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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:MAP2K4-MYH3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MAP2K4-MYH3
FusionPDB ID: 51209
FusionGDB2.0 ID: 51209
HgeneTgene
Gene symbol

MAP2K4

MYH3

Gene ID

6416

4621

Gene namemitogen-activated protein kinase kinase 4myosin heavy chain 3
SynonymsJNKK|JNKK1|MAPKK4|MEK4|MKK4|PRKMK4|SAPKK-1|SAPKK1|SEK1|SERK1|SKK1CPSFS1A|CPSFS1B|CPSKF1A|CPSKF1B|DA2A|DA2B|DA2B3|DA8|HEMHC|MYHC-EMB|MYHSE1|SMHCE
Cytomap

17p12

17p13.1

Type of geneprotein-codingprotein-coding
Descriptiondual specificity mitogen-activated protein kinase kinase 4JNK-activated kinase 1JNK-activating kinase 1MAP kinase kinase 4MAPK/ERK kinase 4MAPKK 4MEK 4SAPK/ERK kinase 1c-Jun N-terminal kinase kinase 1stress-activated protein kinase kinase 1myosin-3myosin heavy chain, fast skeletal muscle, embryonicmyosin, heavy chain 3, skeletal muscle, embryonicmyosin, heavy polypeptide 3, skeletal muscle, embryonicmyosin, skeletal, heavy chain, embryonic 1
Modification date2020032920200314
UniProtAcc

P45985

P11055

Ensembl transtripts involved in fusion geneENST idsENST00000353533, ENST00000415385, 
ENST00000581941, 
ENST00000226209, 
ENST00000583535, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 4 X 7=2805 X 5 X 3=75
# samples 135
** MAII scorelog2(13/280*10)=-1.10691520391651
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: MAP2K4 [Title/Abstract] AND MYH3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MAP2K4(11924318)-MYH3(10539170), # samples:3
Anticipated loss of major functional domain due to fusion event.MAP2K4-MYH3 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.
MAP2K4-MYH3 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.
MAP2K4-MYH3 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.
MAP2K4-MYH3 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 MAP2K4 (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 MYH3 (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 Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4OVTCGA-61-1914-01AMAP2K4chr17

11924318

+MYH3chr17

10539170

-
ChimerDB4OVTCGA-61-1914MAP2K4chr17

11924318

+MYH3chr17

10539170

-


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Fusion ORF Analysis


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)
ENST00000353533MAP2K4chr1711924318+ENST00000226209MYH3chr1710539170-2272178632144693
ENST00000353533MAP2K4chr1711924318+ENST00000583535MYH3chr1710539170-2271178632144693
ENST00000415385MAP2K4chr1711924318+ENST00000226209MYH3chr1710539170-2262168532134693
ENST00000415385MAP2K4chr1711924318+ENST00000583535MYH3chr1710539170-2261168532134693

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
ENST00000353533ENST00000226209MAP2K4chr1711924318+MYH3chr1710539170-0.0042783850.9957216
ENST00000353533ENST00000583535MAP2K4chr1711924318+MYH3chr1710539170-0.0042412320.9957587
ENST00000415385ENST00000226209MAP2K4chr1711924318+MYH3chr1710539170-0.0042448650.9957552
ENST00000415385ENST00000583535MAP2K4chr1711924318+MYH3chr1710539170-0.0042108050.99578923

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>51209_51209_1_MAP2K4-MYH3_MAP2K4_chr17_11924318_ENST00000353533_MYH3_chr17_10539170_ENST00000226209_length(amino acids)=693AA_BP=38
MAAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGELSRQLEEKESIVSQLSRSKQAFTQQTEELKRQLEEENKAKNALAHALQSS
RHDCDLLREQYEEEQEGKAELQRALSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQDSEEQVEAVNAKCASLEKTKQRLQGEVE
DLMVDVERANSLAAALDKKQRNFDKVLAEWKTKCEESQAELEASLKESRSLSTELFKLKNAYEEALDQLETVKRENKNLEQEIADLTEQI
AENGKTIHELEKSRKQIELEKADIQLALEEAEAALEHEEAKILRIQLELTQVKSEIDRKIAEKDEEIEQLKRNYQRTVETMQSALDAEVR
SRNEAIRLKKKMEGDLNEIEIQLSHANRQAAETLKHLRSVQGQLKDTQLHLDDALRGQEDLKEQLAIVERRANLLQAEVEELRATLEQTE
RARKLAEQELLDSNERVQLLHTQNTSLIHTKKKLETDLMQLQSEVEDASRDARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNL
EQTVKDLQHRLDEAEQLALKGGKKQIQKLETRIRELEFELEGEQKKNTESVKGLRKYERRVKELTYQSEEDRKNVLRLQDLVDKLQVKVK

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

>51209_51209_2_MAP2K4-MYH3_MAP2K4_chr17_11924318_ENST00000353533_MYH3_chr17_10539170_ENST00000583535_length(amino acids)=693AA_BP=38
MAAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGELSRQLEEKESIVSQLSRSKQAFTQQTEELKRQLEEENKAKNALAHALQSS
RHDCDLLREQYEEEQEGKAELQRALSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQDSEEQVEAVNAKCASLEKTKQRLQGEVE
DLMVDVERANSLAAALDKKQRNFDKVLAEWKTKCEESQAELEASLKESRSLSTELFKLKNAYEEALDQLETVKRENKNLEQEIADLTEQI
AENGKTIHELEKSRKQIELEKADIQLALEEAEAALEHEEAKILRIQLELTQVKSEIDRKIAEKDEEIEQLKRNYQRTVETMQSALDAEVR
SRNEAIRLKKKMEGDLNEIEIQLSHANRQAAETLKHLRSVQGQLKDTQLHLDDALRGQEDLKEQLAIVERRANLLQAEVEELRATLEQTE
RARKLAEQELLDSNERVQLLHTQNTSLIHTKKKLETDLMQLQSEVEDASRDARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNL
EQTVKDLQHRLDEAEQLALKGGKKQIQKLETRIRELEFELEGEQKKNTESVKGLRKYERRVKELTYQSEEDRKNVLRLQDLVDKLQVKVK

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

>51209_51209_3_MAP2K4-MYH3_MAP2K4_chr17_11924318_ENST00000415385_MYH3_chr17_10539170_ENST00000226209_length(amino acids)=693AA_BP=38
MAAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGELSRQLEEKESIVSQLSRSKQAFTQQTEELKRQLEEENKAKNALAHALQSS
RHDCDLLREQYEEEQEGKAELQRALSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQDSEEQVEAVNAKCASLEKTKQRLQGEVE
DLMVDVERANSLAAALDKKQRNFDKVLAEWKTKCEESQAELEASLKESRSLSTELFKLKNAYEEALDQLETVKRENKNLEQEIADLTEQI
AENGKTIHELEKSRKQIELEKADIQLALEEAEAALEHEEAKILRIQLELTQVKSEIDRKIAEKDEEIEQLKRNYQRTVETMQSALDAEVR
SRNEAIRLKKKMEGDLNEIEIQLSHANRQAAETLKHLRSVQGQLKDTQLHLDDALRGQEDLKEQLAIVERRANLLQAEVEELRATLEQTE
RARKLAEQELLDSNERVQLLHTQNTSLIHTKKKLETDLMQLQSEVEDASRDARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNL
EQTVKDLQHRLDEAEQLALKGGKKQIQKLETRIRELEFELEGEQKKNTESVKGLRKYERRVKELTYQSEEDRKNVLRLQDLVDKLQVKVK

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

>51209_51209_4_MAP2K4-MYH3_MAP2K4_chr17_11924318_ENST00000415385_MYH3_chr17_10539170_ENST00000583535_length(amino acids)=693AA_BP=38
MAAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGELSRQLEEKESIVSQLSRSKQAFTQQTEELKRQLEEENKAKNALAHALQSS
RHDCDLLREQYEEEQEGKAELQRALSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQDSEEQVEAVNAKCASLEKTKQRLQGEVE
DLMVDVERANSLAAALDKKQRNFDKVLAEWKTKCEESQAELEASLKESRSLSTELFKLKNAYEEALDQLETVKRENKNLEQEIADLTEQI
AENGKTIHELEKSRKQIELEKADIQLALEEAEAALEHEEAKILRIQLELTQVKSEIDRKIAEKDEEIEQLKRNYQRTVETMQSALDAEVR
SRNEAIRLKKKMEGDLNEIEIQLSHANRQAAETLKHLRSVQGQLKDTQLHLDDALRGQEDLKEQLAIVERRANLLQAEVEELRATLEQTE
RARKLAEQELLDSNERVQLLHTQNTSLIHTKKKLETDLMQLQSEVEDASRDARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNL
EQTVKDLQHRLDEAEQLALKGGKKQIQKLETRIRELEFELEGEQKKNTESVKGLRKYERRVKELTYQSEEDRKNVLRLQDLVDKLQVKVK

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Fusion Protein Functional Features


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/chr17:11924318/chr17:10539170)
- 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
MAP2K4

P45985

MYH3

P11055

FUNCTION: Dual specificity protein kinase which acts as an essential component of the MAP kinase signal transduction pathway. Essential component of the stress-activated protein kinase/c-Jun N-terminal kinase (SAP/JNK) signaling pathway. With MAP2K7/MKK7, is the one of the only known kinase to directly activate the stress-activated protein kinase/c-Jun N-terminal kinases MAPK8/JNK1, MAPK9/JNK2 and MAPK10/JNK3. MAP2K4/MKK4 and MAP2K7/MKK7 both activate the JNKs by phosphorylation, but they differ in their preference for the phosphorylation site in the Thr-Pro-Tyr motif. MAP2K4 shows preference for phosphorylation of the Tyr residue and MAP2K7/MKK7 for the Thr residue. The phosphorylation of the Thr residue by MAP2K7/MKK7 seems to be the prerequisite for JNK activation at least in response to proinflammatory cytokines, while other stimuli activate both MAP2K4/MKK4 and MAP2K7/MKK7 which synergistically phosphorylate JNKs. MAP2K4 is required for maintaining peripheral lymphoid homeostasis. The MKK/JNK signaling pathway is also involved in mitochondrial death signaling pathway, including the release cytochrome c, leading to apoptosis. Whereas MAP2K7/MKK7 exclusively activates JNKs, MAP2K4/MKK4 additionally activates the p38 MAPKs MAPK11, MAPK12, MAPK13 and MAPK14. {ECO:0000269|PubMed:7716521}.FUNCTION: Muscle contraction.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000353533+1115_1938.333333333333336400.0Compositional biasNote=Gly/Ser-rich
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000415385+1125_1938.333333333333336411.0Compositional biasNote=Gly/Ser-rich

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000353533+111102_36738.333333333333336400.0DomainProtein kinase
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000415385+112102_36738.333333333333336411.0DomainProtein kinase
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000353533+111108_11638.333333333333336400.0Nucleotide bindingATP
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000415385+112108_11638.333333333333336411.0Nucleotide bindingATP
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000353533+111364_38738.333333333333336400.0RegionNote=DVD domain
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000353533+11137_5238.333333333333336400.0RegionNote=D domain
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000415385+112364_38738.333333333333336411.0RegionNote=DVD domain
HgeneMAP2K4chr17:11924318chr17:10539170ENST00000415385+11237_5238.333333333333336411.0RegionNote=D domain
TgeneMYH3chr17:11924318chr17:10539170ENST000002262092640840_19331285.33333333333331941.0Coiled coilOntology_term=ECO:0000255
TgeneMYH3chr17:11924318chr17:10539170ENST000005835352741840_19331285.33333333333331941.0Coiled coilOntology_term=ECO:0000255
TgeneMYH3chr17:11924318chr17:10539170ENST00000226209264033_821285.33333333333331941.0DomainMyosin N-terminal SH3-like
TgeneMYH3chr17:11924318chr17:10539170ENST000002262092640782_8111285.33333333333331941.0DomainIQ
TgeneMYH3chr17:11924318chr17:10539170ENST00000226209264086_7791285.33333333333331941.0DomainMyosin motor
TgeneMYH3chr17:11924318chr17:10539170ENST00000583535274133_821285.33333333333331941.0DomainMyosin N-terminal SH3-like
TgeneMYH3chr17:11924318chr17:10539170ENST000005835352741782_8111285.33333333333331941.0DomainIQ
TgeneMYH3chr17:11924318chr17:10539170ENST00000583535274186_7791285.33333333333331941.0DomainMyosin motor
TgeneMYH3chr17:11924318chr17:10539170ENST000002262092640179_1861285.33333333333331941.0Nucleotide bindingATP
TgeneMYH3chr17:11924318chr17:10539170ENST000005835352741179_1861285.33333333333331941.0Nucleotide bindingATP
TgeneMYH3chr17:11924318chr17:10539170ENST000002262092640656_6781285.33333333333331941.0RegionNote=Actin-binding
TgeneMYH3chr17:11924318chr17:10539170ENST000002262092640758_7721285.33333333333331941.0RegionNote=Actin-binding
TgeneMYH3chr17:11924318chr17:10539170ENST000005835352741656_6781285.33333333333331941.0RegionNote=Actin-binding
TgeneMYH3chr17:11924318chr17:10539170ENST000005835352741758_7721285.33333333333331941.0RegionNote=Actin-binding


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1421_MAP2K4_11924318_MYH3_10539170_ranked_0.pdbMAP2K41192431811924318ENST00000583535MYH3chr1710539170-
MAAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGELSRQLEEKESIVSQLSRSKQAFTQQTEELKRQLEEENKAKNALAHALQSS
RHDCDLLREQYEEEQEGKAELQRALSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQDSEEQVEAVNAKCASLEKTKQRLQGEVE
DLMVDVERANSLAAALDKKQRNFDKVLAEWKTKCEESQAELEASLKESRSLSTELFKLKNAYEEALDQLETVKRENKNLEQEIADLTEQI
AENGKTIHELEKSRKQIELEKADIQLALEEAEAALEHEEAKILRIQLELTQVKSEIDRKIAEKDEEIEQLKRNYQRTVETMQSALDAEVR
SRNEAIRLKKKMEGDLNEIEIQLSHANRQAAETLKHLRSVQGQLKDTQLHLDDALRGQEDLKEQLAIVERRANLLQAEVEELRATLEQTE
RARKLAEQELLDSNERVQLLHTQNTSLIHTKKKLETDLMQLQSEVEDASRDARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNL
EQTVKDLQHRLDEAEQLALKGGKKQIQKLETRIRELEFELEGEQKKNTESVKGLRKYERRVKELTYQSEEDRKNVLRLQDLVDKLQVKVK
693


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
MAP2K4_pLDDT.png
all structure
all structure
MYH3_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
MAP2K4
MYH3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to MAP2K4-MYH3


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 MAP2K4-MYH3


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