Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:XRCC5-RPL37A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: XRCC5-RPL37A
	FusionPDB ID: 99770
	FusionGDB2.0 ID: 99770
		Hgene	Tgene
	Gene symbol	XRCC5	RPL37A
	Gene ID	7520	6168
	Gene name	X-ray repair cross complementing 5	ribosomal protein L37a
	Synonyms	KARP-1\|KARP1\|KU80\|KUB2\|Ku86\|NFIV	L37A
	Cytomap	2q35	2q35
	Type of gene	protein-coding	protein-coding
	Description	X-ray repair cross-complementing protein 586 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 2ATP-dependent DNA helicase II 80 kDa subunitCTC box-binding factor 85 kDa subunitCTC85CTCBFDNA repair protein XRCC5Ku autoantigen, 80kDaKu	60S ribosomal protein L37alarge ribosomal subunit protein eL43
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000392132, ENST00000392133, ENST00000471649,	ENST00000427280, ENST00000441179, ENST00000456586, ENST00000598925, ENST00000446558, ENST00000491306, ENST00000600880,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 10 X 7=910	23 X 13 X 5=1495
	# samples	12	26
	** MAII score	log2(12/910*10)=-2.92283213947754 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(26/1495*10)=-2.52356195605701 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: XRCC5 [Title/Abstract] AND RPL37A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: XRCC5 [Title/Abstract] AND RPL37A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	XRCC5(216974180)-RPL37A(217363992), # samples:1 XRCC5(216974180)-RPL37A(217364672), # samples:1
Anticipated loss of major functional domain due to fusion event.	XRCC5-RPL37A 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. XRCC5-RPL37A 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. XRCC5-RPL37A 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. XRCC5-RPL37A 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	XRCC5	GO:0002218	activation of innate immune response	28712728
Hgene	XRCC5	GO:0006303	double-strand break repair via nonhomologous end joining	26359349
Hgene	XRCC5	GO:0045860	positive regulation of protein kinase activity	22504299
Hgene	XRCC5	GO:0071480	cellular response to gamma radiation	26359349

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:216974180/chr2:217363992)
- 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.

Retention analysis results 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, are available here.

Fusion gene breakpoints across XRCC5 (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 RPL37A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

Fusion Amino Acid Sequences

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)
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000491306	RPL37A	chr2	217363992	+	2905	482	71	757	228
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000600880	RPL37A	chr2	217363992	+	879	482	71	697	208
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000446558	RPL37A	chr2	217363992	+	954	482	71	706	211
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000491306	RPL37A	chr2	217363992	+	2584	161	983	585	132
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000600880	RPL37A	chr2	217363992	+	558	161	406	2	135
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000446558	RPL37A	chr2	217363992	+	633	161	391	2	130
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000491306	RPL37A	chr2	217364672	+	2776	482	71	628	185
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000600880	RPL37A	chr2	217364672	+	750	482	71	568	165
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000446558	RPL37A	chr2	217364672	+	825	482	71	577	168
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000456586	RPL37A	chr2	217364672	+	688	482	71	628	185
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000598925	RPL37A	chr2	217364672	+	805	482	71	604	177
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000427280	RPL37A	chr2	217364672	+	867	482	71	688	205
ENST00000392133	XRCC5	chr2	216974180	+	ENST00000441179	RPL37A	chr2	217364672	+	841	482	71	604	177
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000491306	RPL37A	chr2	217364672	+	2455	161	854	456	132
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000600880	RPL37A	chr2	217364672	+	429	161	277	2	92
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000446558	RPL37A	chr2	217364672	+	504	161	362	24	112
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000456586	RPL37A	chr2	217364672	+	367	161	56	307	83
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000598925	RPL37A	chr2	217364672	+	484	161	338	24	104
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000427280	RPL37A	chr2	217364672	+	546	161	397	2	132
ENST00000392132	XRCC5	chr2	216974180	+	ENST00000441179	RPL37A	chr2	217364672	+	520	161	338	24	104

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
ENST00000392133	ENST00000491306	XRCC5	chr2	216974180	+	RPL37A	chr2	217363992	+	0.043702617	0.9562974
ENST00000392133	ENST00000600880	XRCC5	chr2	216974180	+	RPL37A	chr2	217363992	+	0.13846989	0.86153007
ENST00000392133	ENST00000446558	XRCC5	chr2	216974180	+	RPL37A	chr2	217363992	+	0.13040823	0.8695917
ENST00000392132	ENST00000491306	XRCC5	chr2	216974180	+	RPL37A	chr2	217363992	+	0.03209786	0.96790206
ENST00000392132	ENST00000600880	XRCC5	chr2	216974180	+	RPL37A	chr2	217363992	+	0.109270096	0.89072984
ENST00000392132	ENST00000446558	XRCC5	chr2	216974180	+	RPL37A	chr2	217363992	+	0.12764795	0.87235206
ENST00000392133	ENST00000491306	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.29122514	0.70877486
ENST00000392133	ENST00000600880	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.2812059	0.71879417
ENST00000392133	ENST00000446558	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.28796554	0.7120345
ENST00000392133	ENST00000456586	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.22382131	0.7761787
ENST00000392133	ENST00000598925	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.22342402	0.776576
ENST00000392133	ENST00000427280	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.20197077	0.79802924
ENST00000392133	ENST00000441179	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.17498675	0.8250133
ENST00000392132	ENST00000491306	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.46290764	0.5370923
ENST00000392132	ENST00000600880	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.5696201	0.43037996
ENST00000392132	ENST00000446558	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.5040573	0.4959427
ENST00000392132	ENST00000456586	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.5276632	0.47233683
ENST00000392132	ENST00000598925	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.29836774	0.7016322
ENST00000392132	ENST00000427280	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.18518233	0.81481767
ENST00000392132	ENST00000441179	XRCC5	chr2	216974180	+	RPL37A	chr2	217364672	+	0.22073281	0.7792672

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

Top

Fusion Protein Breakpoint Sequences for XRCC5-RPL37A

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

Length(fusion protein)

BP in fusion protein

Peptide

Top

Potential FusionNeoAntigen Information of XRCC5-RPL37A in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA I

FusionNeoAntigen peptide

Binding score

Immunogenic score

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

Top

Potential FusionNeoAntigen Information of XRCC5-RPL37A in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

Top

Fusion breakpoint peptide structures of XRCC5-RPL37A

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of XRCC5-RPL37A

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele

PDB ID

File name

BPseq

Docking score

Glide score

Top

Vaccine Design for the FusionNeoAntigens of XRCC5-RPL37A

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide sequence

FusionNeoAntigen RNA sequence

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

Top

Information of the samples that have these potential fusion neoantigens of XRCC5-RPL37A

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type

Fusion gene

Hchr

Hbp

Henst

Tchr

Tbp

Tenst

Sample

Top

Potential target of CAR-T therapy development for XRCC5-RPL37A

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

Top

Related Drugs to XRCC5-RPL37A

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to XRCC5-RPL37A

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

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)