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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:C1orf35-PGA4 (FusionGDB2 ID:HG79169TG643847)

Fusion Gene Summary for C1orf35-PGA4

check button Fusion gene summary
Fusion gene informationFusion gene name: C1orf35-PGA4
Fusion gene ID: hg79169tg643847
HgeneTgene
Gene symbol

C1orf35

PGA4

Gene ID

79169

643847

Gene namechromosome 1 open reading frame 35pepsinogen A4
SynonymsMMTAG2-
Cytomap('C1orf35')('PGA4')

1q42.13

11q12.2

Type of geneprotein-codingprotein-coding
Descriptionmultiple myeloma tumor-associated protein 2multiple myeloma transforming 2pepsin A-4pepsinogen 4, group I (pepsinogen A)pepsinogen-4pregnancy-associated glycoprotein
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000272139, ENST00000472617, 
Fusion gene scores* DoF score3 X 2 X 2=1212 X 27 X 5=1620
# samples 214
** MAII scorelog2(2/12*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(14/1620*10)=-3.53249508082702
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: C1orf35 [Title/Abstract] AND PGA4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC1orf35(228290835)-PGA4(60992809), # samples:1
Anticipated loss of major functional domain due to fusion event.C1orf35-PGA4 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.
C1orf35-PGA4 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.
C1orf35-PGA4 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.
C1orf35-PGA4 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

check buttonFusion gene breakpoints across C1orf35 (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 PGA4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4ESCATCGA-JY-A939C1orf35chr1

228290835

-PGA4chr11

60992809

+


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Fusion Gene ORF analysis for C1orf35-PGA4

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-intronENST00000272139ENST00000537932C1orf35chr1

228290835

-PGA4chr11

60992809

+
5CDS-intronENST00000272139ENST00000544899C1orf35chr1

228290835

-PGA4chr11

60992809

+
5UTR-3CDSENST00000472617ENST00000378149C1orf35chr1

228290835

-PGA4chr11

60992809

+
5UTR-3CDSENST00000472617ENST00000422676C1orf35chr1

228290835

-PGA4chr11

60992809

+
5UTR-intronENST00000472617ENST00000537932C1orf35chr1

228290835

-PGA4chr11

60992809

+
5UTR-intronENST00000472617ENST00000544899C1orf35chr1

228290835

-PGA4chr11

60992809

+
In-frameENST00000272139ENST00000378149C1orf35chr1

228290835

-PGA4chr11

60992809

+
In-frameENST00000272139ENST00000422676C1orf35chr1

228290835

-PGA4chr11

60992809

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000272139C1orf35chr1228290835-ENST00000378149PGA4chr1160992809+16733293021276324
ENST00000272139C1orf35chr1228290835-ENST00000422676PGA4chr1160992809+14533293021276324

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
ENST00000272139ENST00000378149C1orf35chr1228290835-PGA4chr1160992809+0.004036170.9959638
ENST00000272139ENST00000422676C1orf35chr1228290835-PGA4chr1160992809+0.0048432950.9951567

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Fusion Genomic Features for C1orf35-PGA4


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
C1orf35chr1228290834-PGA4chr1160992810+0.0017986830.99820125
C1orf35chr1228290834-PGA4chr1160992810+0.0017986830.99820125

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for C1orf35-PGA4


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/chr1:228290835/chr11:60992809)
- 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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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, 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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgenePGA4chr1:228290835chr11:60992809ENST000003781491976_38573389.0DomainPeptidase A1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneC1orf35chr1:228290835chr11:60992809ENST00000272139-18184_20631264.0Compositional biasNote=Lys-rich
HgeneC1orf35chr1:228290835chr11:60992809ENST00000272139-18226_22931264.0Compositional biasNote=Poly-His


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Fusion Gene Sequence for C1orf35-PGA4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>11361_11361_1_C1orf35-PGA4_C1orf35_chr1_228290835_ENST00000272139_PGA4_chr11_60992809_ENST00000378149_length(transcript)=1673nt_BP=329nt
AGGCGCAGTGCGCAGGCGCCCAAAGCCGACGTGGAGGTGATGCGCGGGAGCACAGATCCGGGGCAGTGCGCTGCGCAGAGGCGCGCGGCG
AAGCCGAGTGGGCGCGGGAGTGACGTCACGGCGCGCGACGCGGAGGCGGGGTCGGGCCTGGGTCCGACGGTAGTGGGTAGCGGGTCTCGG
GTTGCGGGTTGCAGGTTGCAAGCCGCAGGCCCCAGGCAACTGCCTTCCCGGCGCCATGTTCGGCTCCAGTCGTGGAGGCGTGCGCGGCGG
GCAGGACCAGTTCAACTGGGAGGACGTGAAGACTGACAAGCAGCGGGAGAACTACCTGGATGGAGTACTTCGGCACTATCGGCATCGGAA
CTCCTGCCCAGGATTTCACCGTCGTCTTTGACACCGGCTCCTCCAACCTGTGGGTGCCCTCAGTCTACTGCTCCAGTCTTGCCTGCACCA
ACCACAACCGCTTCAACCCTGAGGATTCTTCCACCTACCAGTCCACCAGCGAGACAGTCTCCATCACCTACGGCACCGGCAGCATGACAG
GCATCCTCGGATACGACACTGTCCAGGTTGGAGGCATCTCTGACACCAATCAGATCTTCGGCCTGAGCGAGACGGAACCTGGCTCCTTCC
TGTATTATGCTCCCTTCGATGGCATCCTGGGGCTGGCCTACCCCAGCATTTCCTCCTCCGGGGCCACACCCGTCTTTGACAACATCTGGA
ACCAGGGCCTGGTTTCTCAGGACCTCTTCTCTGTCTACCTCAGCGCCGATGACCAGAGTGGCAGCGTGGTGATCTTTGGTGGCATTGACT
CTTCTTACTACACTGGAAGTCTGAACTGGGTGCCTGTTACCGTCGAGGGTTACTGGCAGATCACCGTGGACAGCATCACCATGAACGGAG
AGGCCATCGCCTGCGCTGAGGGCTGCCAGGCCATTGTTGACACCGGCACCTCTCTGCTGACCGGCCCAACCAGCCCCATTGCCAACATCC
AGAGCGACATCGGAGCCAGCGAGAACTCAGATGGCGACATGGTGGTCAGCTGCTCAGCCATCAGCAGCCTGCCCGACATCGTCTTCACCA
TCAATGGAGTCCAGTACCCCGTGCCACCCAGTGCCTACATCCTGCAGAGCGAGGGGAGCTGCATCAGTGGCTTCCAGGGCATGAACCTCC
CCACCGAATCTGGAGAGCTTTGGATCCTGGGTGATGTCTTCATCCGCCAGTACTTTACCGTCTTCGACAGGGCAAACAACCAGGTCGGCC
TGGCCCCCGTGGCTTAAGCCTAAGTCTCTTCAGCCACCTCCCAGGAAGATCTGGCCTCTGTCCTGTGCCCACTTTAGATGTATCTAATTC
TCCTGACTGTTCTTCCCAGGGGAGTGTGGAGGTCTTGGCCCTGTTCCCTGTCCTACCAATAACGTAGAATAAAAACATAACCCACTGAAA
CAGGTTTTGTGGAGCTGCTTCTCTTTGCTGGTCTTTTTCCTTCACATTACTGGGGTTAGAACGCCAGGGCAGGGATGAAAATGACCACAT
CCATTTGGATGGCACCCAACATAGTGACCCCAGCAGCTGACACTTCATGATGGAGCCAAGAAGACAGAGAGGCTTCGGGGGTTGTGCTGG

>11361_11361_1_C1orf35-PGA4_C1orf35_chr1_228290835_ENST00000272139_PGA4_chr11_60992809_ENST00000378149_length(amino acids)=324AA_BP=9
MTSSGRTTWMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTNHNRFNPEDSSTYQSTSETVSITYGTGSMTGILGYDTVQVG
GISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISSSGATPVFDNIWNQGLVSQDLFSVYLSADDQSGSVVIFGGIDSSYYTGSLNWV
PVTVEGYWQITVDSITMNGEAIACAEGCQAIVDTGTSLLTGPTSPIANIQSDIGASENSDGDMVVSCSAISSLPDIVFTINGVQYPVPPS

--------------------------------------------------------------
>11361_11361_2_C1orf35-PGA4_C1orf35_chr1_228290835_ENST00000272139_PGA4_chr11_60992809_ENST00000422676_length(transcript)=1453nt_BP=329nt
AGGCGCAGTGCGCAGGCGCCCAAAGCCGACGTGGAGGTGATGCGCGGGAGCACAGATCCGGGGCAGTGCGCTGCGCAGAGGCGCGCGGCG
AAGCCGAGTGGGCGCGGGAGTGACGTCACGGCGCGCGACGCGGAGGCGGGGTCGGGCCTGGGTCCGACGGTAGTGGGTAGCGGGTCTCGG
GTTGCGGGTTGCAGGTTGCAAGCCGCAGGCCCCAGGCAACTGCCTTCCCGGCGCCATGTTCGGCTCCAGTCGTGGAGGCGTGCGCGGCGG
GCAGGACCAGTTCAACTGGGAGGACGTGAAGACTGACAAGCAGCGGGAGAACTACCTGGATGGAGTACTTCGGCACTATCGGCATCGGAA
CTCCTGCCCAGGATTTCACCGTCGTCTTTGACACCGGCTCCTCCAACCTGTGGGTGCCCTCAGTCTACTGCTCCAGTCTTGCCTGCACCA
ACCACAACCGCTTCAACCCTGAGGATTCTTCCACCTACCAGTCCACCAGCGAGACAGTCTCCATCACCTACGGCACCGGCAGCATGACAG
GCATCCTCGGATACGACACTGTCCAGGTTGGAGGCATCTCTGACACCAATCAGATCTTCGGCCTGAGCGAGACGGAACCTGGCTCCTTCC
TGTATTATGCTCCCTTCGATGGCATCCTGGGGCTGGCCTACCCCAGCATTTCCTCCTCCGGGGCCACACCCGTCTTTGACAACATCTGGA
ACCAGGGCCTGGTTTCTCAGGACCTCTTCTCTGTCTACCTCAGCGCCGATGACAAGAGTGGCAGCGTGGTGATCTTTGGTGGCATTGACT
CTTCTTACTACACTGGAAGTCTGAACTGGGTGCCTGTTACCGTCGAGGGTTACTGGCAGATCACCGTGGACAGCATCACCATGAACGGAG
AGACCATCGCCTGTGCTGAGGGCTGCCAGGCCATTGTTGACACCGGCACCTCTCTGCTGACCGGCCCAACCAGCCCCATTGCCAACATCC
AGAGCGACATCGGAGCCAGCGAGAACTCAGATGGCGACATGGTGGTCAGCTGCTCAGCCATCAGCAGCCTGCCCGACATCGTCTTCACCA
TCAATGGAGTCCAGTACCCCGTGCCACCCAGTGCCTACATCCTGCAGAGCGAGGGGAGCTGCATCAGTGGCTTCCAGGGCATGAACGTCC
CCACCGAATCTGGAGAGCTTTGGATCCTGGGTGATGTCTTCATCCGCCAGTACTTTACCGTCTTCGACAGGGCAAACAACCAGGTCGGCC
TGGCCCCTGTGGCTTAAGCCTAAGTCTCTTCAGCCACCTCCCAGGAAGATCTGGCCTCCGTCCTATGCCCACTTTAGATGTATCTAATTC
TCCTGACTGTTCTTCCCAGGGGAGTGTGAAGGTCTTGGCCCTGTTCCCTGTCCTACCAATAACGTAGAATAAAAACATAACCCACTGAAA

>11361_11361_2_C1orf35-PGA4_C1orf35_chr1_228290835_ENST00000272139_PGA4_chr11_60992809_ENST00000422676_length(amino acids)=324AA_BP=9
MTSSGRTTWMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTNHNRFNPEDSSTYQSTSETVSITYGTGSMTGILGYDTVQVG
GISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISSSGATPVFDNIWNQGLVSQDLFSVYLSADDKSGSVVIFGGIDSSYYTGSLNWV
PVTVEGYWQITVDSITMNGETIACAEGCQAIVDTGTSLLTGPTSPIANIQSDIGASENSDGDMVVSCSAISSLPDIVFTINGVQYPVPPS

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

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Fusion Gene PPI Analysis for C1orf35-PGA4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for C1orf35-PGA4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for C1orf35-PGA4


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