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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:MSL1-KRT24

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MSL1-KRT24
	FusionPDB ID: 55344
	FusionGDB2.0 ID: 55344
		Hgene	Tgene
	Gene symbol	MSL1	KRT24
	Gene ID	339287	192666
	Gene name	MSL complex subunit 1	keratin 24
	Synonyms	MSL-1	K24\|KA24
	Cytomap	17q21.1	17q21.2
	Type of gene	protein-coding	protein-coding
	Description	male-specific lethal 1 homologMSL1-like 1male specific lethal 1 homologmale-specific lethal 1-like 1male-specific lethal-1 homolog 1	keratin, type I cytoskeletal 24CK-24cytokeratin-24keratin 24, type Itype I keratin-24
	Modification date	20200313	20200313
	UniProtAcc	Q68DK7	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000579565, ENST00000398532, ENST00000577454, ENST00000578648,	ENST00000264651,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 6 X 5=270	4 X 1 X 3=12
	# samples	9	4
	** MAII score	log2(9/270*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/12*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: MSL1 [Title/Abstract] AND KRT24 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MSL1(38279633)-KRT24(38858185), # samples:2
Anticipated loss of major functional domain due to fusion event.	MSL1-KRT24 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. MSL1-KRT24 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. MSL1-KRT24 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. MSL1-KRT24 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	MSL1	GO:0043984	histone H4-K16 acetylation	20018852

Fusion gene breakpoints across MSL1 (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 KRT24 (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	STAD	TCGA-D7-8573-01A	MSL1	chr17	38279633	+	KRT24	chr17	38858185	-
ChimerDB4	STAD	TCGA-D7-8573	MSL1	chr17	38279633	+	KRT24	chr17	38858185	-

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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)
ENST00000398532	MSL1	chr17	38279633	+	ENST00000264651	KRT24	chr17	38858185	-	2292	1083	300	2045	581
ENST00000577454	MSL1	chr17	38279633	+	ENST00000264651	KRT24	chr17	38858185	-	2017	808	25	1770	581
ENST00000578648	MSL1	chr17	38279633	+	ENST00000264651	KRT24	chr17	38858185	-	2006	797	14	1759	581

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
ENST00000398532	ENST00000264651	MSL1	chr17	38279633	+	KRT24	chr17	38858185	-	0.011654982	0.988345
ENST00000577454	ENST00000264651	MSL1	chr17	38279633	+	KRT24	chr17	38858185	-	0.010532321	0.9894677
ENST00000578648	ENST00000264651	MSL1	chr17	38279633	+	KRT24	chr17	38858185	-	0.010541548	0.98945844

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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

>55344_55344_1_MSL1-KRT24_MSL1_chr17_38279633_ENST00000398532_KRT24_chr17_38858185_ENST00000264651_length(amino acids)=581AA_BP=248
MLRTTMTMRSAVFKAAAAPAGGNPEQRLDYERAAALGGPEDEPGAAEAHFLPRHRKLKEPGPPLASSQGGSPAPSPAGCGGKGRGLLLPA
GAAPGQQEESWGGSVPLPCPPPATKQAGIGGEPAAAGAGCSPRPKYQAVLPIQTGSLVAAAKEPTPWAGDKGGAASPAATASDPAGPPPL
PLPGPPPLAPTATAGTLAASEGRWKSMRKSPLGGGGGSGASSQAACLKQILLLQLDLIEQQQQQLQAKEKEIEELKSERDTIIAATVENA
GIILHIDNARLAADDFRLKYENELCLRQSVEADINGLRKVLDDLTMTRSDLEMQIESFTEELAYLRKNHEEEMKNMQGSSGGEVTVEMNA
APGTDLTKLLNDMRAQYEELAEQNRREAEERFNKQSASLQAQISTDAGAATSAKNEITELKRTLQALEIELQSQLAMKSSLEGTLADTEA
GYVAQLSEIQTQISALEEEICQIWGETKCQNAEYKQLLDIKTRLEVEIETYRRLLDGEGGGSSFAEFGGRNSGSVNMGSRDLVSGDSRSG

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

>55344_55344_2_MSL1-KRT24_MSL1_chr17_38279633_ENST00000577454_KRT24_chr17_38858185_ENST00000264651_length(amino acids)=581AA_BP=248
MLRTTMTMRSAVFKAAAAPAGGNPEQRLDYERAAALGGPEDEPGAAEAHFLPRHRKLKEPGPPLASSQGGSPAPSPAGCGGKGRGLLLPA
GAAPGQQEESWGGSVPLPCPPPATKQAGIGGEPAAAGAGCSPRPKYQAVLPIQTGSLVAAAKEPTPWAGDKGGAASPAATASDPAGPPPL
PLPGPPPLAPTATAGTLAASEGRWKSMRKSPLGGGGGSGASSQAACLKQILLLQLDLIEQQQQQLQAKEKEIEELKSERDTIIAATVENA
GIILHIDNARLAADDFRLKYENELCLRQSVEADINGLRKVLDDLTMTRSDLEMQIESFTEELAYLRKNHEEEMKNMQGSSGGEVTVEMNA
APGTDLTKLLNDMRAQYEELAEQNRREAEERFNKQSASLQAQISTDAGAATSAKNEITELKRTLQALEIELQSQLAMKSSLEGTLADTEA
GYVAQLSEIQTQISALEEEICQIWGETKCQNAEYKQLLDIKTRLEVEIETYRRLLDGEGGGSSFAEFGGRNSGSVNMGSRDLVSGDSRSG

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

>55344_55344_3_MSL1-KRT24_MSL1_chr17_38279633_ENST00000578648_KRT24_chr17_38858185_ENST00000264651_length(amino acids)=581AA_BP=248
MLRTTMTMRSAVFKAAAAPAGGNPEQRLDYERAAALGGPEDEPGAAEAHFLPRHRKLKEPGPPLASSQGGSPAPSPAGCGGKGRGLLLPA
GAAPGQQEESWGGSVPLPCPPPATKQAGIGGEPAAAGAGCSPRPKYQAVLPIQTGSLVAAAKEPTPWAGDKGGAASPAATASDPAGPPPL
PLPGPPPLAPTATAGTLAASEGRWKSMRKSPLGGGGGSGASSQAACLKQILLLQLDLIEQQQQQLQAKEKEIEELKSERDTIIAATVENA
GIILHIDNARLAADDFRLKYENELCLRQSVEADINGLRKVLDDLTMTRSDLEMQIESFTEELAYLRKNHEEEMKNMQGSSGGEVTVEMNA
APGTDLTKLLNDMRAQYEELAEQNRREAEERFNKQSASLQAQISTDAGAATSAKNEITELKRTLQALEIELQSQLAMKSSLEGTLADTEA
GYVAQLSEIQTQISALEEEICQIWGETKCQNAEYKQLLDIKTRLEVEIETYRRLLDGEGGGSSFAEFGGRNSGSVNMGSRDLVSGDSRSG

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

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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/chr17:38279633/chr17:38858185)
- 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
MSL1 Q68DK7	.
FUNCTION: Component of histone acetyltransferase complex responsible for the majority of histone H4 acetylation at 'Lys-16' (H4K16ac) which is implicated in the formation of higher-order chromatin structure (PubMed:16227571). Greatly enhances MSL2 E3 ubiquitin ligase activity, promoting monoubiquitination of histone H2B at 'Lys-34' (H2BK34Ub) (PubMed:21726816). This modification in turn stimulates histone H3 methylation at 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) and leads to gene activation, including that of HOXA9 and MEIS1 (PubMed:21726816). In the MSL complex, acts as a scaffold to tether MSL3 and KAT8 together for enzymatic activity regulation (PubMed:22547026). {ECO:0000269\|PubMed:16227571, ECO:0000269\|PubMed:21726816, ECO:0000269\|PubMed:22547026}.	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

MSL1

chr17:38279633

chr17:38858185

ENST00000398532

10_15

256.0

615.0

Compositional bias

Note=Poly-Ala

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000398532

208_214

256.0

615.0

Compositional bias

Note=Poly-Gly

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000398532

55_185

256.0

615.0

Compositional bias

Note=Pro-rich

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

291_313

205.0

526.0

Region

Note=Linker 12

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

314_452

205.0

526.0

Region

Note=Coil 2

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

453_525

205.0

526.0

Region

Note=Tail

- 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

MSL1

chr17:38279633

chr17:38858185

ENST00000398532

213_282

256.0

615.0

Coiled coil

Ontology_term=ECO:0000269

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000579565

213_282

352.0

Coiled coil

Ontology_term=ECO:0000269

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000579565

10_15

352.0

Compositional bias

Note=Poly-Ala

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000579565

208_214

352.0

Compositional bias

Note=Poly-Gly

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000579565

55_185

352.0

Compositional bias

Note=Pro-rich

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000398532

317_346

256.0

615.0

Motif

Nuclear localization signal

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000398532

505_519

256.0

615.0

Motif

Bipartite nuclear localization signal

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000579565

317_346

352.0

Motif

Nuclear localization signal

Hgene

MSL1

chr17:38279633

chr17:38858185

ENST00000579565

505_519

352.0

Motif

Bipartite nuclear localization signal

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

13_138

205.0

526.0

Compositional bias

Note=Gly-rich

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

140_456

205.0

526.0

Domain

IF rod

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

140_175

205.0

526.0

Region

Note=Coil 1A

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

176_198

205.0

526.0

Region

Note=Linker 1

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

199_290

205.0

526.0

Region

Note=Coil 1B

Tgene

KRT24

chr17:38279633

chr17:38858185

ENST00000264651

1_139

205.0

526.0

Region

Note=Head

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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 >>>1238_MSL1_38279633_KRT24_38858185_1238_MSL1_38279633_KRT24_38858185_ranked_0.pdb	MSL1	38279633	38279633	ENST00000264651	KRT24	chr17	38858185	-	MLRTTMTMRSAVFKAAAAPAGGNPEQRLDYERAAALGGPEDEPGAAEAHFLPRHRKLKEPGPPLASSQGGSPAPSPAGCGGKGRGLLLPA GAAPGQQEESWGGSVPLPCPPPATKQAGIGGEPAAAGAGCSPRPKYQAVLPIQTGSLVAAAKEPTPWAGDKGGAASPAATASDPAGPPPL PLPGPPPLAPTATAGTLAASEGRWKSMRKSPLGGGGGSGASSQAACLKQILLLQLDLIEQQQQQLQAKEKEIEELKSERDTIIAATVENA GIILHIDNARLAADDFRLKYENELCLRQSVEADINGLRKVLDDLTMTRSDLEMQIESFTEELAYLRKNHEEEMKNMQGSSGGEVTVEMNA APGTDLTKLLNDMRAQYEELAEQNRREAEERFNKQSASLQAQISTDAGAATSAKNEITELKRTLQALEIELQSQLAMKSSLEGTLADTEA GYVAQLSEIQTQISALEEEICQIWGETKCQNAEYKQLLDIKTRLEVEIETYRRLLDGEGGGSSFAEFGGRNSGSVNMGSRDLVSGDSRSG	581

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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.

MSL1_pLDDT.png

KRT24_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
MSL1
KRT24

- 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	MSL1	chr17:38279633	chr17:38858185	ENST00000398532	+	1	9	498_518	256.0	615.0	KAT8
Hgene	MSL1	chr17:38279633	chr17:38858185	ENST00000579565	+	2	10	498_518	0	352.0	KAT8
Hgene	MSL1	chr17:38279633	chr17:38858185	ENST00000579565	+	2	10	223_237	0	352.0	MSL2

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Related Drugs to MSL1-KRT24

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 MSL1-KRT24

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