4_MSI2-SLC39A11_MSI2_chr17_55339553_ENST00000322684_SLC39A11_chr17_71027853_ENST00000542342_length(amino acids)=393AA_BP=100
MADLTSVLTSVMFSPSSKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPK
VAFPRRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALNFGSTLMKKKSDPEG
PALLFPESELSIRIGRAGLLSDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHNVPEGLAVGVGFGAI
EKTASATFESARNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYALAFAAGAMVYVVMDD

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

>55331_55331_5_MSI2-SLC39A11_MSI2_chr17_55339553_ENST00000416426_SLC39A11_chr17_71027853_ENST00000255559_length(amino acids)=382AA_BP=96
MGRLGGRQRSARVKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFP
RRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALNFGSTLMKKKSDPEGPALL
FPESELSIRIDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHNVPEGLAVGVGFGAIEKTASATFESA
RNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYALAFAAGAMVYVVMDDIIPEAQISGNG

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

>55331_55331_6_MSI2-SLC39A11_MSI2_chr17_55339553_ENST00000416426_SLC39A11_chr17_71027853_ENST00000542342_length(amino acids)=389AA_BP=96
MGRLGGRQRSARVKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFP
RRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALNFGSTLMKKKSDPEGPALL
FPESELSIRIGRAGLLSDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHNVPEGLAVGVGFGAIEKTA
SATFESARNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYALAFAAGAMVYVVMDDIIPE

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

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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/chr17:55339553/chr17:71027853)
- 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
MSI2 Q96DH6	.
FUNCTION: RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system (By similarity). {ECO:0000250}.	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

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

194_214

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

263_285

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

290_307

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

322_342

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

72_92

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

194_214

49.0

343.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

263_285

49.0

343.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

290_307

49.0

343.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

322_342

49.0

343.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

72_92

49.0

343.0

Transmembrane

Helical

- 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

MSI2

chr17:55339553

chr17:71027853

ENST00000284073

253_260

104.0

1951.0

Compositional bias

Note=Poly-Ala

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000322684

253_260

100.0

252.0

Compositional bias

Note=Poly-Ala

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000579180

253_260

152.0

Compositional bias

Note=Poly-Ala

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000284073

110_187

104.0

1951.0

Domain

RRM 2

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000284073

21_111

104.0

1951.0

Domain

RRM 1

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000322684

110_187

100.0

252.0

Domain

RRM 2

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000322684

21_111

100.0

252.0

Domain

RRM 1

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000579180

110_187

152.0

Domain

RRM 2

Hgene

MSI2

chr17:55339553

chr17:71027853

ENST00000579180

21_111

152.0

Domain

RRM 1

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

12_32

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000255559

44_64

49.0

336.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

12_32

49.0

343.0

Transmembrane

Helical

Tgene

SLC39A11

chr17:55339553

chr17:71027853

ENST00000542342

44_64

49.0

343.0

Transmembrane

Helical

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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 >>>828_MSI2_55339553_SLC39A11_71027853_ranked_0.pdb	MSI2	55339553	55339553	ENST00000542342	SLC39A11	chr17	71027853	-	MGVGGRGGSDMEANGSQGTSGSANDSQHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLG QPHHELDSKTIDPKVAFPRRAQPKVMLAASYWSLLAPAVEMATSSGGFGAFAFFPVAVGFTLGAAFVYLADLLMPHLGAAEDPQTTLALN FGSTLMKKKSDPEGPALLFPESELSIRIGRAGLLSDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRIALLILAITIHN VPEGLAVGVGFGAIEKTASATFESARNLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYAL	407

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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.

MSI2_pLDDT.png

SLC39A11_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
MSI2
SLC39A11

- 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 MSI2-SLC39A11

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 MSI2-SLC39A11

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