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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ITGA7-PCBP2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ITGA7-PCBP2
FusionPDB ID: 40454
FusionGDB2.0 ID: 40454
HgeneTgene
Gene symbol

ITGA7

PCBP2

Gene ID

3679

5094

Gene nameintegrin subunit alpha 7poly(rC) binding protein 2
Synonyms-HNRNPE2|HNRPE2|hnRNP-E2
Cytomap

12q13.2

12q13.13

Type of geneprotein-codingprotein-coding
Descriptionintegrin alpha-7integrin alpha 7 chainpoly(rC)-binding protein 2alpha-CP2epididymis secretory sperm binding proteinheterogeneous nuclear ribonucleoprotein E2heterogenous nuclear ribonucleoprotein E2hnRNP E2
Modification date2020032820200313
UniProtAcc

Q13683

Main function of 5'-partner protein: FUNCTION: Integrin alpha-7/beta-1 is the primary laminin receptor on skeletal myoblasts and adult myofibers. During myogenic differentiation, it may induce changes in the shape and mobility of myoblasts, and facilitate their localization at laminin-rich sites of secondary fiber formation. It is involved in the maintenance of the myofibers cytoarchitecture as well as for their anchorage, viability and functional integrity. Isoform Alpha-7X2B and isoform Alpha-7X1B promote myoblast migration on laminin 1 and laminin 2/4, but isoform Alpha-7X1B is less active on laminin 1 (In vitro). Acts as Schwann cell receptor for laminin-2. Acts as a receptor of COMP and mediates its effect on vascular smooth muscle cells (VSMCs) maturation (By similarity). Required to promote contractile phenotype acquisition in differentiated airway smooth muscle (ASM) cells. {ECO:0000250, ECO:0000269|PubMed:10694445, ECO:0000269|PubMed:17641293, ECO:0000269|PubMed:9307969}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000257879, ENST00000257880, 
ENST00000347027, ENST00000394229, 
ENST00000394230, ENST00000553804, 
ENST00000555728, ENST00000452168, 
ENST00000359282, ENST00000359462, 
ENST00000437231, ENST00000439930, 
ENST00000447282, ENST00000455667, 
ENST00000541275, ENST00000546463, 
ENST00000548933, ENST00000549863, 
ENST00000552296, ENST00000552819, 
ENST00000603815, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 8 X 5=28027 X 26 X 9=6318
# samples 830
** MAII scorelog2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(30/6318*10)=-4.39643353125099
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ITGA7 [Title/Abstract] AND PCBP2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ITGA7 [Title/Abstract] AND PCBP2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ITGA7(56096655)-PCBP2(53856276), # samples:1
Anticipated loss of major functional domain due to fusion event.ITGA7-PCBP2 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.
ITGA7-PCBP2 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.
ITGA7-PCBP2 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.
ITGA7-PCBP2 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgenePCBP2

GO:0039694

viral RNA genome replication

12414943

TgenePCBP2

GO:0075522

IRES-dependent viral translational initiation

12414943



check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:56096655/chr12:53856276)
- 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.
FGviewer

check buttonRetention 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.

check buttonFusion gene breakpoints across ITGA7 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PCBP2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000553804ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+130943319924301
ENST00000553804ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2734433191014331
ENST00000553804ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+260543319885288
ENST00000553804ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+264443319924301
ENST00000553804ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+121043319882287
ENST00000553804ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1408433191017332
ENST00000553804ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1259433191017332
ENST00000553804ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1187433191014331
ENST00000553804ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+126843319885288
ENST00000553804ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+260643319885288
ENST00000553804ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1191433191014331
ENST00000553804ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+110343319924301
ENST00000553804ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+95143319834271
ENST00000257879ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+1506630781121347
ENST00000257879ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2931630781211377
ENST00000257879ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+2802630781082334
ENST00000257879ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+2841630781121347
ENST00000257879ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+1407630781079333
ENST00000257879ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1605630781214378
ENST00000257879ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1456630781214378
ENST00000257879ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1384630781211377
ENST00000257879ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+1465630781082334
ENST00000257879ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+2803630781082334
ENST00000257879ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1388630781211377
ENST00000257879ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+1300630781121347
ENST00000257879ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+1148630781031317
ENST00000347027ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+1492616641107347
ENST00000347027ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2917616641197377
ENST00000347027ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+2788616641068334
ENST00000347027ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+2827616641107347
ENST00000347027ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+1393616641065333
ENST00000347027ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1591616641200378
ENST00000347027ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1442616641200378
ENST00000347027ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1370616641197377
ENST00000347027ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+1451616641068334
ENST00000347027ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+2789616641068334
ENST00000347027ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1374616641197377
ENST00000347027ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+1286616641107347
ENST00000347027ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+1134616641017317
ENST00000394229ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+1510634821125347
ENST00000394229ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2935634821215377
ENST00000394229ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+2806634821086334
ENST00000394229ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+2845634821125347
ENST00000394229ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+1411634821083333
ENST00000394229ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1609634821218378
ENST00000394229ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1460634821218378
ENST00000394229ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1388634821215377
ENST00000394229ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+1469634821086334
ENST00000394229ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+2807634821086334
ENST00000394229ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1392634821215377
ENST00000394229ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+1304634821125347
ENST00000394229ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+1152634821035317
ENST00000257880ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+1510634821125347
ENST00000257880ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2935634821215377
ENST00000257880ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+2806634821086334
ENST00000257880ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+2845634821125347
ENST00000257880ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+1411634821083333
ENST00000257880ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1609634821218378
ENST00000257880ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1460634821218378
ENST00000257880ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1388634821215377
ENST00000257880ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+1469634821086334
ENST00000257880ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+2807634821086334
ENST00000257880ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1392634821215377
ENST00000257880ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+1304634821125347
ENST00000257880ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+1152634821035317
ENST00000394230ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+1510634821125347
ENST00000394230ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2935634821215377
ENST00000394230ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+2806634821086334
ENST00000394230ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+2845634821125347
ENST00000394230ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+1411634821083333
ENST00000394230ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1609634821218378
ENST00000394230ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1460634821218378
ENST00000394230ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1388634821215377
ENST00000394230ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+1469634821086334
ENST00000394230ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+2807634821086334
ENST00000394230ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1392634821215377
ENST00000394230ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+1304634821125347
ENST00000394230ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+1152634821035317
ENST00000555728ITGA7chr1256096655-ENST00000359282PCBP2chr1253856276+131944329934301
ENST00000555728ITGA7chr1256096655-ENST00000603815PCBP2chr1253856276+2744443291024331
ENST00000555728ITGA7chr1256096655-ENST00000437231PCBP2chr1253856276+261544329895288
ENST00000555728ITGA7chr1256096655-ENST00000447282PCBP2chr1253856276+265444329934301
ENST00000555728ITGA7chr1256096655-ENST00000549863PCBP2chr1253856276+122044329892287
ENST00000555728ITGA7chr1256096655-ENST00000359462PCBP2chr1253856276+1418443291027332
ENST00000555728ITGA7chr1256096655-ENST00000546463PCBP2chr1253856276+1269443291027332
ENST00000555728ITGA7chr1256096655-ENST00000552296PCBP2chr1253856276+1197443291024331
ENST00000555728ITGA7chr1256096655-ENST00000552819PCBP2chr1253856276+127844329895288
ENST00000555728ITGA7chr1256096655-ENST00000455667PCBP2chr1253856276+261644329895288
ENST00000555728ITGA7chr1256096655-ENST00000439930PCBP2chr1253856276+1201443291024331
ENST00000555728ITGA7chr1256096655-ENST00000548933PCBP2chr1253856276+111344329934301
ENST00000555728ITGA7chr1256096655-ENST00000541275PCBP2chr1253856276+96144329844271

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000553804ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0441992540.9558007
ENST00000553804ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0052040110.994796
ENST00000553804ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.0088303120.9911697
ENST00000553804ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0107344640.98926556
ENST00000553804ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.0380368230.96196324
ENST00000553804ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0254072230.9745928
ENST00000553804ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.0375059770.962494
ENST00000553804ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.0391430630.960857
ENST00000553804ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.0369541460.96304584
ENST00000553804ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.0087608660.99123913
ENST00000553804ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.0398372820.96016276
ENST00000553804ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.0449562370.9550438
ENST00000553804ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.125310730.8746893
ENST00000257879ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0501617450.9498383
ENST00000257879ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0065808780.9934191
ENST00000257879ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.012279850.9877201
ENST00000257879ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0141809170.9858191
ENST00000257879ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.04348530.9565147
ENST00000257879ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0272858930.9727141
ENST00000257879ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.0380705040.9619295
ENST00000257879ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.040754230.95924574
ENST00000257879ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.044364150.95563585
ENST00000257879ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.0122273180.98777264
ENST00000257879ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.0414643030.95853573
ENST00000257879ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.0597517640.94024825
ENST00000257879ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.133291620.8667084
ENST00000347027ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0461748020.9538252
ENST00000347027ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0059319940.994068
ENST00000347027ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.0116425090.9883575
ENST00000347027ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0126915770.98730844
ENST00000347027ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.039966140.9600339
ENST00000347027ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0247699250.97523004
ENST00000347027ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.035676160.9643239
ENST00000347027ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.038367620.96163243
ENST00000347027ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.0409735930.95902646
ENST00000347027ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.0115749730.988425
ENST00000347027ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.038975110.96102494
ENST00000347027ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.0590688180.94093114
ENST00000347027ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.12631420.87368584
ENST00000394229ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0498936440.9501064
ENST00000394229ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0065327190.9934673
ENST00000394229ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.011862770.9881372
ENST00000394229ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0139708110.9860292
ENST00000394229ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.043035290.9569647
ENST00000394229ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0268495620.9731504
ENST00000394229ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.0376191360.9623808
ENST00000394229ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.040550780.9594492
ENST00000394229ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.043153960.95684606
ENST00000394229ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.0118226550.98817736
ENST00000394229ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.041233460.9587665
ENST00000394229ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.0607197250.9392803
ENST00000394229ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.13271360.8672864
ENST00000257880ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0498936440.9501064
ENST00000257880ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0065327190.9934673
ENST00000257880ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.011862770.9881372
ENST00000257880ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0139708110.9860292
ENST00000257880ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.043035290.9569647
ENST00000257880ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0268495620.9731504
ENST00000257880ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.0376191360.9623808
ENST00000257880ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.040550780.9594492
ENST00000257880ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.043153960.95684606
ENST00000257880ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.0118226550.98817736
ENST00000257880ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.041233460.9587665
ENST00000257880ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.0607197250.9392803
ENST00000257880ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.13271360.8672864
ENST00000394230ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0498936440.9501064
ENST00000394230ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0065327190.9934673
ENST00000394230ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.011862770.9881372
ENST00000394230ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0139708110.9860292
ENST00000394230ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.043035290.9569647
ENST00000394230ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0268495620.9731504
ENST00000394230ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.0376191360.9623808
ENST00000394230ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.040550780.9594492
ENST00000394230ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.043153960.95684606
ENST00000394230ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.0118226550.98817736
ENST00000394230ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.041233460.9587665
ENST00000394230ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.0607197250.9392803
ENST00000394230ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.13271360.8672864
ENST00000555728ENST00000359282ITGA7chr1256096655-PCBP2chr1253856276+0.0491622760.95083773
ENST00000555728ENST00000603815ITGA7chr1256096655-PCBP2chr1253856276+0.0057110280.9942889
ENST00000555728ENST00000437231ITGA7chr1256096655-PCBP2chr1253856276+0.0096260760.99037397
ENST00000555728ENST00000447282ITGA7chr1256096655-PCBP2chr1253856276+0.0123844040.9876155
ENST00000555728ENST00000549863ITGA7chr1256096655-PCBP2chr1253856276+0.0420792030.9579208
ENST00000555728ENST00000359462ITGA7chr1256096655-PCBP2chr1253856276+0.0267161630.9732838
ENST00000555728ENST00000546463ITGA7chr1256096655-PCBP2chr1253856276+0.0406520930.9593479
ENST00000555728ENST00000552296ITGA7chr1256096655-PCBP2chr1253856276+0.044094580.9559054
ENST00000555728ENST00000552819ITGA7chr1256096655-PCBP2chr1253856276+0.0408168250.95918316
ENST00000555728ENST00000455667ITGA7chr1256096655-PCBP2chr1253856276+0.009565310.99043465
ENST00000555728ENST00000439930ITGA7chr1256096655-PCBP2chr1253856276+0.0449450870.9550549
ENST00000555728ENST00000548933ITGA7chr1256096655-PCBP2chr1253856276+0.056499670.94350034
ENST00000555728ENST00000541275ITGA7chr1256096655-PCBP2chr1253856276+0.146383230.8536168

check button 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

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Fusion Protein Breakpoint Sequences for ITGA7-PCBP2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ITGA7chr1256096655PCBP2chr1253856276433138VSVRSQGPGGKIVSPPKGVTIPYRPK
ITGA7chr1256096655PCBP2chr1253856276443138VSVRSQGPGGKIVSPPKGVTIPYRPK
ITGA7chr1256096655PCBP2chr1253856276616184VSVRSQGPGGKIVSPPKGVTIPYRPK
ITGA7chr1256096655PCBP2chr1253856276630184VSVRSQGPGGKIVSPPKGVTIPYRPK
ITGA7chr1256096655PCBP2chr1253856276634184VSVRSQGPGGKIVSPPKGVTIPYRPK

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Potential FusionNeoAntigen Information of ITGA7-PCBP2 in HLA I

check button 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.
ITGA7-PCBP2_56096655_53856276.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
ITGA7-PCBP2chr1256096655chr1253856276630HLA-B52:01VSPPKGVTI0.97250.51321221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A02:38KIVSPPKGV0.83420.59631019
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A30:08KIVSPPKGV0.830.90121019
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A02:13KIVSPPKGV0.75690.60081019
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A02:35KIVSPPKGV0.72910.5381019
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A02:20KIVSPPKGV0.72370.5211019
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C15:06VSPPKGVTI0.9950.84611221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:07VSPPKGVTI0.99450.95881221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C12:04VSPPKGVTI0.99180.98231221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C06:03VSPPKGVTI0.99170.97661221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C12:12VSPPKGVTI0.98440.75951221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C04:06VSPPKGVTI0.97320.63581221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:08VSPPKGVTI0.95220.71321221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C04:14VSPPKGVTI0.95210.59571221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:19VSPPKGVTI0.93250.96981221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:17VSPPKGVTI0.80360.86481221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:30VSPPKGVTI0.79530.89251221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C08:04VSPPKGVTI0.75340.85891221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C08:13VSPPKGVTI0.75340.85891221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C07:29VSPPKGVTI0.61280.80841221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C07:13VSPPKGVTI0.58070.70951221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C02:06VSPPKGVTI0.54010.88551221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C08:03VSPPKGVTI0.25660.93591221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:17IVSPPKGVTI0.97550.83051121
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:30IVSPPKGVTI0.94240.8621121
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:17KIVSPPKGVTI0.99370.84391021
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C15:05VSPPKGVTI0.99480.84821221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C15:02VSPPKGVTI0.99420.80511221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A30:01GGKIVSPPK0.99310.7794817
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:05VSPPKGVTI0.98860.7591221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C06:17VSPPKGVTI0.9870.98111221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C06:02VSPPKGVTI0.9870.98111221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:17VSPPKGVTI0.98620.92011221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C12:03VSPPKGVTI0.97770.93281221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:67VSPPKGVTI0.97550.94921221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C06:06VSPPKGVTI0.96970.98081221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C04:03VSPPKGVTI0.94250.63871221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C18:01VSPPKGVTI0.94190.62171221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:04VSPPKGVTI0.94170.97181221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:03VSPPKGVTI0.94170.97181221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C03:06VSPPKGVTI0.89370.97231221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-A02:03KIVSPPKGV0.88240.59731019
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C16:04VSPPKGVTI0.86330.91311221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C07:04VSPPKGVTI0.84440.78221221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C16:02VSPPKGVTI0.82290.98191221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:02VSPPKGVTI0.80260.84971221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:03VSPPKGVTI0.77790.78761221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C16:01VSPPKGVTI0.77230.94431221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-B57:02VSPPKGVTI0.69830.67711221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C06:08VSPPKGVTI0.61080.97341221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C08:01VSPPKGVTI0.25660.93591221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C17:01VSPPKGVTI0.24150.60561221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-B07:13VSPPKGVTI0.14070.50791221
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:03IVSPPKGVTI0.98550.80821121
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:02IVSPPKGVTI0.97440.82581121
ITGA7-PCBP2chr1256096655chr1253856276630HLA-B15:08VSPPKGVTIPY0.99930.5181223
ITGA7-PCBP2chr1256096655chr1253856276630HLA-B15:11VSPPKGVTIPY0.99930.51711223
ITGA7-PCBP2chr1256096655chr1253856276630HLA-C01:02KIVSPPKGVTI0.99480.84461021

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Potential FusionNeoAntigen Information of ITGA7-PCBP2 in HLA II

check button 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.

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of ITGA7-PCBP2

check button3D 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.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
3019GPGGKIVSPPKGVTITGA7PCBP2chr1256096655chr1253856276630

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ITGA7-PCBP2

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN3019GPGGKIVSPPKGVT-7.9962-8.1096
HLA-B14:023BVN3019GPGGKIVSPPKGVT-5.70842-6.74372
HLA-B52:013W393019GPGGKIVSPPKGVT-6.83737-6.95077
HLA-B52:013W393019GPGGKIVSPPKGVT-4.4836-5.5189
HLA-A11:014UQ23019GPGGKIVSPPKGVT-10.0067-10.1201
HLA-A11:014UQ23019GPGGKIVSPPKGVT-9.03915-10.0745
HLA-A24:025HGA3019GPGGKIVSPPKGVT-6.56204-6.67544
HLA-A24:025HGA3019GPGGKIVSPPKGVT-5.42271-6.45801
HLA-B44:053DX83019GPGGKIVSPPKGVT-7.85648-8.89178
HLA-B44:053DX83019GPGGKIVSPPKGVT-5.3978-5.5112
HLA-A02:016TDR3019GPGGKIVSPPKGVT-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ITGA7-PCBP2

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
ITGA7-PCBP2chr1256096655chr12538562761019KIVSPPKGVAAGATTGTTTCCCCCCCGAAGGGCGTG
ITGA7-PCBP2chr1256096655chr12538562761021KIVSPPKGVTIAAGATTGTTTCCCCCCCGAAGGGCGTGACCATC
ITGA7-PCBP2chr1256096655chr12538562761121IVSPPKGVTIATTGTTTCCCCCCCGAAGGGCGTGACCATC
ITGA7-PCBP2chr1256096655chr12538562761221VSPPKGVTIGTTTCCCCCCCGAAGGGCGTGACCATC
ITGA7-PCBP2chr1256096655chr12538562761223VSPPKGVTIPYGTTTCCCCCCCGAAGGGCGTGACCATCCCGTAC
ITGA7-PCBP2chr1256096655chr1253856276817GGKIVSPPKGGGGGCAAGATTGTTTCCCCCCCGAAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of ITGA7-PCBP2

check button 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 typeFusion geneHchrHbpHenstTchrTbpTenstSample
STADITGA7-PCBP2chr1256096655ENST00000257879chr1253856276ENST00000359282TCGA-RD-A8N4

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Potential target of CAR-T therapy development for ITGA7-PCBP2

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention 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'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button 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.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to ITGA7-PCBP2

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

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Related Diseases to ITGA7-PCBP2

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource