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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:TMX1-TRIM9 (FusionGDB2 ID:92555)

Fusion Gene Summary for TMX1-TRIM9

check button Fusion gene summary
Fusion gene informationFusion gene name: TMX1-TRIM9
Fusion gene ID: 92555
HgeneTgene
Gene symbol

TMX1

TRIM9

Gene ID

81542

114088

Gene namethioredoxin related transmembrane protein 1tripartite motif containing 9
SynonymsPDIA11|TMX|TXNDC|TXNDC1RNF91|SPRING
Cytomap

14q22.1

14q22.1

Type of geneprotein-codingprotein-coding
Descriptionthioredoxin-related transmembrane protein 1protein disulfide isomerase family A, member 11thioredoxin domain containing 1thioredoxin domain-containing protein 1transmembrane Trx-related proteinE3 ubiquitin-protein ligase TRIM9RING finger protein 91RING-type E3 ubiquitin transferase TRIM9SNAP-25-interacting RING finger proteinhomolog of rat RING finger Springtripartite motif-containing protein 9
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000457354, ENST00000338969, 
ENST00000360392, ENST00000557456, 
ENST00000298355, 
Fusion gene scores* DoF score4 X 3 X 4=485 X 4 X 5=100
# samples 45
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TMX1 [Title/Abstract] AND TRIM9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTMX1(51710689)-TRIM9(51467558), # samples:3
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneTRIM9

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

20085810


check buttonFusion gene breakpoints across TMX1 (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 TRIM9 (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 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SKCMTCGA-GN-A265-06ATMX1chr14

51710689

-TRIM9chr14

51467558

-
ChimerDB4SKCMTCGA-GN-A265-06ATMX1chr14

51710689

+TRIM9chr14

51467558

-


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Fusion Gene ORF analysis for TMX1-TRIM9

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-intronENST00000457354ENST00000338969TMX1chr14

51710689

+TRIM9chr14

51467558

-
5CDS-intronENST00000457354ENST00000360392TMX1chr14

51710689

+TRIM9chr14

51467558

-
5CDS-intronENST00000457354ENST00000557456TMX1chr14

51710689

+TRIM9chr14

51467558

-
In-frameENST00000457354ENST00000298355TMX1chr14

51710689

+TRIM9chr14

51467558

-

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)
ENST00000457354TMX1chr1451710689+ENST00000298355TRIM9chr1451467558-32493931251219364

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
ENST00000457354ENST00000298355TMX1chr1451710689+TRIM9chr1451467558-0.0001877170.9998123

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Fusion Genomic Features for TMX1-TRIM9


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)

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.

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Fusion Protein Features for TMX1-TRIM9


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/chr14:51710689/chr14:51467558)
- 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
TgeneTRIM9chr14:51710689chr14:51467558ENST00000338969012273_3400803.0Coiled coilOntology_term=ECO:0000255
TgeneTRIM9chr14:51710689chr14:51467558ENST00000298355410440_535435711.0DomainFibronectin type-III
TgeneTRIM9chr14:51710689chr14:51467558ENST00000298355410533_702435711.0DomainB30.2/SPRY
TgeneTRIM9chr14:51710689chr14:51467558ENST00000338969012374_4320803.0DomainCOS
TgeneTRIM9chr14:51710689chr14:51467558ENST00000338969012440_5350803.0DomainFibronectin type-III
TgeneTRIM9chr14:51710689chr14:51467558ENST00000338969012533_7020803.0DomainB30.2/SPRY
TgeneTRIM9chr14:51710689chr14:51467558ENST0000036039247440_535435551.0DomainFibronectin type-III
TgeneTRIM9chr14:51710689chr14:51467558ENST0000036039247533_702435551.0DomainB30.2/SPRY
TgeneTRIM9chr14:51710689chr14:51467558ENST0000033896901210_500803.0Zinc fingerRING-type
TgeneTRIM9chr14:51710689chr14:51467558ENST00000338969012163_2120803.0Zinc fingerB box-type 1
TgeneTRIM9chr14:51710689chr14:51467558ENST00000338969012224_2660803.0Zinc fingerB box-type 2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTMX1chr14:51710689chr14:51467558ENST00000457354+2827_13289281.0DomainThioredoxin
HgeneTMX1chr14:51710689chr14:51467558ENST00000457354+28204_28089281.0Topological domainCytoplasmic
HgeneTMX1chr14:51710689chr14:51467558ENST00000457354+2827_18089281.0Topological domainExtracellular
HgeneTMX1chr14:51710689chr14:51467558ENST00000457354+28181_20389281.0TransmembraneHelical
TgeneTRIM9chr14:51710689chr14:51467558ENST00000298355410273_340435711.0Coiled coilOntology_term=ECO:0000255
TgeneTRIM9chr14:51710689chr14:51467558ENST0000036039247273_340435551.0Coiled coilOntology_term=ECO:0000255
TgeneTRIM9chr14:51710689chr14:51467558ENST00000298355410374_432435711.0DomainCOS
TgeneTRIM9chr14:51710689chr14:51467558ENST0000036039247374_432435551.0DomainCOS
TgeneTRIM9chr14:51710689chr14:51467558ENST0000029835541010_50435711.0Zinc fingerRING-type
TgeneTRIM9chr14:51710689chr14:51467558ENST00000298355410163_212435711.0Zinc fingerB box-type 1
TgeneTRIM9chr14:51710689chr14:51467558ENST00000298355410224_266435711.0Zinc fingerB box-type 2
TgeneTRIM9chr14:51710689chr14:51467558ENST000003603924710_50435551.0Zinc fingerRING-type
TgeneTRIM9chr14:51710689chr14:51467558ENST0000036039247163_212435551.0Zinc fingerB box-type 1
TgeneTRIM9chr14:51710689chr14:51467558ENST0000036039247224_266435551.0Zinc fingerB box-type 2


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Fusion Gene Sequence for TMX1-TRIM9


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.
>92555_92555_1_TMX1-TRIM9_TMX1_chr14_51710689_ENST00000457354_TRIM9_chr14_51467558_ENST00000298355_length(transcript)=3249nt_BP=393nt
ATGCGCATTGAGAGTCCTCTAGACAGGCGCTCCTCGCAGCACCGTAGTGCGCTTGCGCTGAGCAGCCCGCGAGGGCGGAAGTGGGAGCTG
CGACCGCGCTCCCTGTGAGGTGGGCAAGCGGCGAAATGGCGCCCTCCGGGAGTCTTGCAGTTCCCCTGGCAGTCCTGGTGCTGTTGCTTT
GGGGTGCTCCCTGGACGCACGGGCGGCGGAGCAACGTTCGCGTCATCACGGACGAGAACTGGAGAGAACTGCTGGAAGGAGACTGGATGA
TAGAATTTTATGCCCCGTGGTGCCCTGCTTGTCAAAATCTTCAACCGGAATGGGAAAGTTTTGCTGAATGGGGAGAAGATCTTGAGGTTA
ATATTGCGAAAGTAGATGTCACAGAGCAGCCAGCTTCCTCTCCAGTCCCAGCAACCCCTATCCTACAGCTGGAGGAATGTTGTACCCACA
ACAACAGCGCTACGTTGTCCTGGAAACAGCCACCTCTGTCCACGGTGCCCGCCGATGGATACATTCTGGAGCTGGATGATGGCAACGGTG
GTCAATTCCGGGAGGTGTATGTGGGGAAGGAGACAATGTGCACTGTGGATGGTCTTCACTTCAACAGCACATACAACGCTCGGGTCAAGG
CCTTCAACAAAACAGGAGTCAGCCCGTACAGCAAGACCCTGGTCCTCCAAACGTCTGAGGTGGCCTGGTTTGCTTTCGACCCTGGCTCGG
CGCACTCGGACATCATCCTCTCCAATGACAACCTGACAGTGACCTGTAGTAGCTATGATGACCGGGTGGTGCTAGGGAAGACTGGCTTCT
CCAAGGGCATCCACTACTGGGAGCTCACGGTAGATCGCTATGACAACCACCCTGATCCTGCCTTTGGTGTGGCTCGCATGGACGTGATGA
AGGATGTGATGTTAGGAAAAGACGACAAAGCTTGGGCAATGTATGTGGACAATAACCGGAGCTGGTTCATGCACAACAACTCGCACACCA
ACAGAACTGAGGGAGGGATCACAAAAGGGGCCACAATTGGGGTCCTCCTCGACTTAAATAGAAAAAACTTGACATTTTTTATCAACGATG
AACAACAAGGTCCCATAGCATTTGATAACGTGGAGGGCCTCTTCTTCCCTGCGGTCAGCCTGAACAGGAACGTGCAGGTCACGCTGCACA
CCGGGCTCCCAGTCCCCGACTTCTACTCCAGCAGAGCATCAATAGCCTAAGGATGTGCCGTGGAGGCGCCAGCTGCCTGTTCTTACCTCC
GCCTGCGAGAGCCACAGCAAGGAGCTCAGCCAGCCGTGGTGGGGTGCAGAGTTGGCAGGAGTGGGAGAAGGAGGAGAGAAAAGCTGGTCC
TCTGCAGTCTTTACACCCACAGCTCTGCCCTTTTCCCTTTCAACCTCTCCTCCGCTGTCATGCCTGCTTCCGCTTCCATGTCCAACAATT
CTAACCAACAAAGGACCTAGACAGCCCACCAAGTCACTTGGTTCCCACTCCCAGATTTTGCTTTTATTTAACTTAATTTTTTATGTAGGT
GAGTTATATTTTCTTTCTTTTCTGATCAGGTTATTGGTGACTTACTGGACTGGCACCGCCAGGAGAAAATTCTCCTGCTAACTTTTTTTC
TTAAGCTTTCTGTCAAACAATGAGGTTGTAGGGGGAGGTAGGGAAGAATGAGCTGAATTTGTAGCATACAGCTTACCTGCTAGAATGTTC
TTACCCTCTTACCTCTCCTGTAGCGTTAGCTCTGCAGAGCTAAGCTTTGGGAGAATGAATCTATCACTGAGAAGTTTTACTACTCATTGA
AGCACAAAAATATCCGCTACACAGGTTCACATCAGGGTAGGATCGTTAGGATGGCTCTATAATTAGGATAGGCCAGAACCCTGGCCACTG
TATAAAATTGGAAAGTCTCTAAGACACAGGCAAACCAGGGGACTTAATGATTTGGTTCGTTTATTTAATAAAAGCTTTTAATTGAGAACC
TACTATTGACCAGGCACTGTTCAAGACACTAGAACATTATGTTCTAGACACTGTGGGGACACAGTGGTGAACAGACAGGCATGGTCTCTG
CCCTTCGGAGCTTATATTCCAGTAGGAGAAAAAGCAAAAATAAAATAATTATAAATGGTCATATGTACTAGAAAGGAAATGGGCAAGGGT
CAAAGAGACTCATGGGCAAGATCTTTCAGGCTTCCTAGAATGATGCTAAAAATCCACACATTCTGGCCATAGCACCAGAAATGTACCAAC
TCAATGCCTTTTCAGCTGCACTATTTAATTATGGTACCTGCTGCCACTCATCACAGAGCCCTTCTTGGTAGAAATGATGTCAGCATTCTT
ATTTGCTGATGCTGCTATGATACCACGCCTTAAAAATTGACAGTTGAAAAAAAAAAGAGTGACCAGAGGGCAAAGGACCCATTCTCAGTA
ATGGGAGATCTTGAGTTGCAGTCCACAGCATTCACATTCTCAGGATAAACATGCTTGTCTCCATATATACTATCTGTGCCTGTTATGAAT
GAAAAATCCATCCACTCTGCTGCCATTCACAGCCTAATTTTCTGGAGTAGTCCAAACAATGTTTGGAAAAACATGGGACTGTATGTCATT
ACTATGACTGATAGCAGAATAATAATGCATCTTACTTCTATATAGAGATAGACTTACATAGGTTACCCTTGAAATTCATTAGTTTGTCAT
AAAGTTTTAGGAAAGGTAGGACCCGGAAAGAAGTTCTAATTAGTTGTCTAAATATTTTTCAGTGAGCCAAGAAATTCACCATGAAAAAAC
AAGAATAACAAATAGAAGGGAAGAGATAGGATGGGAAAGCTAACAAATTAAAGTTTTGGCAAAAAGGAATATATGTAAATAGCTAATTAT
TTACTTTTGTGCTTACTTTATTTAGATTATTTCTATCAGTTACAATCTTTTTCTAGTTAAGTGTACCTAATTTATGGAATGGGTGCTATC
CTGTTTATGTGTGTCTTGGTTTTTCTTGGCTACAGAAAAACTGTTGCAGGGCAACACTAGTTTGATATTTGATTTACTCTCCAATGAGAC
TCAATGGCTGGGCCGTGGTAGACTCATAGTTCCTCTTGTTCTTTATTAAATTCATCCTGCTAATTAGATTTCTAGTGACTTGTAACATGT
AGTTTACACTGAATTGCAATTACAGATGCATACAACTACTATACTAGAAAAAATTGTCATTTCTGATGTGCCAATAAATGATTTTTATGA

>92555_92555_1_TMX1-TRIM9_TMX1_chr14_51710689_ENST00000457354_TRIM9_chr14_51467558_ENST00000298355_length(amino acids)=364AA_BP=89
MAPSGSLAVPLAVLVLLLWGAPWTHGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEWESFAEWGEDLEVNIAKVDVTEQPA
SSPVPATPILQLEECCTHNNSATLSWKQPPLSTVPADGYILELDDGNGGQFREVYVGKETMCTVDGLHFNSTYNARVKAFNKTGVSPYSK
TLVLQTSEVAWFAFDPGSAHSDIILSNDNLTVTCSSYDDRVVLGKTGFSKGIHYWELTVDRYDNHPDPAFGVARMDVMKDVMLGKDDKAW
AMYVDNNRSWFMHNNSHTNRTEGGITKGATIGVLLDLNRKNLTFFINDEQQGPIAFDNVEGLFFPAVSLNRNVQVTLHTGLPVPDFYSSR

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Fusion Gene PPI Analysis for TMX1-TRIM9


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 TMX1-TRIM9


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 TMX1-TRIM9


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