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:CRK-STX8

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CRK-STX8
	FusionPDB ID: 19504
	FusionGDB2.0 ID: 19504
		Hgene	Tgene
	Gene symbol	CRK	STX8
	Gene ID	1398	9482
	Gene name	CRK proto-oncogene, adaptor protein	syntaxin 8
	Synonyms	CRKII\|p38	CARB
	Cytomap	17p13.3	17p13.1
	Type of gene	protein-coding	protein-coding
	Description	adapter molecule crkproto-oncogene c-Crkv-crk avian sarcoma virus CT10 oncogene homologv-crk sarcoma virus CT10 oncogene-like protein	syntaxin-8CIP-1-associated regulator of cyclin B
	Modification date	20200327	20200313
	UniProtAcc	P46109	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000300574, ENST00000398970, ENST00000574295, ENST00000572145,	ENST00000573373, ENST00000306357, ENST00000574431,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 11 X 7=1155	24 X 16 X 8=3072
	# samples	18	29
	** MAII score	log2(18/1155*10)=-2.68182403997375 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(29/3072*10)=-3.40505341070622 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CRK [Title/Abstract] AND STX8 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CRK(1359171)-STX8(9153962), # samples:3
Anticipated loss of major functional domain due to fusion event.	CRK-STX8 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. CRK-STX8 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	CRK	GO:0009966	regulation of signal transduction	17515907
Hgene	CRK	GO:0032956	regulation of actin cytoskeleton organization	11870224
Hgene	CRK	GO:0043087	regulation of GTPase activity	11870224
Hgene	CRK	GO:0048013	ephrin receptor signaling pathway	11870224
Hgene	CRK	GO:0061045	negative regulation of wound healing	17515907
Hgene	CRK	GO:2000146	negative regulation of cell motility	17515907
Tgene	STX8	GO:0045022	early endosome to late endosome transport	10564279
Tgene	STX8	GO:1903076	regulation of protein localization to plasma membrane	18570918

Fusion gene breakpoints across CRK (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 STX8 (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	LUSC	TCGA-85-A4CN-01A	CRK	chr17	1359171	-	STX8	chr17	9153962	-
ChimerDB4	LUSC	TCGA-85-A4CN	CRK	chr17	1359170	-	STX8	chr17	9153962	-
ChimerDB4	LUSC	TCGA-85-A4CN	CRK	chr17	1359171	-	STX8	chr17	9153962	-

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)
ENST00000398970	CRK	chr17	1359171	-	ENST00000306357	STX8	chr17	9153962	-	522	347	141	503	120
ENST00000398970	CRK	chr17	1359171	-	ENST00000574431	STX8	chr17	9153962	-	506	347	141	503	120
ENST00000300574	CRK	chr17	1359171	-	ENST00000306357	STX8	chr17	9153962	-	557	382	176	538	120
ENST00000300574	CRK	chr17	1359171	-	ENST00000574431	STX8	chr17	9153962	-	541	382	176	538	120
ENST00000574295	CRK	chr17	1359171	-	ENST00000306357	STX8	chr17	9153962	-	448	273	67	429	120
ENST00000574295	CRK	chr17	1359171	-	ENST00000574431	STX8	chr17	9153962	-	432	273	67	429	120
ENST00000398970	CRK	chr17	1359170	-	ENST00000306357	STX8	chr17	9153962	-	522	347	141	503	120
ENST00000398970	CRK	chr17	1359170	-	ENST00000574431	STX8	chr17	9153962	-	506	347	141	503	120
ENST00000300574	CRK	chr17	1359170	-	ENST00000306357	STX8	chr17	9153962	-	557	382	176	538	120
ENST00000300574	CRK	chr17	1359170	-	ENST00000574431	STX8	chr17	9153962	-	541	382	176	538	120
ENST00000574295	CRK	chr17	1359170	-	ENST00000306357	STX8	chr17	9153962	-	448	273	67	429	120
ENST00000574295	CRK	chr17	1359170	-	ENST00000574431	STX8	chr17	9153962	-	432	273	67	429	120

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
ENST00000398970	ENST00000306357	CRK	chr17	1359171	-	STX8	chr17	9153962	-	0.07384653	0.9261534
ENST00000398970	ENST00000574431	CRK	chr17	1359171	-	STX8	chr17	9153962	-	0.06789588	0.9321041
ENST00000300574	ENST00000306357	CRK	chr17	1359171	-	STX8	chr17	9153962	-	0.05475993	0.9452401
ENST00000300574	ENST00000574431	CRK	chr17	1359171	-	STX8	chr17	9153962	-	0.051723946	0.94827604
ENST00000574295	ENST00000306357	CRK	chr17	1359171	-	STX8	chr17	9153962	-	0.06283575	0.93716425
ENST00000574295	ENST00000574431	CRK	chr17	1359171	-	STX8	chr17	9153962	-	0.053475134	0.94652486
ENST00000398970	ENST00000306357	CRK	chr17	1359170	-	STX8	chr17	9153962	-	0.07384653	0.9261534
ENST00000398970	ENST00000574431	CRK	chr17	1359170	-	STX8	chr17	9153962	-	0.06789588	0.9321041
ENST00000300574	ENST00000306357	CRK	chr17	1359170	-	STX8	chr17	9153962	-	0.05475993	0.9452401
ENST00000300574	ENST00000574431	CRK	chr17	1359170	-	STX8	chr17	9153962	-	0.051723946	0.94827604
ENST00000574295	ENST00000306357	CRK	chr17	1359170	-	STX8	chr17	9153962	-	0.06283575	0.93716425
ENST00000574295	ENST00000574431	CRK	chr17	1359170	-	STX8	chr17	9153962	-	0.053475134	0.94652486

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

>19504_19504_1_CRK-STX8_CRK_chr17_1359170_ENST00000300574_STX8_chr17_9153962_ENST00000306357_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_2_CRK-STX8_CRK_chr17_1359170_ENST00000300574_STX8_chr17_9153962_ENST00000574431_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_3_CRK-STX8_CRK_chr17_1359170_ENST00000398970_STX8_chr17_9153962_ENST00000306357_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_4_CRK-STX8_CRK_chr17_1359170_ENST00000398970_STX8_chr17_9153962_ENST00000574431_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_5_CRK-STX8_CRK_chr17_1359170_ENST00000574295_STX8_chr17_9153962_ENST00000306357_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_6_CRK-STX8_CRK_chr17_1359170_ENST00000574295_STX8_chr17_9153962_ENST00000574431_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_7_CRK-STX8_CRK_chr17_1359171_ENST00000300574_STX8_chr17_9153962_ENST00000306357_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_8_CRK-STX8_CRK_chr17_1359171_ENST00000300574_STX8_chr17_9153962_ENST00000574431_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_9_CRK-STX8_CRK_chr17_1359171_ENST00000398970_STX8_chr17_9153962_ENST00000306357_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_10_CRK-STX8_CRK_chr17_1359171_ENST00000398970_STX8_chr17_9153962_ENST00000574431_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_11_CRK-STX8_CRK_chr17_1359171_ENST00000574295_STX8_chr17_9153962_ENST00000306357_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

>19504_19504_12_CRK-STX8_CRK_chr17_1359171_ENST00000574295_STX8_chr17_9153962_ENST00000574431_length(amino acids)=120AA_BP=68
MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ

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

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/chr17:1359171/chr17:9153962)
- 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
CRK P46109	.
FUNCTION: May mediate the transduction of intracellular signals.	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

STX8

chr17:1359170

chr17:9153962

ENST00000306357

233_236

214.33333333333334

237.0

Topological domain

Vesicular

Tgene

STX8

chr17:1359171

chr17:9153962

ENST00000306357

233_236

214.33333333333334

237.0

Topological domain

Vesicular

Tgene

STX8

chr17:1359170

chr17:9153962

ENST00000306357

216_232

214.33333333333334

237.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

Tgene

STX8

chr17:1359171

chr17:9153962

ENST00000306357

216_232

214.33333333333334

237.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

- 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

CRK

chr17:1359170

chr17:9153962

ENST00000300574

132_192

80.33333333333333

305.0

Domain

SH3 1

Hgene

CRK

chr17:1359170

chr17:9153962

ENST00000300574

13_118

80.33333333333333

305.0

Domain

SH2

Hgene

CRK

chr17:1359170

chr17:9153962

ENST00000300574

235_296

80.33333333333333

305.0

Domain

SH3 2

Hgene

CRK

chr17:1359170

chr17:9153962

ENST00000398970

132_192

80.33333333333333

205.0

Domain

SH3 1

Hgene

CRK

chr17:1359170

chr17:9153962

ENST00000398970

13_118

80.33333333333333

205.0

Domain

SH2

Hgene

CRK

chr17:1359170

chr17:9153962

ENST00000398970

235_296

80.33333333333333

205.0

Domain

SH3 2

Hgene

CRK

chr17:1359171

chr17:9153962

ENST00000300574

132_192

80.33333333333333

305.0

Domain

SH3 1

Hgene

CRK

chr17:1359171

chr17:9153962

ENST00000300574

13_118

80.33333333333333

305.0

Domain

SH2

Hgene

CRK

chr17:1359171

chr17:9153962

ENST00000300574

235_296

80.33333333333333

305.0

Domain

SH3 2

Hgene

CRK

chr17:1359171

chr17:9153962

ENST00000398970

132_192

80.33333333333333

205.0

Domain

SH3 1

Hgene

CRK

chr17:1359171

chr17:9153962

ENST00000398970

13_118

80.33333333333333

205.0

Domain

SH2

Hgene

CRK

chr17:1359171

chr17:9153962

ENST00000398970

235_296

80.33333333333333

205.0

Domain

SH3 2

Tgene

STX8

chr17:1359170

chr17:9153962

ENST00000306357

42_65

214.33333333333334

237.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

STX8

chr17:1359171

chr17:9153962

ENST00000306357

42_65

214.33333333333334

237.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

STX8

chr17:1359170

chr17:9153962

ENST00000306357

145_207

214.33333333333334

237.0

Domain

t-SNARE coiled-coil homology

Tgene

STX8

chr17:1359171

chr17:9153962

ENST00000306357

145_207

214.33333333333334

237.0

Domain

t-SNARE coiled-coil homology

Tgene

STX8

chr17:1359170

chr17:9153962

ENST00000306357

1_215

214.33333333333334

237.0

Topological domain

Cytoplasmic

Tgene

STX8

chr17:1359171

chr17:9153962

ENST00000306357

1_215

214.33333333333334

237.0

Topological domain

Cytoplasmic

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 >>>48_CRK_1359171_STX8_9153962_ranked_0.pdb	CRK	1359170	1359171	ENST00000574431	STX8	chr17	9153962	-	MVLGEVESAGGGGAAAGPAARGVPGAGLEHQPRGLCAQRLRELARLPLHHQQQRPAPAGATVARPASARDDHGDFTAACGYRGCCSLADQ	120

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.

CRK_pLDDT.png

STX8_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
CRK
STX8

- 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 CRK-STX8

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to CRK-STX8

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