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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:MICALL1-EIF3L (FusionGDB2 ID:53537)

Fusion Gene Summary for MICALL1-EIF3L

check button Fusion gene summary
Fusion gene informationFusion gene name: MICALL1-EIF3L
Fusion gene ID: 53537
HgeneTgene
Gene symbol

MICALL1

EIF3L

Gene ID

85377

51386

Gene nameMICAL like 1eukaryotic translation initiation factor 3 subunit L
SynonymsMICAL-L1|MIRAB13EIF3EIP|EIF3S11|EIF3S6IP|HSPC021|HSPC025|MSTP005
Cytomap

22q13.1

22q13.1

Type of geneprotein-codingprotein-coding
DescriptionMICAL-like protein 1molecule interacting with Rab13eukaryotic translation initiation factor 3 subunit LeIEF associated protein HSPC021eukaryotic translation initiation factor 3 subunit 6-interacting proteineukaryotic translation initiation factor 3 subunit E-interacting protein
Modification date2020031320200322
UniProtAcc

Q8N3F8

Q9Y262

Ensembl transtripts involved in fusion geneENST00000215957, ENST00000402631, 
ENST00000412331, ENST00000381683, 
ENST00000406934, ENST00000476955, 
Fusion gene scores* DoF score10 X 11 X 8=88010 X 13 X 6=780
# samples 1313
** MAII scorelog2(13/880*10)=-2.75899190049621
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/780*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MICALL1 [Title/Abstract] AND EIF3L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMICALL1(38338350)-EIF3L(38259012), # samples:2
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
HgeneMICALL1

GO:0097320

plasma membrane tubulation

23596323

TgeneEIF3L

GO:0006413

translational initiation

17581632

TgeneEIF3L

GO:0075525

viral translational termination-reinitiation

21347434


check buttonFusion gene breakpoints across MICALL1 (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 EIF3L (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
ChimerDB4LUSCTCGA-77-7338-01AMICALL1chr22

38323833

+EIF3Lchr22

38266183

+
ChimerDB4OVTCGA-36-1570-01AMICALL1chr22

38337540

+EIF3Lchr22

38259279

+
ChimerDB4OVTCGA-36-1570-01AMICALL1chr22

38338350

+EIF3Lchr22

38259012

+
ChimerDB4UCECTCGA-EO-A22U-01AMICALL1chr22

38323833

+EIF3Lchr22

38282772

+


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Fusion Gene ORF analysis for MICALL1-EIF3L

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
3UTR-3CDSENST00000215957ENST00000412331MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-3CDSENST00000215957ENST00000412331MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
3UTR-3CDSENST00000402631ENST00000381683MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
3UTR-3CDSENST00000402631ENST00000381683MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
3UTR-3CDSENST00000402631ENST00000406934MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
3UTR-3CDSENST00000402631ENST00000406934MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
3UTR-3CDSENST00000402631ENST00000412331MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
3UTR-3CDSENST00000402631ENST00000412331MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-3CDSENST00000402631ENST00000412331MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
3UTR-3UTRENST00000402631ENST00000476955MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
3UTR-intronENST00000215957ENST00000381683MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-intronENST00000215957ENST00000381683MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
3UTR-intronENST00000215957ENST00000406934MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-intronENST00000215957ENST00000406934MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
3UTR-intronENST00000215957ENST00000476955MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-intronENST00000215957ENST00000476955MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
3UTR-intronENST00000402631ENST00000381683MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-intronENST00000402631ENST00000406934MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-intronENST00000402631ENST00000476955MICALL1chr22

38337540

+EIF3Lchr22

38259279

+
3UTR-intronENST00000402631ENST00000476955MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
5CDS-3UTRENST00000215957ENST00000476955MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
5CDS-intronENST00000215957ENST00000476955MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
In-frameENST00000215957ENST00000381683MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
In-frameENST00000215957ENST00000381683MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
In-frameENST00000215957ENST00000406934MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
In-frameENST00000215957ENST00000406934MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
In-frameENST00000215957ENST00000412331MICALL1chr22

38323833

+EIF3Lchr22

38266183

+
In-frameENST00000215957ENST00000412331MICALL1chr22

38323833

+EIF3Lchr22

38282772

+
intron-3CDSENST00000402631ENST00000412331MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
intron-intronENST00000402631ENST00000381683MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
intron-intronENST00000402631ENST00000406934MICALL1chr22

38338350

+EIF3Lchr22

38259012

+
intron-intronENST00000402631ENST00000476955MICALL1chr22

38338350

+EIF3Lchr22

38259012

+

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)

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

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Fusion Genomic Features for MICALL1-EIF3L


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 MICALL1-EIF3L


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/chr22:38338350/chr22:38259012)
- 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
MICALL1

Q8N3F8

EIF3L

Q9Y262

FUNCTION: Probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. On endosome membranes, may act as a downstream effector of Rab proteins recruiting cytosolic proteins to regulate membrane tubulation. May be involved in a late step of receptor-mediated endocytosis regulating for instance endocytosed-EGF receptor trafficking. Alternatively, may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. May indirectly play a role in neurite outgrowth. {ECO:0000269|PubMed:19864458, ECO:0000269|PubMed:20801876, ECO:0000269|PubMed:21795389, ECO:0000269|PubMed:23596323}.FUNCTION: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). {ECO:0000255|HAMAP-Rule:MF_03011, ECO:0000269|PubMed:17581632, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.; FUNCTION: (Microbial infection) In case of FCV infection, plays a role in the ribosomal termination-reinitiation event leading to the translation of VP2 (PubMed:18056426). {ECO:0000269|PubMed:18056426}.

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
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+916162_225627864.0DomainLIM zinc-binding
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+9162_108627864.0DomainCalponin-homology (CH)
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+916162_225627864.0DomainLIM zinc-binding
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+9162_108627864.0DomainCalponin-homology (CH)
TgeneEIF3Lchr22:38323833chr22:38266183ENST00000381683411331_537145517.0DomainPCI
TgeneEIF3Lchr22:38323833chr22:38266183ENST00000412331613331_537193565.0DomainPCI

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+916682_711627864.0Coiled coilOntology_term=ECO:0000255
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+916785_830627864.0Coiled coilOntology_term=ECO:0000255
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+916682_711627864.0Coiled coilOntology_term=ECO:0000255
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+916785_830627864.0Coiled coilOntology_term=ECO:0000255
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+916253_667627864.0Compositional biasNote=Pro-rich
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+916253_667627864.0Compositional biasNote=Pro-rich
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+916671_818627864.0DomainbMERB
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+916671_818627864.0DomainbMERB
HgeneMICALL1chr22:38323833chr22:38266183ENST00000215957+916700_863627864.0RegionNote=Necessary and sufficient to associate with tubular recycling endosome membranes%2C mediate phosphatidic acid-binding and membrane tubulation
HgeneMICALL1chr22:38323833chr22:38282772ENST00000215957+916700_863627864.0RegionNote=Necessary and sufficient to associate with tubular recycling endosome membranes%2C mediate phosphatidic acid-binding and membrane tubulation
TgeneEIF3Lchr22:38323833chr22:38282772ENST00000381683811331_537477517.0DomainPCI
TgeneEIF3Lchr22:38323833chr22:38282772ENST000004123311013331_537525565.0DomainPCI


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Fusion Gene Sequence for MICALL1-EIF3L


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.

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Fusion Gene PPI Analysis for MICALL1-EIF3L


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 MICALL1-EIF3L


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 MICALL1-EIF3L


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