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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:FAF1-SKI

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FAF1-SKI
	FusionPDB ID: 28249
	FusionGDB2.0 ID: 28249
		Hgene	Tgene
	Gene symbol	FAF1	SKI
	Gene ID	11124	6497
	Gene name	Fas associated factor 1	SKI proto-oncogene
	Synonyms	CGI-03\|HFAF1s\|UBXD12\|UBXN3A\|hFAF1	SGS\|SKV
	Cytomap	1p32.3	1p36.33-p36.32
	Type of gene	protein-coding	protein-coding
	Description	FAS-associated factor 1Fas (TNFRSF6) associated factor 1TNFRSF6-associated factor 1UBX domain protein 3AUBX domain-containing protein 12UBX domain-containing protein 3A	ski oncogeneproto-oncogene c-Skiski oncoproteinv-ski avian sarcoma viral oncogene homolog
	Modification date	20200313	20200329
	UniProtAcc	Q9UNN5	SKIDA1,C10orf140
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000371778, ENST00000396153, ENST00000472808, ENST00000545823,	ENST00000478223, ENST00000378536,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	23 X 21 X 9=4347	17 X 5 X 6=510
	# samples	31	17
	** MAII score	log2(31/4347*10)=-3.80967997500385 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(17/510*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: FAF1 [Title/Abstract] AND SKI [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FAF1(51425439)-SKI(2234417), # samples:2 SKI(2161174)-FAF1(51267349), # samples:3
Anticipated loss of major functional domain due to fusion event.	FAF1-SKI 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. FAF1-SKI 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. SKI-FAF1 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. SKI-FAF1 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. FAF1-SKI seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. FAF1-SKI seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. FAF1-SKI seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
Hgene	FAF1	GO:0010942	positive regulation of cell death	15596450
Tgene	SKI	GO:0000122	negative regulation of transcription by RNA polymerase II	17469184
Tgene	SKI	GO:0008285	negative regulation of cell proliferation	11430826
Tgene	SKI	GO:0014902	myotube differentiation	19008232
Tgene	SKI	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	17469184
Tgene	SKI	GO:0030514	negative regulation of BMP signaling pathway	14699069
Tgene	SKI	GO:0032926	negative regulation of activin receptor signaling pathway	14699069
Tgene	SKI	GO:0043388	positive regulation of DNA binding	15107821
Tgene	SKI	GO:0045668	negative regulation of osteoblast differentiation	14699069
Tgene	SKI	GO:0060395	SMAD protein signal transduction	12874272

Fusion gene breakpoints across FAF1 (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 SKI (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-D7-6822-01A	FAF1	chr1	51425439	-	SKI	chr1	2234417	+
ChimerDB4	STAD	TCGA-D7-6822	FAF1	chr1	51425438	-	SKI	chr1	2234416	+

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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)

ENST00000396153

FAF1

chr1

51425439

ENST00000378536

SKI

chr1

2234417

5069

497

140

1714

524

ENST00000396153

FAF1

chr1

51425438

ENST00000378536

SKI

chr1

2234416

5069

497

140

1714

524

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
ENST00000396153	ENST00000378536	FAF1	chr1	51425439	-	SKI	chr1	2234417	+	0.003975577	0.99602437
ENST00000396153	ENST00000378536	FAF1	chr1	51425438	-	SKI	chr1	2234416	+	0.003975577	0.99602437

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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

>28249_28249_1_FAF1-SKI_FAF1_chr1_51425438_ENST00000396153_SKI_chr1_2234416_ENST00000378536_length(amino acids)=524AA_BP=48
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQVSSEPPASIRPKTDDTSSQSPAPSEKDKPSSWLRTLAGSSNKSLGCVHPRQRLSAFRPWSP
AVSASEKELSPHLPALIRDSFYSYKSFETAVAPNVALAPPAQQKVVSSPPCAAAVSRAPEPLATCTQPRKRKLTVDTPGAPETLAPVAAP
EEDKDSEAEVEVESREEFTSSLSSLSSPSFTSSSSAKDLGSPGARALPSAVPDAAAPADAPSGLEAELEHLRQALEGGLDTKEAKEKFLH
EVVKMRVKQEEKLSAALQAKRSLHQELEFLRVAKKEKLREATEAKRNLRKEIERLRAENEKKMKEANESRLRLKRELEQARQARVCDKGC

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

>28249_28249_2_FAF1-SKI_FAF1_chr1_51425439_ENST00000396153_SKI_chr1_2234417_ENST00000378536_length(amino acids)=524AA_BP=48
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQVSSEPPASIRPKTDDTSSQSPAPSEKDKPSSWLRTLAGSSNKSLGCVHPRQRLSAFRPWSP
AVSASEKELSPHLPALIRDSFYSYKSFETAVAPNVALAPPAQQKVVSSPPCAAAVSRAPEPLATCTQPRKRKLTVDTPGAPETLAPVAAP
EEDKDSEAEVEVESREEFTSSLSSLSSPSFTSSSSAKDLGSPGARALPSAVPDAAAPADAPSGLEAELEHLRQALEGGLDTKEAKEKFLH
EVVKMRVKQEEKLSAALQAKRSLHQELEFLRVAKKEKLREATEAKRNLRKEIERLRAENEKKMKEANESRLRLKRELEQARQARVCDKGC

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

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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/chr1:51425439/chr1:2234417)
- 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
FAF1 Q9UNN5	SKI SKIDA1,C10orf140
FUNCTION: Ubiquitin-binding protein (PubMed:19722279). Required for the progression of DNA replication forks by targeting DNA replication licensing factor CDT1 for degradation (PubMed:26842564). Potentiates but cannot initiate FAS-induced apoptosis (By similarity). {ECO:0000250\|UniProtKB:P54731, ECO:0000269\|PubMed:19722279, ECO:0000269\|PubMed:26842564}.	908

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

SKI

chr1:51425438

chr1:2234416

ENST00000378536

536_710

323.0

729.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

SKI

chr1:51425439

chr1:2234417

ENST00000378536

536_710

323.0

729.0

Coiled coil

Ontology_term=ECO:0000255

- 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

FAF1

chr1:51425438

chr1:2234416

ENST00000371778

1_57

15.0

651.0

Domain

UBA

Hgene

FAF1

chr1:51425438

chr1:2234416

ENST00000371778

569_646

15.0

651.0

Domain

UBX

Hgene

FAF1

chr1:51425438

chr1:2234416

ENST00000396153

1_57

15.0

651.0

Domain

UBA

Hgene

FAF1

chr1:51425438

chr1:2234416

ENST00000396153

569_646

15.0

651.0

Domain

UBX

Hgene

FAF1

chr1:51425439

chr1:2234417

ENST00000371778

1_57

15.0

651.0

Domain

UBA

Hgene

FAF1

chr1:51425439

chr1:2234417

ENST00000371778

569_646

15.0

651.0

Domain

UBX

Hgene

FAF1

chr1:51425439

chr1:2234417

ENST00000396153

1_57

15.0

651.0

Domain

UBA

Hgene

FAF1

chr1:51425439

chr1:2234417

ENST00000396153

569_646

15.0

651.0

Domain

UBX

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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
FAF1
SKI

- 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

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Related Drugs to FAF1-SKI

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 FAF1-SKI

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