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Fusion Protein:ZNF544-CCDC61

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ZNF544-CCDC61
	FusionPDB ID: 102328
	FusionGDB2.0 ID: 102328
		Hgene	Tgene
	Gene symbol	ZNF544	CCDC61
	Gene ID	27300	729440
	Gene name	zinc finger protein 544	coiled-coil domain containing 61
	Synonyms	-	-
	Cytomap	19q13.43	19q13.32
	Type of gene	protein-coding	protein-coding
	Description	zinc finger protein 544	coiled-coil domain-containing protein 61
	Modification date	20200313	20200313
	UniProtAcc	.	Q9Y6R9 Main function of 5'-partner protein: FUNCTION: Microtubule-binding centrosomal protein required for centriole cohesion, independently of the centrosome-associated protein/CEP250 and rootletin/CROCC linker (PubMed:31789463). In interphase, required for anchoring microtubule at the mother centriole subdistal appendages and for centrosome positioning (PubMed:31789463). During mitosis, may be involved in spindle assembly and chromatin alignment by regulating the organization of spindle microtubules into a symmetrical structure (PubMed:30354798). Has been proposed to play a role in CEP170 recruitment to centrosomes (PubMed:30354798). However, this function could not be confirmed (PubMed:31789463). Plays a non-essential role in ciliogenesis (PubMed:31789463, PubMed:32375023). {ECO:0000269\|PubMed:30354798, ECO:0000269\|PubMed:31789463, ECO:0000269\|PubMed:32375023}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000596597, ENST00000269829, ENST00000333581, ENST00000594384, ENST00000595981, ENST00000596652, ENST00000596825, ENST00000596929, ENST00000599227, ENST00000599953, ENST00000415203, ENST00000600044, ENST00000600220,	ENST00000263284, ENST00000536603, ENST00000594087, ENST00000595358, ENST00000601763,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 4 X 6=192	4 X 4 X 4=64
	# samples	11	5
	** MAII score	log2(11/192*10)=-0.803602787196497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/64*10)=-0.356143810225275 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ZNF544 [Title/Abstract] AND CCDC61 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ZNF544 [Title/Abstract] AND CCDC61 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ZNF544(58758160)-CCDC61(46506266), # samples:3
Anticipated loss of major functional domain due to fusion event.	ZNF544-CCDC61 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. ZNF544-CCDC61 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. ZNF544-CCDC61 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. ZNF544-CCDC61 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:58758160/chr19:46506266)
- 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.

Retention analysis results 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, are available here.

Fusion gene breakpoints across ZNF544 (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 CCDC61 (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 Amino Acid Sequences

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)
ENST00000269829	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506266	+	2383	718	372	2153	593
ENST00000333581	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506266	+	2143	478	132	1913	593
ENST00000596652	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506266	+	2143	478	132	1913	593
ENST00000596929	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506266	+	2143	478	132	1913	593
ENST00000595981	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506266	+	2140	475	129	1910	593
ENST00000269829	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506265	+	2383	718	372	2153	593
ENST00000333581	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506265	+	2143	478	132	1913	593
ENST00000596652	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506265	+	2143	478	132	1913	593
ENST00000596929	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506265	+	2143	478	132	1913	593
ENST00000595981	ZNF544	chr19	58758160	+	ENST00000263284	CCDC61	chr19	46506265	+	2140	475	129	1910	593

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
ENST00000269829	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506266	+	0.03252036	0.9674797
ENST00000333581	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506266	+	0.026528554	0.97347146
ENST00000596652	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506266	+	0.026528554	0.97347146
ENST00000596929	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506266	+	0.026528554	0.97347146
ENST00000595981	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506266	+	0.026492005	0.97350794
ENST00000269829	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506265	+	0.03252036	0.9674797
ENST00000333581	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506265	+	0.026528554	0.97347146
ENST00000596652	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506265	+	0.026528554	0.97347146
ENST00000596929	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506265	+	0.026528554	0.97347146
ENST00000595981	ENST00000263284	ZNF544	chr19	58758160	+	CCDC61	chr19	46506265	+	0.026492005	0.97350794

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

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for ZNF544-CCDC61

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
ZNF544	chr19	58758160	CCDC61	chr19	46506265	475	115	EEDLCRAEQEAPRATLAMDQPAGLQV
ZNF544	chr19	58758160	CCDC61	chr19	46506265	478	115	EEDLCRAEQEAPRATLAMDQPAGLQV
ZNF544	chr19	58758160	CCDC61	chr19	46506265	718	115	EEDLCRAEQEAPRATLAMDQPAGLQV
ZNF544	chr19	58758160	CCDC61	chr19	46506266	475	115	EEDLCRAEQEAPRATLAMDQPAGLQV
ZNF544	chr19	58758160	CCDC61	chr19	46506266	478	115	EEDLCRAEQEAPRATLAMDQPAGLQV
ZNF544	chr19	58758160	CCDC61	chr19	46506266	718	115	EEDLCRAEQEAPRATLAMDQPAGLQV

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Potential FusionNeoAntigen Information of ZNF544-CCDC61 in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

ZNF544-CCDC61_58758160_46506265.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B45:01	AEQEAPRA	0.9999	0.9764	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:02	AEQEAPRA	0.9999	0.8324	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B07:02	APRATLAM	0.9998	0.5955	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:01	QEAPRATL	0.9992	0.7157	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:05	QEAPRATL	0.9987	0.517	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:05	QEAPRATL	0.9962	0.5417	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:13	QEAPRATL	0.9949	0.9955	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:01	AEQEAPRA	0.9913	0.9854	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B18:01	QEAPRATL	0.9798	0.9803	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:01	AEQEAPRA	0.935	0.973	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B14:02	EQEAPRATL	0.9983	0.9596	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B14:01	EQEAPRATL	0.9983	0.9596	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B45:01	QEAPRATLA	0.9979	0.9885	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:02	QEAPRATLA	0.9973	0.8749	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:24	EQEAPRATL	0.997	0.7172	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:01	EQEAPRATL	0.9967	0.9868	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B45:01	AEQEAPRAT	0.9947	0.9937	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-A26:02	EAPRATLAM	0.9935	0.7097	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:02	AEQEAPRAT	0.9909	0.9188	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B38:02	EQEAPRATL	0.9906	0.9932	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:13	EQEAPRATL	0.99	0.9894	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:02	AEQEAPRAT	0.9893	0.6967	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-A26:15	EAPRATLAM	0.9826	0.8038	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-A26:14	EAPRATLAM	0.9826	0.8038	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B38:01	EQEAPRATL	0.9781	0.9918	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:10	EQEAPRATL	0.9766	0.7798	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:37	EQEAPRATL	0.9281	0.8237	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:03	EAPRATLAM	0.8793	0.6512	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:01	QEAPRATLA	0.7925	0.9773	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:02	EAPRATLAM	0.5935	0.8219	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:04	EAPRATLAM	0.5935	0.8219	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:01	QEAPRATLA	0.5924	0.9906	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:01	AEQEAPRAT	0.4068	0.9919	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:02	AEQEAPRAT	0.3082	0.6201	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:01	AEQEAPRAT	0.2185	0.9845	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:05	AEQEAPRAT	0.2112	0.8761	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B48:01	AEQEAPRATL	0.9994	0.738	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:01	AEQEAPRATL	0.9983	0.6458	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:03	AEQEAPRATL	0.9968	0.9806	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:02	AEQEAPRATL	0.9961	0.8369	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:03	QEAPRATLAM	0.9956	0.9866	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:05	AEQEAPRATL	0.9953	0.5603	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:02	QEAPRATLAM	0.9947	0.6301	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:05	QEAPRATLAM	0.9943	0.7578	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B13:01	AEQEAPRATL	0.9943	0.9933	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B47:01	QEAPRATLAM	0.9928	0.8035	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B47:01	AEQEAPRATL	0.9912	0.7946	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:01	QEAPRATLAM	0.9899	0.8697	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:13	AEQEAPRATL	0.984	0.9952	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:02	QEAPRATLAM	0.9804	0.564	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B45:01	AEQEAPRATL	0.9777	0.9747	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:02	EQEAPRATLA	0.9763	0.767	7	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B45:01	EQEAPRATLA	0.9752	0.9793	7	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:05	QEAPRATLAM	0.9668	0.7379	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:01	AEQEAPRATL	0.9221	0.9778	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:01	AEQEAPRATL	0.8556	0.9828	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:01	RAEQEAPRAT	0.5752	0.981	5	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B45:01	AEQEAPRATLA	0.9998	0.9962	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:02	AEQEAPRATLA	0.9997	0.8812	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B48:01	RAEQEAPRATL	0.9986	0.8661	5	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:01	AEQEAPRATLA	0.9968	0.9833	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:01	AEQEAPRATLA	0.9924	0.9758	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:06	AEQEAPRA	0.9999	0.9439	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B48:03	QEAPRATL	0.9995	0.7785	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B07:12	APRATLAM	0.9986	0.7097	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:09	QEAPRATL	0.9985	0.5665	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:08	QEAPRATL	0.9984	0.981	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B07:04	APRATLAM	0.9821	0.524	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:10	APRATLAM	0.6229	0.9483	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:09	EQEAPRATL	0.9972	0.935	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:12	EQEAPRATL	0.9953	0.9872	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:06	QEAPRATLA	0.9937	0.962	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:06	AEQEAPRAT	0.9913	0.9842	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:08	EQEAPRATL	0.9912	0.9191	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:05	EQEAPRATL	0.9883	0.9841	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-A26:01	EAPRATLAM	0.9826	0.8038	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B14:03	EQEAPRATL	0.9824	0.9561	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:09	QEAPRATLA	0.918	0.7554	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:09	AEQEAPRAT	0.9117	0.8885	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-C01:30	EAPRATLAM	0.8751	0.9655	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-C01:17	EAPRATLAM	0.8616	0.9405	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:12	EAPRATLAM	0.5935	0.8219	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:06	AEQEAPRATL	0.9995	0.9604	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B48:03	AEQEAPRATL	0.9985	0.7125	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:10	AEQEAPRATL	0.9973	0.9026	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:09	AEQEAPRATL	0.9967	0.553	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:09	QEAPRATLAM	0.9965	0.8219	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:04	QEAPRATLAM	0.9949	0.6101	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:08	AEQEAPRATL	0.9943	0.5057	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:08	AEQEAPRATL	0.9936	0.9746	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:08	QEAPRATLAM	0.9935	0.7862	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:03	AEQEAPRATL	0.9911	0.7903	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:10	QEAPRATLAM	0.9827	0.9187	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:06	AEQEAPRATLA	0.9998	0.9644	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B48:03	RAEQEAPRATL	0.9852	0.8256	5	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B07:22	APRATLAM	0.9998	0.5955	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:04	QEAPRATL	0.9998	0.9204	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B07:09	APRATLAM	0.9998	0.5745	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:12	QEAPRATL	0.9995	0.7785	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:36	QEAPRATL	0.9993	0.6803	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:49	QEAPRATL	0.9991	0.739	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:02	QEAPRATL	0.9955	0.9954	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:03	QEAPRATL	0.9939	0.8648	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B18:11	QEAPRATL	0.9879	0.9793	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B18:05	QEAPRATL	0.9798	0.9803	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B18:03	QEAPRATL	0.976	0.9784	8	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:05	AEQEAPRA	0.935	0.973	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:04	AEQEAPRA	0.935	0.973	6	14
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B67:01	APRATLAM	0.5898	0.8948	10	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:02	EQEAPRATL	0.9971	0.9896	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:31	EQEAPRATL	0.9971	0.9865	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:11	EQEAPRATL	0.9885	0.8994	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-A25:01	EAPRATLAM	0.9863	0.8851	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B38:05	EQEAPRATL	0.9781	0.9918	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:11	EAPRATLAM	0.9307	0.7658	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:04	AEQEAPRAT	0.929	0.976	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:09	EQEAPRATL	0.9125	0.775	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:23	EAPRATLAM	0.888	0.6623	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-C01:02	EAPRATLAM	0.8516	0.9422	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:03	QEAPRATLA	0.7738	0.8677	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-C01:03	EAPRATLAM	0.7076	0.9035	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:73	EQEAPRATL	0.6537	0.9742	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:30	EQEAPRATL	0.6263	0.9693	7	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:09	EAPRATLAM	0.5935	0.8219	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:05	QEAPRATLA	0.5924	0.9906	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:04	QEAPRATLA	0.5924	0.9906	8	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:08	EAPRATLAM	0.5353	0.6426	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B35:43	EAPRATLAM	0.5332	0.6505	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:11	EAPRATLAM	0.529	0.6338	9	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:03	AEQEAPRAT	0.3562	0.9277	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:05	AEQEAPRAT	0.2185	0.9845	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:04	AEQEAPRAT	0.2185	0.9845	6	15
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:04	AEQEAPRATL	0.9991	0.9124	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:12	AEQEAPRATL	0.9985	0.7125	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:36	AEQEAPRATL	0.9984	0.6078	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:49	AEQEAPRATL	0.9981	0.6613	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:26	AEQEAPRATL	0.9968	0.9806	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:13	AEQEAPRATL	0.9968	0.9806	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:07	AEQEAPRATL	0.9968	0.9806	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:13	QEAPRATLAM	0.9956	0.9866	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:26	QEAPRATLAM	0.9956	0.9866	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:07	QEAPRATLAM	0.9956	0.9866	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B44:22	QEAPRATLAM	0.9947	0.6301	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:21	AEQEAPRATL	0.9921	0.7297	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:04	QEAPRATLAM	0.9919	0.9658	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:36	QEAPRATLAM	0.9904	0.8581	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:49	QEAPRATLAM	0.9898	0.8821	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:30	AEQEAPRATL	0.9889	0.989	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B39:02	AEQEAPRATL	0.9888	0.9951	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:53	QEAPRATLAM	0.9876	0.9745	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B15:73	AEQEAPRATL	0.9823	0.9889	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B18:11	QEAPRATLAM	0.9685	0.9697	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:03	AEQEAPRATL	0.9366	0.895	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:05	AEQEAPRATL	0.9221	0.9778	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:04	AEQEAPRATL	0.9221	0.9778	6	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B41:03	QEAPRATLAM	0.8926	0.9332	8	18
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B48:05	RAEQEAPRATL	0.9998	0.6954	5	16
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:04	AEQEAPRATLA	0.9924	0.9758	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B50:05	AEQEAPRATLA	0.9924	0.9758	6	17
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	HLA-B40:12	RAEQEAPRATL	0.9852	0.8256	5	16

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Potential FusionNeoAntigen Information of ZNF544-CCDC61 in HLA II

ZNF544-CCDC61_58758160_46506265.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	DRB1-1476	PRATLAMDQPAGLQV	11	26
ZNF544-CCDC61	chr19	58758160	chr19	46506265	718	DRB1-1479	PRATLAMDQPAGLQV	11	26

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Fusion breakpoint peptide structures of ZNF544-CCDC61

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
169	AEQEAPRATLAMDQ	ZNF544	CCDC61	chr19	58758160	chr19	46506265	718

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ZNF544-CCDC61

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	169	AEQEAPRATLAMDQ	-7.15543	-7.26883
HLA-B14:02	3BVN	169	AEQEAPRATLAMDQ	-4.77435	-5.80965
HLA-B52:01	3W39	169	AEQEAPRATLAMDQ	-6.80875	-6.92215
HLA-B52:01	3W39	169	AEQEAPRATLAMDQ	-4.20386	-5.23916
HLA-A11:01	4UQ2	169	AEQEAPRATLAMDQ	-7.5194	-8.5547
HLA-A11:01	4UQ2	169	AEQEAPRATLAMDQ	-6.9601	-7.0735
HLA-A24:02	5HGA	169	AEQEAPRATLAMDQ	-7.52403	-7.63743
HLA-A24:02	5HGA	169	AEQEAPRATLAMDQ	-5.82433	-6.85963
HLA-B27:05	6PYJ	169	AEQEAPRATLAMDQ	-3.28285	-4.31815
HLA-B44:05	3DX8	169	AEQEAPRATLAMDQ	-5.91172	-6.94702
HLA-B44:05	3DX8	169	AEQEAPRATLAMDQ	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of ZNF544-CCDC61

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
ZNF544-CCDC61	chr19	58758160	chr19	46506265	10	18	APRATLAM	CCCCCCGAGCAACCTTGGCCATGG
ZNF544-CCDC61	chr19	58758160	chr19	46506265	5	15	RAEQEAPRAT	GGGCAGAGCAGGAGGCCCCCCGAGCAACCT
ZNF544-CCDC61	chr19	58758160	chr19	46506265	5	16	RAEQEAPRATL	GGGCAGAGCAGGAGGCCCCCCGAGCAACCTTGG
ZNF544-CCDC61	chr19	58758160	chr19	46506265	6	14	AEQEAPRA	CAGAGCAGGAGGCCCCCCGAGCAA
ZNF544-CCDC61	chr19	58758160	chr19	46506265	6	15	AEQEAPRAT	CAGAGCAGGAGGCCCCCCGAGCAACCT
ZNF544-CCDC61	chr19	58758160	chr19	46506265	6	16	AEQEAPRATL	CAGAGCAGGAGGCCCCCCGAGCAACCTTGG
ZNF544-CCDC61	chr19	58758160	chr19	46506265	6	17	AEQEAPRATLA	CAGAGCAGGAGGCCCCCCGAGCAACCTTGGCCA
ZNF544-CCDC61	chr19	58758160	chr19	46506265	7	16	EQEAPRATL	AGCAGGAGGCCCCCCGAGCAACCTTGG
ZNF544-CCDC61	chr19	58758160	chr19	46506265	7	17	EQEAPRATLA	AGCAGGAGGCCCCCCGAGCAACCTTGGCCA
ZNF544-CCDC61	chr19	58758160	chr19	46506265	8	16	QEAPRATL	AGGAGGCCCCCCGAGCAACCTTGG
ZNF544-CCDC61	chr19	58758160	chr19	46506265	8	17	QEAPRATLA	AGGAGGCCCCCCGAGCAACCTTGGCCA
ZNF544-CCDC61	chr19	58758160	chr19	46506265	8	18	QEAPRATLAM	AGGAGGCCCCCCGAGCAACCTTGGCCATGG
ZNF544-CCDC61	chr19	58758160	chr19	46506265	9	18	EAPRATLAM	AGGCCCCCCGAGCAACCTTGGCCATGG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
ZNF544-CCDC61	chr19	58758160	chr19	46506265	11	26	PRATLAMDQPAGLQV	CCCGAGCAACCTTGGCCATGGACCAGCCGGCTGGCCTGCAGGTGG

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Information of the samples that have these potential fusion neoantigens of ZNF544-CCDC61

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
BLCA	ZNF544-CCDC61	chr19	58758160	ENST00000269829	chr19	46506265	ENST00000263284	TCGA-HQ-A2OE

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Potential target of CAR-T therapy development for ZNF544-CCDC61

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to ZNF544-CCDC61

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 ZNF544-CCDC61

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

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)