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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:MIA3-SLAIN1 (FusionGDB2 ID:53472)

Fusion Gene Summary for MIA3-SLAIN1

check button Fusion gene summary
Fusion gene informationFusion gene name: MIA3-SLAIN1
Fusion gene ID: 53472
HgeneTgene
Gene symbol

MIA3

SLAIN1

Gene ID

375056

122060

Gene nameMIA SH3 domain ER export factor 3SLAIN motif family member 1
SynonymsARNT|D320|TANGO|TANGO1|UNQ6077C13orf32
Cytomap

1q41

13q22.3

Type of geneprotein-codingprotein-coding
Descriptiontransport and Golgi organization protein 1 homologC219-reactive peptideMIA family member 3, ER export factormelanoma inhibitory activity family, member 3melanoma inhibitory activity protein 3transport and Golgi organization protein 1SLAIN motif-containing protein 1
Modification date2020031320200313
UniProtAcc

Q5JRA6

.
Ensembl transtripts involved in fusion geneENST00000340535, ENST00000344441, 
ENST00000344922, ENST00000344507, 
ENST00000470521, 		ENST00000267219, 
ENST00000314070, ENST00000351546, 
ENST00000358679, ENST00000418532, 
ENST00000465831, ENST00000466548, 
ENST00000488699, 
Fusion gene scores* DoF score4 X 4 X 2=324 X 4 X 2=32
# samples 44
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: MIA3 [Title/Abstract] AND SLAIN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMIA3(222826620)-SLAIN1(78315658), # samples:1
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
HgeneMIA3

GO:0002687

positive regulation of leukocyte migration

17726152

HgeneMIA3

GO:0007162

negative regulation of cell adhesion

17726152

HgeneMIA3

GO:0030336

negative regulation of cell migration

17044017

HgeneMIA3

GO:0042060

wound healing

17044017


check buttonFusion gene breakpoints across MIA3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SLAIN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChiTaRS5.0N/AAW899124MIA3chr1

222826620

+SLAIN1chr13

78315658

+


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Fusion Gene ORF analysis for MIA3-SLAIN1

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-intronENST00000340535ENST00000267219MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000314070MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000351546MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000358679MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000418532MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000465831MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000466548MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000340535ENST00000488699MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000267219MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000314070MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000351546MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000358679MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000418532MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000465831MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000466548MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344441ENST00000488699MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000267219MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000314070MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000351546MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000358679MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000418532MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000465831MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000466548MIA3chr1

222826620

+SLAIN1chr13

78315658

+
5CDS-intronENST00000344922ENST00000488699MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000267219MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000314070MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000351546MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000358679MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000418532MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000465831MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000466548MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000344507ENST00000488699MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000267219MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000314070MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000351546MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000358679MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000418532MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000465831MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000466548MIA3chr1

222826620

+SLAIN1chr13

78315658

+
intron-intronENST00000470521ENST00000488699MIA3chr1

222826620

+SLAIN1chr13

78315658

+

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 MIA3-SLAIN1


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.

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 MIA3-SLAIN1


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/:222826620/:78315658)
- 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
MIA3

Q5JRA6

.
FUNCTION: Plays a role in the transport of cargos that are too large to fit into COPII-coated vesicles and require specific mechanisms to be incorporated into membrane-bound carriers and exported from the endoplasmic reticulum. This protein is required for collagen VII (COL7A1) secretion by loading COL7A1 into transport carriers. It may participate in cargo loading of COL7A1 at endoplasmic reticulum exit sites by binding to COPII coat subunits Sec23/24 and guiding SH3-bound COL7A1 into a growing carrier. Does not play a role in global protein secretion and is apparently specific to COL7A1 cargo loading. However, it may participate in secretion of other proteins in cells that do not secrete COL7A1. It is also specifically required for the secretion of lipoproteins by participating in their export from the endoplasmic reticulum (PubMed:27138255, PubMed:19269366). Required for correct assembly of COPII coat components at endoplasmic reticulum exit sites (ERES) and for the localization of SEC16A and membrane-bound ER-resident complexes consisting of MIA2 and PREB/SEC12 to ERES (PubMed:28442536). {ECO:0000269|PubMed:19269366, ECO:0000269|PubMed:27138255, ECO:0000269|PubMed:28442536}.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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for MIA3-SLAIN1


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 MIA3-SLAIN1


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 MIA3-SLAIN1


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 MIA3-SLAIN1


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