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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:BCAM-MRPL9 (FusionGDB2 ID:HG4059TG65005)

Fusion Gene Summary for BCAM-MRPL9

check button Fusion gene summary
Fusion gene informationFusion gene name: BCAM-MRPL9
Fusion gene ID: hg4059tg65005
HgeneTgene
Gene symbol

BCAM

MRPL9

Gene ID

4059

65005

Gene namebasal cell adhesion molecule (Lutheran blood group)mitochondrial ribosomal protein L9
SynonymsAU|CD239|LU|MSK19L9mt
Cytomap('BCAM')('MRPL9')

19q13.32

1q21.3

Type of geneprotein-codingprotein-coding
Descriptionbasal cell adhesion moleculeAuberger b antigenB-CAM cell surface glycoproteinB-cell adhesion moleculeF8/G253 antigenLutheran blood group variant LUGAbasal cell adhesion molecule (Lu and Au blood groups)39S ribosomal protein L9, mitochondrialmitochondrial large ribosomal subunit protein bL9m
Modification date2020031320200313
UniProtAcc.

Q9BYD2

Ensembl transtripts involved in fusion geneENST00000270233, ENST00000589651, 
Fusion gene scores* DoF score12 X 12 X 6=8647 X 6 X 5=210
# samples 127
** MAII scorelog2(12/864*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCAM [Title/Abstract] AND MRPL9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCAM(45315805)-MRPL9(151734028), # samples:1
Anticipated loss of major functional domain due to fusion event.BCAM-MRPL9 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.
BCAM-MRPL9 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.
BCAM-MRPL9 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.
BCAM-MRPL9 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 BCAM (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 MRPL9 (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
ChimerDB4STADTCGA-CD-8525-01ABCAMchr19

45315805

+MRPL9chr1

151734028

-


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Fusion Gene ORF analysis for BCAM-MRPL9

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-5UTRENST00000270233ENST00000467306BCAMchr19

45315805

+MRPL9chr1

151734028

-
5CDS-5UTRENST00000589651ENST00000467306BCAMchr19

45315805

+MRPL9chr1

151734028

-
5CDS-intronENST00000270233ENST00000368829BCAMchr19

45315805

+MRPL9chr1

151734028

-
5CDS-intronENST00000589651ENST00000368829BCAMchr19

45315805

+MRPL9chr1

151734028

-
In-frameENST00000270233ENST00000368830BCAMchr19

45315805

+MRPL9chr1

151734028

-
In-frameENST00000589651ENST00000368830BCAMchr19

45315805

+MRPL9chr1

151734028

-

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)
ENST00000589651BCAMchr1945315805+ENST00000368830MRPL9chr1151734028-128355854875273
ENST00000270233BCAMchr1945315805+ENST00000368830MRPL9chr1151734028-125152622843273

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
ENST00000589651ENST00000368830BCAMchr1945315805+MRPL9chr1151734028-0.0035831490.9964168
ENST00000270233ENST00000368830BCAMchr1945315805+MRPL9chr1151734028-0.0029115670.9970885

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Fusion Genomic Features for BCAM-MRPL9


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

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Fusion Protein Features for BCAM-MRPL9


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/chr19:45315805/chr1:151734028)
- 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
.MRPL9

Q9BYD2

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
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+41532_142168629.0DomainNote=Ig-like V-type 1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415147_257168629.0DomainNote=Ig-like V-type 2
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415274_355168629.0DomainNote=Ig-like C2-type 1
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415363_441168629.0DomainNote=Ig-like C2-type 2
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415448_541168629.0DomainNote=Ig-like C2-type 3
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+41532_547168629.0Topological domainExtracellular
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415569_628168629.0Topological domainCytoplasmic
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415548_568168629.0TransmembraneHelical


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Fusion Gene Sequence for BCAM-MRPL9


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.
>9139_9139_1_BCAM-MRPL9_BCAM_chr19_45315805_ENST00000270233_MRPL9_chr1_151734028_ENST00000368830_length(transcript)=1251nt_BP=526nt
AGTCTCCGCCGCCGCCGTGAACATGGAGCCCCCGGACGCACCGGCCCAGGCGCGCGGGGCCCCGCGGCTGCTGTTGCTCGCAGTCCTGCT
GGCGGCGCACCCAGATGCCCAGGCGGAGGTGCGCTTGTCTGTACCCCCGCTGGTGGAGGTGATGCGAGGAAAGTCTGTCATTCTGGACTG
CACCCCTACGGGAACCCACGACCATTATATGCTGGAATGGTTCCTTACCGACCGCTCGGGAGCTCGCCCCCGCCTAGCCTCGGCTGAGAT
GCAGGGCTCTGAGCTCCAGGTCACAATGCACGACACCCGGGGCCGCAGTCCCCCATACCAGCTGGACTCCCAGGGGCGCCTGGTGCTGGC
TGAGGCCCAGGTGGGCGACGAGCGAGACTACGTGTGCGTGGTGAGGGCAGGGGCGGCAGGCACTGCTGAGGCCACTGCGCGGCTCAACGT
GTTTGCAAAGCCAGAGGCCACTGAGGTCTCCCCCAACAAAGGGACACTGTCTGTGATGGAGGACTCTGCCCAGGAGACAGTGAAATTTCT
AAAAAGCTGTCGCCTGGAGGTAGGGATGAAGAACAATGTCAAATGGGAGCTGAACCCTGAAATAGTTGCCCGCCACTTCTTTAAGAATCT
TGGTGTTGTGGTTGCCCCACATACATTAAAGTTACCAGAAGAGCCTATCACACGGTGGGGCGAGTATTGGTGTGAGGTGACGGTAAATGG
GCTTGATACTGTGAGAGTGCCTATGTCTGTCGTGAACTTTGAGAAGCCCAAGACCAAAAGATATAAGTACTGGTTAGCCCAGCAAGCTGC
CAAGGCTATGGCCCCCACCAGCCCCCAGATCTAAATCTACTCTCCCTCCAAGGCAGCAAAGCAGAATCGGGAGCAGTGGAGCAGAAATGT
GCAAGCACCCTGATCTCACTCCCAGCTCTGACCAAATACAGAATTTTAGAGAACATCTGAAGACATCAGACTGCACTGCGTATACATGTT
GAATTCTTCATTTTTGCCATCTTTAACTGTCATCACTGGGGCAGGGAAGTCCTGTTCCAGAAGTACCAGGCTGTAGATTTGATAAGCTAG
ATGCAGTAGACCGAAACCATCCAAAACCTGTTTAGCTTCTTCCTCCATTGGAGTTTATTGGGACAAACAGGAGAGCCAGCCATTGTCTCC

>9139_9139_1_BCAM-MRPL9_BCAM_chr19_45315805_ENST00000270233_MRPL9_chr1_151734028_ENST00000368830_length(amino acids)=273AA_BP=163
MEPPDAPAQARGAPRLLLLAVLLAAHPDAQAEVRLSVPPLVEVMRGKSVILDCTPTGTHDHYMLEWFLTDRSGARPRLASAEMQGSELQV
TMHDTRGRSPPYQLDSQGRLVLAEAQVGDERDYVCVVRAGAAGTAEATARLNVFAKPEATEVSPNKGTLSVMEDSAQETVKFLKSCRLEV
GMKNNVKWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWLAQQAAKAMAPTS

--------------------------------------------------------------
>9139_9139_2_BCAM-MRPL9_BCAM_chr19_45315805_ENST00000589651_MRPL9_chr1_151734028_ENST00000368830_length(transcript)=1283nt_BP=558nt
GCCCCGCAGCGGCCGAGCTGCAGCCCGGGCTCAGTCTCCGCCGCCGCCGTGAACATGGAGCCCCCGGACGCACCGGCCCAGGCGCGCGGG
GCCCCGCGGCTGCTGTTGCTCGCAGTCCTGCTGGCGGCGCACCCAGATGCCCAGGCGGAGGTGCGCTTGTCTGTACCCCCGCTGGTGGAG
GTGATGCGAGGAAAGTCTGTCATTCTGGACTGCACCCCTACGGGAACCCACGACCATTATATGCTGGAATGGTTCCTTACCGACCGCTCG
GGAGCTCGCCCCCGCCTAGCCTCGGCTGAGATGCAGGGCTCTGAGCTCCAGGTCACAATGCACGACACCCGGGGCCGCAGTCCCCCATAC
CAGCTGGACTCCCAGGGGCGCCTGGTGCTGGCTGAGGCCCAGGTGGGCGACGAGCGAGACTACGTGTGCGTGGTGAGGGCAGGGGCGGCA
GGCACTGCTGAGGCCACTGCGCGGCTCAACGTGTTTGCAAAGCCAGAGGCCACTGAGGTCTCCCCCAACAAAGGGACACTGTCTGTGATG
GAGGACTCTGCCCAGGAGACAGTGAAATTTCTAAAAAGCTGTCGCCTGGAGGTAGGGATGAAGAACAATGTCAAATGGGAGCTGAACCCT
GAAATAGTTGCCCGCCACTTCTTTAAGAATCTTGGTGTTGTGGTTGCCCCACATACATTAAAGTTACCAGAAGAGCCTATCACACGGTGG
GGCGAGTATTGGTGTGAGGTGACGGTAAATGGGCTTGATACTGTGAGAGTGCCTATGTCTGTCGTGAACTTTGAGAAGCCCAAGACCAAA
AGATATAAGTACTGGTTAGCCCAGCAAGCTGCCAAGGCTATGGCCCCCACCAGCCCCCAGATCTAAATCTACTCTCCCTCCAAGGCAGCA
AAGCAGAATCGGGAGCAGTGGAGCAGAAATGTGCAAGCACCCTGATCTCACTCCCAGCTCTGACCAAATACAGAATTTTAGAGAACATCT
GAAGACATCAGACTGCACTGCGTATACATGTTGAATTCTTCATTTTTGCCATCTTTAACTGTCATCACTGGGGCAGGGAAGTCCTGTTCC
AGAAGTACCAGGCTGTAGATTTGATAAGCTAGATGCAGTAGACCGAAACCATCCAAAACCTGTTTAGCTTCTTCCTCCATTGGAGTTTAT
TGGGACAAACAGGAGAGCCAGCCATTGTCTCCAGTACTTGCCTCATTCTCATCATCCAAACTGAACATTTGTATCCCAAGCAGAAATAAA

>9139_9139_2_BCAM-MRPL9_BCAM_chr19_45315805_ENST00000589651_MRPL9_chr1_151734028_ENST00000368830_length(amino acids)=273AA_BP=163
MEPPDAPAQARGAPRLLLLAVLLAAHPDAQAEVRLSVPPLVEVMRGKSVILDCTPTGTHDHYMLEWFLTDRSGARPRLASAEMQGSELQV
TMHDTRGRSPPYQLDSQGRLVLAEAQVGDERDYVCVVRAGAAGTAEATARLNVFAKPEATEVSPNKGTLSVMEDSAQETVKFLKSCRLEV
GMKNNVKWELNPEIVARHFFKNLGVVVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWLAQQAAKAMAPTS

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Fusion Gene PPI Analysis for BCAM-MRPL9


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
HgeneBCAMchr19:45315805chr1:151734028ENST00000270233+415309_312168.0629.0laminin alpha5


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 BCAM-MRPL9


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 BCAM-MRPL9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human