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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:PTK7-SRF

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTK7-SRF
	FusionPDB ID: 70080
	FusionGDB2.0 ID: 70080
		Hgene	Tgene
	Gene symbol	PTK7	SRF
	Gene ID	5754	6722
	Gene name	protein tyrosine kinase 7 (inactive)	serum response factor
	Synonyms	CCK-4\|CCK4	MCM1
	Cytomap	6p21.1	6p21.1
	Type of gene	protein-coding	protein-coding
	Description	inactive tyrosine-protein kinase 7PTK7 protein tyrosine kinase 7colon carcinoma kinase 4pseudo tyrosine kinase receptor 7tyrosine-protein kinase-like 7	serum response factorc-fos serum response element-binding transcription factorminichromosome maintenance 1 homolog
	Modification date	20200322	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000230419, ENST00000345201, ENST00000349241, ENST00000352931, ENST00000471863, ENST00000476760, ENST00000481273,	ENST00000265354, ENST00000457278,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 6 X 10=900	3 X 3 X 3=27
	# samples	14	3
	** MAII score	log2(14/900*10)=-2.68449817427207 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PTK7 [Title/Abstract] AND SRF [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTK7(43044305)-SRF(43146544), # samples:2
Anticipated loss of major functional domain due to fusion event.	PTK7-SRF 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. PTK7-SRF 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
Tgene	SRF	GO:0001829	trophectodermal cell differentiation	17576768
Tgene	SRF	GO:0009725	response to hormone	17975004
Tgene	SRF	GO:0045597	positive regulation of cell differentiation	17576768
Tgene	SRF	GO:0045944	positive regulation of transcription by RNA polymerase II	3203386\|8887666\|17576768\|19578358
Tgene	SRF	GO:0045987	positive regulation of smooth muscle contraction	17215356
Tgene	SRF	GO:0051091	positive regulation of DNA-binding transcription factor activity	19098903
Tgene	SRF	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	8887666

Fusion gene breakpoints across PTK7 (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 SRF (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	TGCT	TCGA-2G-AAGZ-01A	PTK7	chr6	43044305	+	SRF	chr6	43146544	+
ChimerDB4	TGCT	TCGA-2G-AAGZ	PTK7	chr6	43044305	+	SRF	chr6	43146544	+

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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)
ENST00000230419	PTK7	chr6	43044305	+	ENST00000265354	SRF	chr6	43146544	+	2788	300	1721	1248	157
ENST00000230419	PTK7	chr6	43044305	+	ENST00000457278	SRF	chr6	43146544	+	709	300	8	472	154
ENST00000349241	PTK7	chr6	43044305	+	ENST00000265354	SRF	chr6	43146544	+	2714	226	1647	1174	157
ENST00000349241	PTK7	chr6	43044305	+	ENST00000457278	SRF	chr6	43146544	+	635	226	99	398	99
ENST00000345201	PTK7	chr6	43044305	+	ENST00000265354	SRF	chr6	43146544	+	2714	226	1647	1174	157
ENST00000345201	PTK7	chr6	43044305	+	ENST00000457278	SRF	chr6	43146544	+	635	226	99	398	99
ENST00000352931	PTK7	chr6	43044305	+	ENST00000265354	SRF	chr6	43146544	+	2714	226	1647	1174	157
ENST00000352931	PTK7	chr6	43044305	+	ENST00000457278	SRF	chr6	43146544	+	635	226	99	398	99
ENST00000476760	PTK7	chr6	43044305	+	ENST00000265354	SRF	chr6	43146544	+	2749	261	1682	1209	157
ENST00000476760	PTK7	chr6	43044305	+	ENST00000457278	SRF	chr6	43146544	+	670	261	8	433	141
ENST00000471863	PTK7	chr6	43044305	+	ENST00000265354	SRF	chr6	43146544	+	2717	229	1650	1177	157
ENST00000471863	PTK7	chr6	43044305	+	ENST00000457278	SRF	chr6	43146544	+	638	229	102	401	99

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
ENST00000230419	ENST00000265354	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.8512531	0.14874694
ENST00000230419	ENST00000457278	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.13619134	0.86380863
ENST00000349241	ENST00000265354	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.8913525	0.108647525
ENST00000349241	ENST00000457278	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.091277264	0.90872276
ENST00000345201	ENST00000265354	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.8913525	0.108647525
ENST00000345201	ENST00000457278	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.091277264	0.90872276
ENST00000352931	ENST00000265354	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.8913525	0.108647525
ENST00000352931	ENST00000457278	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.091277264	0.90872276
ENST00000476760	ENST00000265354	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.67741543	0.32258457
ENST00000476760	ENST00000457278	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.102611795	0.89738816
ENST00000471863	ENST00000265354	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.892606	0.10739396
ENST00000471863	ENST00000457278	PTK7	chr6	43044305	+	SRF	chr6	43146544	+	0.0980076	0.90199244

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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

>70080_70080_1_PTK7-SRF_PTK7_chr6_43044305_ENST00000230419_SRF_chr6_43146544_ENST00000265354_length(amino acids)=157AA_BP=
MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV

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

>70080_70080_2_PTK7-SRF_PTK7_chr6_43044305_ENST00000230419_SRF_chr6_43146544_ENST00000457278_length(amino acids)=154AA_BP=1
MAAAAAARGDSEVLGARGSGSGRLGTPRGRAPAAAAAAAPALRCAPPPVPAAERSLRARRAPSAPFPEPAAMGAARGSPARPRRLPLLSV

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

>70080_70080_3_PTK7-SRF_PTK7_chr6_43044305_ENST00000345201_SRF_chr6_43146544_ENST00000265354_length(amino acids)=157AA_BP=
MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV

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

>70080_70080_4_PTK7-SRF_PTK7_chr6_43044305_ENST00000345201_SRF_chr6_43146544_ENST00000457278_length(amino acids)=99AA_BP=1
MRARRAPSAPFPEPAAMGAARGSPARPRRLPLLSVLLLPLLGGGVPQVFLTASSGTVQIPVSAVQLHQMAVIGQQAGSSSNLTELQVVNL

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

>70080_70080_5_PTK7-SRF_PTK7_chr6_43044305_ENST00000349241_SRF_chr6_43146544_ENST00000265354_length(amino acids)=157AA_BP=
MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV

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

>70080_70080_6_PTK7-SRF_PTK7_chr6_43044305_ENST00000349241_SRF_chr6_43146544_ENST00000457278_length(amino acids)=99AA_BP=1
MRARRAPSAPFPEPAAMGAARGSPARPRRLPLLSVLLLPLLGGGVPQVFLTASSGTVQIPVSAVQLHQMAVIGQQAGSSSNLTELQVVNL

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

>70080_70080_7_PTK7-SRF_PTK7_chr6_43044305_ENST00000352931_SRF_chr6_43146544_ENST00000265354_length(amino acids)=157AA_BP=
MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV

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

>70080_70080_8_PTK7-SRF_PTK7_chr6_43044305_ENST00000352931_SRF_chr6_43146544_ENST00000457278_length(amino acids)=99AA_BP=1
MRARRAPSAPFPEPAAMGAARGSPARPRRLPLLSVLLLPLLGGGVPQVFLTASSGTVQIPVSAVQLHQMAVIGQQAGSSSNLTELQVVNL

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

>70080_70080_9_PTK7-SRF_PTK7_chr6_43044305_ENST00000471863_SRF_chr6_43146544_ENST00000265354_length(amino acids)=157AA_BP=
MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV

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

>70080_70080_10_PTK7-SRF_PTK7_chr6_43044305_ENST00000471863_SRF_chr6_43146544_ENST00000457278_length(amino acids)=99AA_BP=1
MRARRAPSAPFPEPAAMGAARGSPARPRRLPLLSVLLLPLLGGGVPQVFLTASSGTVQIPVSAVQLHQMAVIGQQAGSSSNLTELQVVNL

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

>70080_70080_11_PTK7-SRF_PTK7_chr6_43044305_ENST00000476760_SRF_chr6_43146544_ENST00000265354_length(amino acids)=157AA_BP=
MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV

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

>70080_70080_12_PTK7-SRF_PTK7_chr6_43044305_ENST00000476760_SRF_chr6_43146544_ENST00000457278_length(amino acids)=141AA_BP=1
MGARGSGSGRLGTPRGRAPAAAAAAAPALRCAPPPVPAAERSLRARRAPSAPFPEPAAMGAARGSPARPRRLPLLSVLLLPLLGGGVPQV

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

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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/chr6:43044305/chr6:43146544)
- 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

- 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

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

128_218

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 2

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

225_317

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 3

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

309_407

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 4

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

31_120

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 1

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

412_497

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 5

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

503_586

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 6

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

578_680

26.333333333333332

1071.0

Domain

Note=Ig-like C2-type 7

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

796_1066

26.333333333333332

1071.0

Domain

Protein kinase%3B inactive

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

128_218

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 2

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

225_317

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 3

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

309_407

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 4

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

31_120

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 1

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

412_497

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 5

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

503_586

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 6

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

578_680

26.333333333333332

1031.0

Domain

Note=Ig-like C2-type 7

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

796_1066

26.333333333333332

1031.0

Domain

Protein kinase%3B inactive

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

128_218

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 2

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

225_317

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 3

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

309_407

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 4

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

31_120

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 1

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

412_497

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 5

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

503_586

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 6

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

578_680

26.333333333333332

941.0

Domain

Note=Ig-like C2-type 7

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

796_1066

26.333333333333332

941.0

Domain

Protein kinase%3B inactive

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

128_218

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 2

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

225_317

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 3

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

309_407

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 4

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

31_120

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 1

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

412_497

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 5

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

503_586

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 6

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

578_680

26.333333333333332

1015.0

Domain

Note=Ig-like C2-type 7

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

796_1066

26.333333333333332

1015.0

Domain

Protein kinase%3B inactive

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

128_218

1079.0

Domain

Note=Ig-like C2-type 2

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

225_317

1079.0

Domain

Note=Ig-like C2-type 3

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

309_407

1079.0

Domain

Note=Ig-like C2-type 4

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

31_120

1079.0

Domain

Note=Ig-like C2-type 1

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

412_497

1079.0

Domain

Note=Ig-like C2-type 5

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

503_586

1079.0

Domain

Note=Ig-like C2-type 6

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

578_680

1079.0

Domain

Note=Ig-like C2-type 7

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

796_1066

1079.0

Domain

Protein kinase%3B inactive

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

31_704

26.333333333333332

1071.0

Topological domain

Extracellular

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

726_1070

26.333333333333332

1071.0

Topological domain

Cytoplasmic

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

31_704

26.333333333333332

1031.0

Topological domain

Extracellular

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

726_1070

26.333333333333332

1031.0

Topological domain

Cytoplasmic

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

31_704

26.333333333333332

941.0

Topological domain

Extracellular

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

726_1070

26.333333333333332

941.0

Topological domain

Cytoplasmic

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

31_704

26.333333333333332

1015.0

Topological domain

Extracellular

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

726_1070

26.333333333333332

1015.0

Topological domain

Cytoplasmic

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

31_704

1079.0

Topological domain

Extracellular

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

726_1070

1079.0

Topological domain

Cytoplasmic

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000230419

705_725

26.333333333333332

1071.0

Transmembrane

Helical

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000345201

705_725

26.333333333333332

1031.0

Transmembrane

Helical

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000349241

705_725

26.333333333333332

941.0

Transmembrane

Helical

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000352931

705_725

26.333333333333332

1015.0

Transmembrane

Helical

Hgene

PTK7

chr6:43044305

chr6:43146544

ENST00000481273

705_725

1079.0

Transmembrane

Helical

Tgene

SRF

chr6:43044305

chr6:43146544

ENST00000265354

13_142

451.3333333333333

509.0

Compositional bias

Note=Gly-rich

Tgene

SRF

chr6:43044305

chr6:43146544

ENST00000265354

242_258

451.3333333333333

509.0

Compositional bias

Note=Asp/Glu-rich (acidic)

Tgene

SRF

chr6:43044305

chr6:43146544

ENST00000265354

80_90

451.3333333333333

509.0

Compositional bias

Note=Asp/Glu-rich (acidic)

Tgene

SRF

chr6:43044305

chr6:43146544

ENST00000265354

133_222

451.3333333333333

509.0

DNA binding

Tgene

SRF

chr6:43044305

chr6:43146544

ENST00000265354

141_201

451.3333333333333

509.0

Domain

MADS-box

Tgene

SRF

chr6:43044305

chr6:43146544

ENST00000265354

168_222

451.3333333333333

509.0

Region

Note=Involved in dimerization

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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 >>>137_PTK7_43044305_SRF_43146544_ranked_0.pdb	PTK7	43044305	43044305	ENST00000457278	SRF	chr6	43146544	+	MLPLLLTPIPASHPLPDPTLLTATWAPGSCMPGTAQGCNAHACGTNEVSCLCLTPSHPNPDIWSPSSLSLATALKGKKRPRAVGHPPHPV	157

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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.

PTK7_pLDDT.png

SRF_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
PTK7
SRF

- 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	PTK7	chr6:43044305	chr6:43146544	ENST00000230419	+	1	20	794_1070	26.333333333333332	1071.0	CTNNB1
Hgene	PTK7	chr6:43044305	chr6:43146544	ENST00000345201	+	1	19	794_1070	26.333333333333332	1031.0	CTNNB1
Hgene	PTK7	chr6:43044305	chr6:43146544	ENST00000349241	+	1	17	794_1070	26.333333333333332	941.0	CTNNB1
Hgene	PTK7	chr6:43044305	chr6:43146544	ENST00000352931	+	1	19	794_1070	26.333333333333332	1015.0	CTNNB1
Hgene	PTK7	chr6:43044305	chr6:43146544	ENST00000481273	+	1	20	794_1070	0	1079.0	CTNNB1

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Related Drugs to PTK7-SRF

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 PTK7-SRF

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