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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:MIER3-KIF2A (FusionGDB2 ID:53642)

Fusion Gene Summary for MIER3-KIF2A

check button Fusion gene summary
Fusion gene informationFusion gene name: MIER3-KIF2A
Fusion gene ID: 53642
HgeneTgene
Gene symbol

MIER3

KIF2A

Gene ID

166968

3796

Gene nameMIER family member 3kinesin family member 2A
Synonyms-CDCBM3|HK2|KIF2
Cytomap

5q11.2

5q12.1

Type of geneprotein-codingprotein-coding
Descriptionmesoderm induction early response protein 3mesoderm induction early response 1, family member 3mi-er3kinesin-like protein KIF2AKinesin, heavy chain, 2kinesin heavy chain member 2Akinesin-2
Modification date2020031320200318
UniProtAcc.

O00139

Ensembl transtripts involved in fusion geneENST00000381199, ENST00000381213, 
ENST00000381226, ENST00000409421, 
ENST00000546593, 		ENST00000381103, 
ENST00000407818, ENST00000506857, 
ENST00000509663, ENST00000401507, 
Fusion gene scores* DoF score4 X 4 X 4=643 X 4 X 3=36
# samples 54
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: MIER3 [Title/Abstract] AND KIF2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMIER3(56231255)-KIF2A(61681311), # samples:2
Anticipated loss of major functional domain due to fusion event.MIER3-KIF2A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted 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
HgeneMIER3

GO:0016575

histone deacetylation

28046085

TgeneKIF2A

GO:0007052

mitotic spindle organization

18411309


check buttonFusion gene breakpoints across MIER3 (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 KIF2A (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
ChimerDB4ACCTCGA-OR-A5J1-01AMIER3chr5

56231255

-KIF2Achr5

61681311

+


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Fusion Gene ORF analysis for MIER3-KIF2A

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-intronENST00000381199ENST00000381103MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381199ENST00000407818MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381199ENST00000506857MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381199ENST00000509663MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381213ENST00000381103MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381213ENST00000407818MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381213ENST00000506857MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381213ENST00000509663MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381226ENST00000381103MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381226ENST00000407818MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381226ENST00000506857MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000381226ENST00000509663MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000409421ENST00000381103MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000409421ENST00000407818MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000409421ENST00000506857MIER3chr5

56231255

-KIF2Achr5

61681311

+
5CDS-intronENST00000409421ENST00000509663MIER3chr5

56231255

-KIF2Achr5

61681311

+
Frame-shiftENST00000409421ENST00000401507MIER3chr5

56231255

-KIF2Achr5

61681311

+
In-frameENST00000381199ENST00000401507MIER3chr5

56231255

-KIF2Achr5

61681311

+
In-frameENST00000381213ENST00000401507MIER3chr5

56231255

-KIF2Achr5

61681311

+
In-frameENST00000381226ENST00000401507MIER3chr5

56231255

-KIF2Achr5

61681311

+
intron-3CDSENST00000546593ENST00000401507MIER3chr5

56231255

-KIF2Achr5

61681311

+
intron-intronENST00000546593ENST00000381103MIER3chr5

56231255

-KIF2Achr5

61681311

+
intron-intronENST00000546593ENST00000407818MIER3chr5

56231255

-KIF2Achr5

61681311

+
intron-intronENST00000546593ENST00000506857MIER3chr5

56231255

-KIF2Achr5

61681311

+
intron-intronENST00000546593ENST00000509663MIER3chr5

56231255

-KIF2Achr5

61681311

+

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)
ENST00000381226MIER3chr556231255-ENST00000401507KIF2Achr561681311+81962616711231
ENST00000381213MIER3chr556231255-ENST00000401507KIF2Achr561681311+81161823703226
ENST00000381199MIER3chr556231255-ENST00000401507KIF2Achr561681311+79960611691226

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
ENST00000381226ENST00000401507MIER3chr556231255-KIF2Achr561681311+0.0001898730.99981016
ENST00000381213ENST00000401507MIER3chr556231255-KIF2Achr561681311+0.0003203510.9996797
ENST00000381199ENST00000401507MIER3chr556231255-KIF2Achr561681311+0.0003134770.9996866

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Fusion Genomic Features for MIER3-KIF2A


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.
genomic feature of top 1%

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Fusion Protein Features for MIER3-KIF2A


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/chr5:56231255/chr5:61681311)
- 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
.KIF2A

O00139

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: Plus end-directed microtubule-dependent motor required for normal brain development. May regulate microtubule dynamics during axonal growth. Required for normal progression through mitosis. Required for normal congress of chromosomes at the metaphase plate. Required for normal spindle dynamics during mitosis. Promotes spindle turnover. Implicated in formation of bipolar mitotic spindles. Has microtubule depolymerization activity. {ECO:0000269|PubMed:15843429, ECO:0000269|PubMed:17538014, ECO:0000269|PubMed:18411309}.

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
TgeneKIF2Achr5:56231255chr5:61681311ENST000003811031921660_699658687.0Coiled coilOntology_term=ECO:0000255
TgeneKIF2Achr5:56231255chr5:61681311ENST000005068571820660_699632661.0Coiled coilOntology_term=ECO:0000255

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMIER3chr5:56231255chr5:61681311ENST00000381199-713174_272198551.0DomainELM2
HgeneMIER3chr5:56231255chr5:61681311ENST00000381199-713277_329198551.0DomainSANT
HgeneMIER3chr5:56231255chr5:61681311ENST00000381213-713174_272198550.0DomainELM2
HgeneMIER3chr5:56231255chr5:61681311ENST00000381213-713277_329198550.0DomainSANT
HgeneMIER3chr5:56231255chr5:61681311ENST00000381226-713174_272203556.0DomainELM2
HgeneMIER3chr5:56231255chr5:61681311ENST00000381226-713277_329203556.0DomainSANT
HgeneMIER3chr5:56231255chr5:61681311ENST00000409421-511174_272135488.0DomainELM2
HgeneMIER3chr5:56231255chr5:61681311ENST00000409421-511277_329135488.0DomainSANT
TgeneKIF2Achr5:56231255chr5:61681311ENST000004015071820660_699678707.0Coiled coilOntology_term=ECO:0000255
TgeneKIF2Achr5:56231255chr5:61681311ENST000004078181921660_699716745.0Coiled coilOntology_term=ECO:0000255
TgeneKIF2Achr5:56231255chr5:61681311ENST000003811031921223_553658687.0DomainKinesin motor
TgeneKIF2Achr5:56231255chr5:61681311ENST000004015071820223_553678707.0DomainKinesin motor
TgeneKIF2Achr5:56231255chr5:61681311ENST000004078181921223_553716745.0DomainKinesin motor
TgeneKIF2Achr5:56231255chr5:61681311ENST000005068571820223_553632661.0DomainKinesin motor
TgeneKIF2Achr5:56231255chr5:61681311ENST000003811031921313_320658687.0Nucleotide bindingNote=ATP
TgeneKIF2Achr5:56231255chr5:61681311ENST000004015071820313_320678707.0Nucleotide bindingNote=ATP
TgeneKIF2Achr5:56231255chr5:61681311ENST000004078181921313_320716745.0Nucleotide bindingNote=ATP
TgeneKIF2Achr5:56231255chr5:61681311ENST000005068571820313_320632661.0Nucleotide bindingNote=ATP
TgeneKIF2Achr5:56231255chr5:61681311ENST0000038110319211_217658687.0RegionGlobular
TgeneKIF2Achr5:56231255chr5:61681311ENST0000040150718201_217678707.0RegionGlobular
TgeneKIF2Achr5:56231255chr5:61681311ENST0000040781819211_217716745.0RegionGlobular
TgeneKIF2Achr5:56231255chr5:61681311ENST0000050685718201_217632661.0RegionGlobular


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Fusion Gene Sequence for MIER3-KIF2A


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.
>53642_53642_1_MIER3-KIF2A_MIER3_chr5_56231255_ENST00000381199_KIF2A_chr5_61681311_ENST00000401507_length(transcript)=799nt_BP=606nt
AAGGTACCAATATGGCGGAGGCTTCTTTTGGAAGTTCGAGCCCAGTTGGGTCTTTGTCTTCTGAGGATCATGATTTTGACCCCACTGCTG
AGATGTTGGTCCATGACTATGATGATGAAAGAACTCTTGAAGAAGAGGAAATGATGGATGAGGGTAAAAACTTCAGTTCAGAAATTGAAG
ACTTAGAAAAGGAAGGAACCATGCCTCTAGAAGATTTACTGGCATTCTATGGCTATGAACCTACAATTCCAGCAGTTGCAAATTCCAGTG
CAAATAGTTCCCCAAGTGAACTGGCAGATGAACTACCAGACATGACACTAGACAAAGAGGAAATAGCAAAAGACCTGTTGTCAGGTGATG
ACGAGGAAACTCAGTCTTCTGCGGATGATCTGACGCCATCTGTGACTTCCCATGAAACTTCTGATTTCTTCCCTAGGCCTTTACGATCAA
ATACTGCATGTGATGGTGATAAGGAATCAGAGGTTGAAGATGTTGAAACAGACAGTGGTAATTCACCTGAAGATTTGAGGAAGGAAATAA
TGATTGGTTTACAATATCAGGCAGAGATTCCCCCTTATCTTGGAGAGTACGATGGTAATGAGAAAGATAAAGTGAAATCTTTCCGTGCAG
CTCTACAAGAGGAGGAACAAGCCAGCAAGCAAATCAACCCGAAGAGACCCCGTGCCCTTTAAACCGGCATTTGCTGCTAAAGGATACCCA

>53642_53642_1_MIER3-KIF2A_MIER3_chr5_56231255_ENST00000381199_KIF2A_chr5_61681311_ENST00000401507_length(amino acids)=226AA_BP=198
MAEASFGSSSPVGSLSSEDHDFDPTAEMLVHDYDDERTLEEEEMMDEGKNFSSEIEDLEKEGTMPLEDLLAFYGYEPTIPAVANSSANSS
PSELADELPDMTLDKEEIAKDLLSGDDEETQSSADDLTPSVTSHETSDFFPRPLRSNTACDGDKESEVEDVETDSGNSPEDLRKEIMIGL

--------------------------------------------------------------
>53642_53642_2_MIER3-KIF2A_MIER3_chr5_56231255_ENST00000381213_KIF2A_chr5_61681311_ENST00000401507_length(transcript)=811nt_BP=618nt
TCGTTCGCCCTAAAGGTACCAATATGGCGGAGGCTTCTTTTGGAAGTTCGAGCCCAGTTGGGTCTTTGTCTTCTGAGGATCATGATTTTG
ACCCCACTGCTGAGATGTTGGTCCATGACTATGATGATGAAAGAACTCTTGAAGAAGAGGAAATGATGGATGAGGGTAAAAACTTCAGTT
CAGAAATTGAAGACTTAGAAAAGGAAGGAACCATGCCTCTAGAAGATTTACTGGCATTCTATGGCTATGAACCTACAATTCCAGCAGTTG
CAAATTCCAGTGCAAATAGTTCCCCAAGTGAACTGGCAGATGAACTACCAGACATGACACTAGACAAAGAGGAAATAGCAAAAGACCTGT
TGTCAGGTGATGACGAGGAAACTCAGTCTTCTGCGGATGATCTGACGCCATCTGTGACTTCCCATGAAACTTCTGATTTCTTCCCTAGGC
CTTTACGATCAAATACTGCATGTGATGGTGATAAGGAATCAGAGGTTGAAGATGTTGAAACAGACAGTGGTAATTCACCTGAAGATTTGA
GGAAGGAAATAATGATTGGTTTACAATATCAGGCAGAGATTCCCCCTTATCTTGGAGAGTACGATGGTAATGAGAAAGATAAAGTGAAAT
CTTTCCGTGCAGCTCTACAAGAGGAGGAACAAGCCAGCAAGCAAATCAACCCGAAGAGACCCCGTGCCCTTTAAACCGGCATTTGCTGCT
AAAGGATACCCAGAACCCTCACTACTGTAACATACAACGGTTCAGCTGTAAGGGCCATTTGAAAGTTTGGAATTTTAAGTGTCTGTGGAA

>53642_53642_2_MIER3-KIF2A_MIER3_chr5_56231255_ENST00000381213_KIF2A_chr5_61681311_ENST00000401507_length(amino acids)=226AA_BP=198
MAEASFGSSSPVGSLSSEDHDFDPTAEMLVHDYDDERTLEEEEMMDEGKNFSSEIEDLEKEGTMPLEDLLAFYGYEPTIPAVANSSANSS
PSELADELPDMTLDKEEIAKDLLSGDDEETQSSADDLTPSVTSHETSDFFPRPLRSNTACDGDKESEVEDVETDSGNSPEDLRKEIMIGL

--------------------------------------------------------------
>53642_53642_3_MIER3-KIF2A_MIER3_chr5_56231255_ENST00000381226_KIF2A_chr5_61681311_ENST00000401507_length(transcript)=819nt_BP=626nt
CCCTAAAGGTACCAATATGGCGGAGGCTTCTTTTGGAAGTTCGAGCCCAGTTTGTTTTATTCCAGTTGGGTCTTTGTCTTCTGAGGATCA
TGATTTTGACCCCACTGCTGAGATGTTGGTCCATGACTATGATGATGAAAGAACTCTTGAAGAAGAGGAAATGATGGATGAGGGTAAAAA
CTTCAGTTCAGAAATTGAAGACTTAGAAAAGGAAGGAACCATGCCTCTAGAAGATTTACTGGCATTCTATGGCTATGAACCTACAATTCC
AGCAGTTGCAAATTCCAGTGCAAATAGTTCCCCAAGTGAACTGGCAGATGAACTACCAGACATGACACTAGACAAAGAGGAAATAGCAAA
AGACCTGTTGTCAGGTGATGACGAGGAAACTCAGTCTTCTGCGGATGATCTGACGCCATCTGTGACTTCCCATGAAACTTCTGATTTCTT
CCCTAGGCCTTTACGATCAAATACTGCATGTGATGGTGATAAGGAATCAGAGGTTGAAGATGTTGAAACAGACAGTGGTAATTCACCTGA
AGATTTGAGGAAGGAAATAATGATTGGTTTACAATATCAGGCAGAGATTCCCCCTTATCTTGGAGAGTACGATGGTAATGAGAAAGATAA
AGTGAAATCTTTCCGTGCAGCTCTACAAGAGGAGGAACAAGCCAGCAAGCAAATCAACCCGAAGAGACCCCGTGCCCTTTAAACCGGCAT
TTGCTGCTAAAGGATACCCAGAACCCTCACTACTGTAACATACAACGGTTCAGCTGTAAGGGCCATTTGAAAGTTTGGAATTTTAAGTGT

>53642_53642_3_MIER3-KIF2A_MIER3_chr5_56231255_ENST00000381226_KIF2A_chr5_61681311_ENST00000401507_length(amino acids)=231AA_BP=203
MAEASFGSSSPVCFIPVGSLSSEDHDFDPTAEMLVHDYDDERTLEEEEMMDEGKNFSSEIEDLEKEGTMPLEDLLAFYGYEPTIPAVANS
SANSSPSELADELPDMTLDKEEIAKDLLSGDDEETQSSADDLTPSVTSHETSDFFPRPLRSNTACDGDKESEVEDVETDSGNSPEDLRKE

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

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Fusion Gene PPI Analysis for MIER3-KIF2A


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 MIER3-KIF2A


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 MIER3-KIF2A


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