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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:TMEM260-MLIP (FusionGDB2 ID:92036)

Fusion Gene Summary for TMEM260-MLIP

check button Fusion gene summary
Fusion gene informationFusion gene name: TMEM260-MLIP
Fusion gene ID: 92036
HgeneTgene
Gene symbol

TMEM260

MLIP

Gene ID

54916

90523

Gene nametransmembrane protein 260muscular LMNA interacting protein
SynonymsC14orf101|SHDRAC6orf142|CIP
Cytomap

14q22.3

6p12.1

Type of geneprotein-codingprotein-coding
Descriptiontransmembrane protein 260UPF0679 protein C14orf101muscular LMNA-interacting proteincardiac ISL1-interacting proteinmuscle-enriched A-type lamin interacting proteinmuscular-enriched A-type laminin-interacting protein
Modification date2020031320200313
UniProtAcc

Q9NX78

Q5VWP3

Ensembl transtripts involved in fusion geneENST00000261556, ENST00000538838, 
ENST00000536419, ENST00000553335, 
ENST00000358276, ENST00000502396, 
ENST00000511744, ENST00000370876, 
ENST00000370877, ENST00000509997, 
ENST00000274897, ENST00000514921, 
Fusion gene scores* DoF score5 X 5 X 2=508 X 7 X 8=448
# samples 511
** MAII scorelog2(5/50*10)=0log2(11/448*10)=-2.02599520853294
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TMEM260 [Title/Abstract] AND MLIP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTMEM260(57052630)-MLIP(53986245), # 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

check buttonFusion gene breakpoints across TMEM260 (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 MLIP (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
ChimerDB4LUSCTCGA-22-1017-01ATMEM260chr14

57052630

+MLIPchr6

53986245

+
ChimerDB4LUSCTCGA-22-1017TMEM260chr14

57052630

+MLIPchr6

53986245

+


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Fusion Gene ORF analysis for TMEM260-MLIP

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-3UTRENST00000261556ENST00000358276TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-3UTRENST00000261556ENST00000502396TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-3UTRENST00000261556ENST00000511744TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-3UTRENST00000538838ENST00000358276TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-3UTRENST00000538838ENST00000502396TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-3UTRENST00000538838ENST00000511744TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-intronENST00000261556ENST00000370876TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-intronENST00000261556ENST00000370877TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-intronENST00000261556ENST00000509997TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-intronENST00000538838ENST00000370876TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-intronENST00000538838ENST00000370877TMEM260chr14

57052630

+MLIPchr6

53986245

+
5CDS-intronENST00000538838ENST00000509997TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-3CDSENST00000536419ENST00000274897TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-3CDSENST00000536419ENST00000514921TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-3UTRENST00000536419ENST00000358276TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-3UTRENST00000536419ENST00000502396TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-3UTRENST00000536419ENST00000511744TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-intronENST00000536419ENST00000370876TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-intronENST00000536419ENST00000370877TMEM260chr14

57052630

+MLIPchr6

53986245

+
5UTR-intronENST00000536419ENST00000509997TMEM260chr14

57052630

+MLIPchr6

53986245

+
Frame-shiftENST00000261556ENST00000274897TMEM260chr14

57052630

+MLIPchr6

53986245

+
Frame-shiftENST00000261556ENST00000514921TMEM260chr14

57052630

+MLIPchr6

53986245

+
Frame-shiftENST00000538838ENST00000274897TMEM260chr14

57052630

+MLIPchr6

53986245

+
Frame-shiftENST00000538838ENST00000514921TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-3CDSENST00000553335ENST00000274897TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-3CDSENST00000553335ENST00000514921TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-3UTRENST00000553335ENST00000358276TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-3UTRENST00000553335ENST00000502396TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-3UTRENST00000553335ENST00000511744TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-intronENST00000553335ENST00000370876TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-intronENST00000553335ENST00000370877TMEM260chr14

57052630

+MLIPchr6

53986245

+
intron-intronENST00000553335ENST00000509997TMEM260chr14

57052630

+MLIPchr6

53986245

+

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 TMEM260-MLIP


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)
TMEM260chr1457052630+MLIPchr653986244+7.94E-050.9999206
TMEM260chr1457052630+MLIPchr653986244+7.94E-050.9999206
TMEM260chr1457052630+MLIPchr653986244+7.94E-050.9999206
TMEM260chr1457052630+MLIPchr653986244+7.94E-050.9999206

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.
genomic feature of top 1%

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Fusion Protein Features for TMEM260-MLIP


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/:57052630/:53986245)
- 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
TMEM260

Q9NX78

MLIP

Q5VWP3

FUNCTION: Required for precocious cardiac adaptation to stress through integrated regulation of the AKT/mTOR pathways and FOXO1. Regulates cardiac homeostasis and plays an important role in protection against cardiac hypertrophy. Acts as a transcriptional cofactor, represses transactivator activity of ISL1 and MYOCD. {ECO:0000250|UniProtKB:A0A096MK47, ECO:0000250|UniProtKB:Q5FW52}.

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 TMEM260-MLIP


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 TMEM260-MLIP


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 TMEM260-MLIP


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 TMEM260-MLIP


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