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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:LIN28A-EXO1 (FusionGDB2 ID:44745)

Fusion Gene Summary for LIN28A-EXO1

Fusion gene summary

Fusion gene information	Fusion gene name: LIN28A-EXO1
	Fusion gene ID: 44745
		Hgene	Tgene
	Gene symbol	LIN28A	EXO1
	Gene ID	79727	9156
	Gene name	lin-28 homolog A	exonuclease 1
	Synonyms	CSDD1\|LIN-28\|LIN28\|ZCCHC1\|lin-28A	HEX1\|hExoI
	Cytomap	1p36.11	1q43
	Type of gene	protein-coding	protein-coding
	Description	protein lin-28 homolog ARNA-binding protein LIN-28zinc finger CCHC domain-containing protein 1zinc finger, CCHC domain containing 1	exonuclease 1rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1
	Modification date	20200322	20200313
	UniProtAcc	Q9H9Z2	Q9UQ84
	Ensembl transtripts involved in fusion gene	ENST00000254231, ENST00000326279,	ENST00000348581, ENST00000366548, ENST00000493702, ENST00000518483,
Fusion gene scores	* DoF score	2 X 6 X 1=12	1 X 2 X 1=2
	# samples	6	5
	** MAII score	log2(6/12*10)=2.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(5/2*10)=4.64385618977472
Context	PubMed: LIN28A [Title/Abstract] AND EXO1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	LIN28A(26755050)-EXO1(242055823), # samples:7
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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	EXO1	GO:0006298	mismatch repair	14636568

Fusion gene breakpoints across LIN28A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across EXO1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	TGCT	TCGA-2G-AAFN	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AAGF	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AAGK	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AAGN	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AAGS	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AAGS	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AAGT	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
ChimerDB4	TGCT	TCGA-2G-AAL7	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-2G-AALY	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-VF-A8A8	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-XY-A8S2	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
ChimerDB4	TGCT	TCGA-XY-A8S3	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+

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Fusion Gene ORF analysis for LIN28A-EXO1

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
3UTR-intron	ENST00000254231	ENST00000348581	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000254231	ENST00000348581	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000348581	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000366548	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000254231	ENST00000366548	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000366548	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000493702	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000254231	ENST00000493702	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000493702	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000518483	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000254231	ENST00000518483	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000254231	ENST00000518483	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000348581	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000326279	ENST00000348581	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000348581	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000366548	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000326279	ENST00000366548	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000366548	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000493702	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000326279	ENST00000493702	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000493702	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000518483	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
3UTR-intron	ENST00000326279	ENST00000518483	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
3UTR-intron	ENST00000326279	ENST00000518483	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000348581	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000348581	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000366548	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000366548	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000493702	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000493702	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000518483	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000254231	ENST00000518483	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000348581	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000348581	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000366548	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000366548	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000493702	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000493702	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000518483	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
intron-intron	ENST00000326279	ENST00000518483	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for LIN28A-EXO1

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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 LIN28A-EXO1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:26755050/:242055823)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
LIN28A Q9H9Z2	EXO1 Q9UQ84
FUNCTION: RNA-binding protein that inhibits processing of pre-let-7 miRNAs and regulates translation of mRNAs that control developmental timing, pluripotency and metabolism (PubMed:21247876). Seems to recognize a common structural G-quartet (G4) feature in its miRNA and mRNA targets (Probable). 'Translational enhancer' that drives specific mRNAs to polysomes and increases the efficiency of protein synthesis. Its association with the translational machinery and target mRNAs results in an increased number of initiation events per molecule of mRNA and, indirectly, in mRNA stabilization. Binds IGF2 mRNA, MYOD1 mRNA, ARBP/36B4 ribosomal protein mRNA and its own mRNA. Essential for skeletal muscle differentiation program through the translational up-regulation of IGF2 expression. Suppressor of microRNA (miRNA) biogenesis, including that of let-7, miR107, miR-143 and miR-200c. Specifically binds the miRNA precursors (pre-miRNAs), recognizing an 5'-GGAG-3' motif found in pre-miRNA terminal loop, and recruits TUT4 AND tut7 uridylyltransferaseS. This results in the terminal uridylation of target pre-miRNAs. Uridylated pre-miRNAs fail to be processed by Dicer and undergo degradation. The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state by preventing let-7-mediated differentiation of embryonic stem cells (PubMed:18951094, PubMed:19703396, PubMed:22118463, PubMed:22898984). Localized to the periendoplasmic reticulum area, binds to a large number of spliced mRNAs and inhibits the translation of mRNAs destined for the ER, reducing the synthesis of transmembrane proteins, ER or Golgi lumen proteins, and secretory proteins. Binds to and enhances the translation of mRNAs for several metabolic enzymes, such as PFKP, PDHA1 or SDHA, increasing glycolysis and oxidative phosphorylation. Which, with the let-7 repression may enhance tissue repair in adult tissue (By similarity). {ECO:0000250\|UniProtKB:Q8K3Y3, ECO:0000269\|PubMed:18951094, ECO:0000269\|PubMed:19703396, ECO:0000269\|PubMed:21247876, ECO:0000269\|PubMed:22118463, ECO:0000269\|PubMed:22898984, ECO:0000305}.	FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch-containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269\|PubMed:10364235, ECO:0000269\|PubMed:10608837, ECO:0000269\|PubMed:11809771, ECO:0000269\|PubMed:11842105, ECO:0000269\|PubMed:12414623, ECO:0000269\|PubMed:12704184, ECO:0000269\|PubMed:14636568, ECO:0000269\|PubMed:14676842, ECO:0000269\|PubMed:15225546, ECO:0000269\|PubMed:15886194, ECO:0000269\|PubMed:16143102, ECO:0000269\|PubMed:9685493}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for LIN28A-EXO1

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 LIN28A-EXO1

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for LIN28A-EXO1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for LIN28A-EXO1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source