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:SCAF8-IL20RA

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SCAF8-IL20RA
	FusionPDB ID: 79439
	FusionGDB2.0 ID: 79439
		Hgene	Tgene
	Gene symbol	SCAF8	IL20RA
	Gene ID	22828	53832
	Gene name	SR-related CTD associated factor 8	interleukin 20 receptor subunit alpha
	Synonyms	RBM16	CRF2-8\|IL-20R-alpha\|IL-20R1\|IL-20RA
	Cytomap	6q25.2	6q23.3
	Type of gene	protein-coding	protein-coding
	Description	SR-related and CTD-associated factor 8CDC5L complex-associated protein 7RNA-binding motif protein 16SR-like CTD-associated factor 8protein SCAF8	interleukin-20 receptor subunit alphaclass II cytokine receptor ZCYTOR7cytokine receptor family 2 member 8interleukin 20 receptor alpha subunitinterleukin 20 receptor, alphainterleukin-20 receptor I
	Modification date	20200314	20200313
	UniProtAcc	.	Q9UHF4
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000367178, ENST00000367186, ENST00000417268, ENST00000461219,	ENST00000367746, ENST00000367748, ENST00000468393, ENST00000541547, ENST00000316649,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 14 X 10=1960	3 X 2 X 3=18
	# samples	19	5
	** MAII score	log2(19/1960*10)=-3.36678233067162 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/18*10)=1.47393118833241 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SCAF8 [Title/Abstract] AND IL20RA [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SCAF8(155114110)-IL20RA(137338240), # samples:3
Anticipated loss of major functional domain due to fusion event.	SCAF8-IL20RA 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. SCAF8-IL20RA 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. SCAF8-IL20RA 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. SCAF8-IL20RA 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	SCAF8	GO:0032786	positive regulation of DNA-templated transcription, elongation	31104839
Hgene	SCAF8	GO:2000805	negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled	31104839

Fusion gene breakpoints across SCAF8 (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 IL20RA (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	SARC	TCGA-HB-A3YV-01A	SCAF8	chr6	155114110	-	IL20RA	chr6	137338240	-
ChimerDB4	SARC	TCGA-HB-A3YV	SCAF8	chr6	155114110	+	IL20RA	chr6	137338240	-
ChimerDB4	SARC	TCGA-X9-A971-01A	SCAF8	chr6	155114110	+	IL20RA	chr6	137338240	-
ChimerDB4	SARC	TCGA-X9-A971-01A	SCAF8	chr6	155114110	+	IL20RA	chr6	137359268	-

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)
ENST00000367178	SCAF8	chr6	155114110	+	ENST00000316649	IL20RA	chr6	137338240	-	4212	1051	576	2624	682
ENST00000417268	SCAF8	chr6	155114110	+	ENST00000316649	IL20RA	chr6	137338240	-	3868	707	13	2280	755
ENST00000367186	SCAF8	chr6	155114110	+	ENST00000316649	IL20RA	chr6	137338240	-	3841	680	7	2253	748

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
ENST00000367178	ENST00000316649	SCAF8	chr6	155114110	+	IL20RA	chr6	137338240	-	0.000451105	0.99954885
ENST00000417268	ENST00000316649	SCAF8	chr6	155114110	+	IL20RA	chr6	137338240	-	0.000386187	0.9996138
ENST00000367186	ENST00000316649	SCAF8	chr6	155114110	+	IL20RA	chr6	137338240	-	0.000470795	0.99952924

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

>79439_79439_1_SCAF8-IL20RA_SCAF8_chr6_155114110_ENST00000367178_IL20RA_chr6_137338240_ENST00000316649_length(amino acids)=682AA_BP=158
MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSN
NIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIPPPVVTPVLASTTTAMSNTPVPCVSGGLPKPANITFLSINMK
NVLQWTPPEGLQGVKVTYTVQYFIYGQKKWLNKSECRNINRTYCDLSAETSDYEHQYYAKVKAIWGTKCSKWAESGRFYPFLETQIGPPE
VALTTDEKSISVVLTAPEKWKRNPEDLPVSMQQIYSNLKYNVSVLNTKSNRTWSQCVTNHTLVLTWLEPNTLYCVHVESFVPGPPRRAQP
SEKQCARTLKDQSSEFKAKIIFWYVLPVSITVFLFSVMGYSIYRYIHVGKEKHPANLILIYGNEFDKRFFVPAEKIVINFITLNISDDSK
ISHQDMSLLGKSSDVSSLNDPQPSGNLRPPQEEEEVKHLGYASHLMEIFCDSEENTEGTSLTQQESLSRTIPPDKTVIEYEYDVRTTDIC
AGPEEQELSLQEEVSTQGTLLESQAALAVLGPQTLQYSYTPQLQDLDPLAQEHTDSEEGPEEEPSTTLVDWDPQTGRLCIPSLSSFDQDS

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

>79439_79439_2_SCAF8-IL20RA_SCAF8_chr6_155114110_ENST00000367186_IL20RA_chr6_137338240_ENST00000316649_length(amino acids)=748AA_BP=224
MPQPLLPALPPLSSPSGAGSCGPSGGECSGRRLFRRRARGLRSDNMEAVKTFNSEDCASTPACTDCFSSSMDTRSILYSLNDYKPPISKA
KMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVL
NLWQKNNVFKSEIIQPLLDMAAGIPPPVVTPVLASTTTAMSNTPVPCVSGGLPKPANITFLSINMKNVLQWTPPEGLQGVKVTYTVQYFI
YGQKKWLNKSECRNINRTYCDLSAETSDYEHQYYAKVKAIWGTKCSKWAESGRFYPFLETQIGPPEVALTTDEKSISVVLTAPEKWKRNP
EDLPVSMQQIYSNLKYNVSVLNTKSNRTWSQCVTNHTLVLTWLEPNTLYCVHVESFVPGPPRRAQPSEKQCARTLKDQSSEFKAKIIFWY
VLPVSITVFLFSVMGYSIYRYIHVGKEKHPANLILIYGNEFDKRFFVPAEKIVINFITLNISDDSKISHQDMSLLGKSSDVSSLNDPQPS
GNLRPPQEEEEVKHLGYASHLMEIFCDSEENTEGTSLTQQESLSRTIPPDKTVIEYEYDVRTTDICAGPEEQELSLQEEVSTQGTLLESQ
AALAVLGPQTLQYSYTPQLQDLDPLAQEHTDSEEGPEEEPSTTLVDWDPQTGRLCIPSLSSFDQDSEGCEPSEGDGLGEEGLLSRLYEEP

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

>79439_79439_3_SCAF8-IL20RA_SCAF8_chr6_155114110_ENST00000417268_IL20RA_chr6_137338240_ENST00000316649_length(amino acids)=755AA_BP=231
MRGPTRVRHIGCRSRCCQRFLLCLRRAGLVPAARAAGSAPSSRPRSSPRLALPTQCSGRRLFRRRARGLRSDNMEAVKTFNSELYSLNDY
KPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDK
SKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIPPPVVTPVLASTTTAMSNTPVPCVSGGLPKPANITFLSINMKNVLQWTPPEGLQGVKVT
YTVQYFIYGQKKWLNKSECRNINRTYCDLSAETSDYEHQYYAKVKAIWGTKCSKWAESGRFYPFLETQIGPPEVALTTDEKSISVVLTAP
EKWKRNPEDLPVSMQQIYSNLKYNVSVLNTKSNRTWSQCVTNHTLVLTWLEPNTLYCVHVESFVPGPPRRAQPSEKQCARTLKDQSSEFK
AKIIFWYVLPVSITVFLFSVMGYSIYRYIHVGKEKHPANLILIYGNEFDKRFFVPAEKIVINFITLNISDDSKISHQDMSLLGKSSDVSS
LNDPQPSGNLRPPQEEEEVKHLGYASHLMEIFCDSEENTEGTSLTQQESLSRTIPPDKTVIEYEYDVRTTDICAGPEEQELSLQEEVSTQ
GTLLESQAALAVLGPQTLQYSYTPQLQDLDPLAQEHTDSEEGPEEEPSTTLVDWDPQTGRLCIPSLSSFDQDSEGCEPSEGDGLGEEGLL

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

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/chr6:155114110/chr6:137338240)
- 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
.	IL20RA Q9UHF4
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: The IL20RA/IL20RB dimer is a receptor for IL19, IL20 and IL24. The IL20RA/IL10RB dimer is a receptor for IL26.

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

SCAF8

chr6:155114110

chr6:137338240

ENST00000367178

1_139

158.33333333333334

1272.0

Domain

CID

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000417268

1_139

158.33333333333334

1272.0

Domain

CID

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000316649

353_356

29.333333333333332

554.0

Compositional bias

Note=Poly-Glu

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000367748

353_356

443.0

Compositional bias

Note=Poly-Glu

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000316649

136_242

29.333333333333332

554.0

Domain

Fibronectin type-III 2

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000316649

37_135

29.333333333333332

554.0

Domain

Fibronectin type-III 1

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000367748

136_242

443.0

Domain

Fibronectin type-III 2

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000367748

37_135

443.0

Domain

Fibronectin type-III 1

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000316649

272_553

29.333333333333332

554.0

Topological domain

Cytoplasmic

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000316649

30_250

29.333333333333332

554.0

Topological domain

Extracellular

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000367748

272_553

443.0

Topological domain

Cytoplasmic

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000367748

30_250

443.0

Topological domain

Extracellular

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000316649

251_271

29.333333333333332

554.0

Transmembrane

Helical

Tgene

IL20RA

chr6:155114110

chr6:137338240

ENST00000367748

251_271

443.0

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

SCAF8

chr6:155114110

chr6:137338240

ENST00000367178

1120_1182

158.33333333333334

1272.0

Compositional bias

Note=Arg-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000367178

193_371

158.33333333333334

1272.0

Compositional bias

Note=Gln-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000367178

397_459

158.33333333333334

1272.0

Compositional bias

Note=Arg-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000367178

635_1064

158.33333333333334

1272.0

Compositional bias

Note=Pro-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000417268

1120_1182

158.33333333333334

1272.0

Compositional bias

Note=Arg-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000417268

193_371

158.33333333333334

1272.0

Compositional bias

Note=Gln-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000417268

397_459

158.33333333333334

1272.0

Compositional bias

Note=Arg-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000417268

635_1064

158.33333333333334

1272.0

Compositional bias

Note=Pro-rich

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000367178

477_551

158.33333333333334

1272.0

Domain

RRM

Hgene

SCAF8

chr6:155114110

chr6:137338240

ENST00000417268

477_551

158.33333333333334

1272.0

Domain

RRM

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 >>>1521_SCAF8_155114110_IL20RA_137338240_ranked_0.pdb	SCAF8	155114110	155114110	ENST00000316649	IL20RA	chr6	137338240	-	MRGPTRVRHIGCRSRCCQRFLLCLRRAGLVPAARAAGSAPSSRPRSSPRLALPTQCSGRRLFRRRARGLRSDNMEAVKTFNSELYSLNDY KPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDK SKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIPPPVVTPVLASTTTAMSNTPVPCVSGGLPKPANITFLSINMKNVLQWTPPEGLQGVKVT YTVQYFIYGQKKWLNKSECRNINRTYCDLSAETSDYEHQYYAKVKAIWGTKCSKWAESGRFYPFLETQIGPPEVALTTDEKSISVVLTAP EKWKRNPEDLPVSMQQIYSNLKYNVSVLNTKSNRTWSQCVTNHTLVLTWLEPNTLYCVHVESFVPGPPRRAQPSEKQCARTLKDQSSEFK AKIIFWYVLPVSITVFLFSVMGYSIYRYIHVGKEKHPANLILIYGNEFDKRFFVPAEKIVINFITLNISDDSKISHQDMSLLGKSSDVSS LNDPQPSGNLRPPQEEEEVKHLGYASHLMEIFCDSEENTEGTSLTQQESLSRTIPPDKTVIEYEYDVRTTDICAGPEEQELSLQEEVSTQ GTLLESQAALAVLGPQTLQYSYTPQLQDLDPLAQEHTDSEEGPEEEPSTTLVDWDPQTGRLCIPSLSSFDQDSEGCEPSEGDGLGEEGLL	755

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.

SCAF8_pLDDT.png

IL20RA_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
SCAF8
IL20RA

- 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 SCAF8-IL20RA

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to SCAF8-IL20RA

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