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:AP5S1-RNF24

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: AP5S1-RNF24
	FusionPDB ID: 5318
	FusionGDB2.0 ID: 11498
		Hgene	Tgene
	Gene symbol	AP5S1	RNF24
	Gene ID	55317	11237
	Gene name	adaptor related protein complex 5 subunit sigma 1	ring finger protein 24
	Synonyms	C20orf29	G1L
	Cytomap	20p13	20p13
	Type of gene	protein-coding	protein-coding
	Description	AP-5 complex subunit sigma-1adapter-related protein complex 5 sigma subunitadaptor related protein complex 5 sigma 1 subunitadaptor-related protein complex 5 sigma subunitprotein C20orf29sigma5	RING finger protein 24
	Modification date	20200313	20200313
	UniProtAcc	Q9NUS5	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000246041, ENST00000379567, ENST00000379573,	ENST00000336095, ENST00000358395, ENST00000432261, ENST00000545616,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 1 X 2=4	9 X 7 X 4=252
	# samples	2	8
	** MAII score	log2(2/4*10)=2.32192809488736	log2(8/252*10)=-1.65535182861255 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: AP5S1 [Title/Abstract] AND RNF24 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	AP5S1(3802940)-RNF24(3928926), # samples:3
Anticipated loss of major functional domain due to fusion event.	AP5S1-RNF24 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. AP5S1-RNF24 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

Fusion gene breakpoints across AP5S1 (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 RNF24 (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	BRCA	TCGA-AR-A0U3-01A	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-
ChimerDB4	BRCA	TCGA-AR-A0U3	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-

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)
ENST00000379573	AP5S1	chr20	3802940	+	ENST00000336095	RNF24	chr20	3928926	-	7478	420	163	723	186
ENST00000379573	AP5S1	chr20	3802940	+	ENST00000358395	RNF24	chr20	3928926	-	3366	420	163	723	186
ENST00000379573	AP5S1	chr20	3802940	+	ENST00000432261	RNF24	chr20	3928926	-	3363	420	163	723	186
ENST00000379573	AP5S1	chr20	3802940	+	ENST00000545616	RNF24	chr20	3928926	-	1220	420	163	723	186
ENST00000379567	AP5S1	chr20	3802940	+	ENST00000336095	RNF24	chr20	3928926	-	7417	359	183	662	159
ENST00000379567	AP5S1	chr20	3802940	+	ENST00000358395	RNF24	chr20	3928926	-	3305	359	183	662	159
ENST00000379567	AP5S1	chr20	3802940	+	ENST00000432261	RNF24	chr20	3928926	-	3302	359	183	662	159
ENST00000379567	AP5S1	chr20	3802940	+	ENST00000545616	RNF24	chr20	3928926	-	1159	359	183	662	159
ENST00000246041	AP5S1	chr20	3802940	+	ENST00000336095	RNF24	chr20	3928926	-	7453	395	138	698	186
ENST00000246041	AP5S1	chr20	3802940	+	ENST00000358395	RNF24	chr20	3928926	-	3341	395	138	698	186
ENST00000246041	AP5S1	chr20	3802940	+	ENST00000432261	RNF24	chr20	3928926	-	3338	395	138	698	186
ENST00000246041	AP5S1	chr20	3802940	+	ENST00000545616	RNF24	chr20	3928926	-	1195	395	138	698	186

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
ENST00000379573	ENST00000336095	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.007454671	0.9925453
ENST00000379573	ENST00000358395	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.013349219	0.9866508
ENST00000379573	ENST00000432261	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.012291336	0.9877087
ENST00000379573	ENST00000545616	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.023834996	0.97616506
ENST00000379567	ENST00000336095	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.007338268	0.9926617
ENST00000379567	ENST00000358395	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.012713979	0.98728603
ENST00000379567	ENST00000432261	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.011688212	0.9883118
ENST00000379567	ENST00000545616	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.019175459	0.9808246
ENST00000246041	ENST00000336095	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.007441008	0.99255896
ENST00000246041	ENST00000358395	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.013326854	0.9866731
ENST00000246041	ENST00000432261	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.012263279	0.9877367
ENST00000246041	ENST00000545616	AP5S1	chr20	3802940	+	RNF24	chr20	3928926	-	0.018823968	0.9811761

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

>5318_5318_1_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000246041_RNF24_chr20_3928926_ENST00000336095_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_2_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000246041_RNF24_chr20_3928926_ENST00000358395_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_3_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000246041_RNF24_chr20_3928926_ENST00000432261_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_4_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000246041_RNF24_chr20_3928926_ENST00000545616_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_5_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379567_RNF24_chr20_3928926_ENST00000336095_length(amino acids)=159AA_BP=58
MVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQAHKEFYAYKQVILKEKVKELNLHELCA

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

>5318_5318_6_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379567_RNF24_chr20_3928926_ENST00000358395_length(amino acids)=159AA_BP=58
MVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQAHKEFYAYKQVILKEKVKELNLHELCA

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

>5318_5318_7_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379567_RNF24_chr20_3928926_ENST00000432261_length(amino acids)=159AA_BP=58
MVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQAHKEFYAYKQVILKEKVKELNLHELCA

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

>5318_5318_8_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379567_RNF24_chr20_3928926_ENST00000545616_length(amino acids)=159AA_BP=58
MVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQAHKEFYAYKQVILKEKVKELNLHELCA

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

>5318_5318_9_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379573_RNF24_chr20_3928926_ENST00000336095_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_10_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379573_RNF24_chr20_3928926_ENST00000358395_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_11_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379573_RNF24_chr20_3928926_ENST00000432261_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

>5318_5318_12_AP5S1-RNF24_AP5S1_chr20_3802940_ENST00000379573_RNF24_chr20_3928926_ENST00000545616_length(amino acids)=186AA_BP=85
MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ
AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP

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

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/chr20:3802940/chr20:3928926)
- 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
AP5S1 Q9NUS5	.
FUNCTION: As part of AP-5, a probable fifth adaptor protein complex it may be involved in endosomal transport. According to PubMed:20613862, it is required for efficient homologous recombination DNA double-strand break repair. {ECO:0000269\|PubMed:20613862, ECO:0000269\|PubMed:22022230}.	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

RNF24

chr20:3802940

chr20:3928926

ENST00000336095

78_119

47.666666666666664

149.0

Zinc finger

RING-type

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000358395

78_119

47.666666666666664

149.0

Zinc finger

RING-type

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000432261

78_119

68.66666666666667

170.0

Zinc finger

RING-type

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000545616

78_119

68.66666666666667

170.0

Zinc finger

RING-type

- 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

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000336095

24_44

47.666666666666664

149.0

Transmembrane

Helical

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000358395

24_44

47.666666666666664

149.0

Transmembrane

Helical

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000432261

24_44

68.66666666666667

170.0

Transmembrane

Helical

Tgene

RNF24

chr20:3802940

chr20:3928926

ENST00000545616

24_44

68.66666666666667

170.0

Transmembrane

Helical

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 >>>222_AP5S1_3802940_RNF24_3928926_ranked_0.pdb	AP5S1	3802940	3802940	ENST00000545616	RNF24	chr20	3928926	-	MTGVRNYNPRSALRLKVTEAVTTHPGAMVHAFLIHTLRAPNTEDTGLCRVLYSCVFGAEKSPDDPRPHGAERDRLLRKEQILAVARLRHQ AHKEFYAYKQVILKEKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLHSKQDRGPPQGPLP	186

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.

AP5S1_pLDDT.png

RNF24_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
AP5S1
RNF24

- 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 AP5S1-RNF24

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to AP5S1-RNF24

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