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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:LSM3-MRPL22 (FusionGDB2 ID:50210)

Fusion Gene Summary for LSM3-MRPL22

Fusion gene summary

Fusion gene information	Fusion gene name: LSM3-MRPL22
	Fusion gene ID: 50210
		Hgene	Tgene
	Gene symbol	LSM3	MRPL22
	Gene ID	27258	64976
	Gene name	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	mitochondrial ribosomal protein L40
	Synonyms	SMX4\|USS2\|YLR438C	L40mt\|MRP-L22\|MRP-L40\|MRPL22\|NLVCF\|URIM
	Cytomap	3p25.1	22q11.21
	Type of gene	protein-coding	protein-coding
	Description	U6 snRNA-associated Sm-like protein LSm3LSM3 U6 small nuclear RNA and mRNA degradation associatedLSM3 homolog, U6 small nuclear RNA associated	39S ribosomal protein L40, mitochondrialmitochondrial large ribosomal subunit protein mL40nuclear localization signal-containing protein deleted in velocardiofacial syndromeup-regulated in metastasis
	Modification date	20200313	20200320
	UniProtAcc	P62310	Q9NWU5
	Ensembl transtripts involved in fusion gene	ENST00000306024,	ENST00000265229, ENST00000439747, ENST00000522038, ENST00000518364, ENST00000523037,
Fusion gene scores	* DoF score	2 X 2 X 2=8	3 X 3 X 3=27
	# samples	2	3
	** MAII score	log2(2/8*10)=1.32192809488736	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: LSM3 [Title/Abstract] AND MRPL22 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	LSM3(14225532)-MRPL22(154335931), # 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)

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
Hgene	LSM3	GO:0000398	mRNA splicing, via spliceosome	10369684\|10523320\|28781166

Fusion gene breakpoints across LSM3 (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 MRPL22 (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	BLCA	TCGA-FD-A3B7-01A	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+

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Fusion Gene ORF analysis for LSM3-MRPL22

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
5CDS-5UTR	ENST00000306024	ENST00000265229	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+
5CDS-5UTR	ENST00000306024	ENST00000439747	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+
5CDS-5UTR	ENST00000306024	ENST00000522038	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+
5CDS-intron	ENST00000306024	ENST00000518364	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+
In-frame	ENST00000306024	ENST00000523037	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+

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)

ENST00000306024

LSM3

chr3

14225532

ENST00000523037

MRPL22

chr5

154335931

3671

731

503

1156

217

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
ENST00000306024	ENST00000523037	LSM3	chr3	14225532	+	MRPL22	chr5	154335931	+	0.000762567	0.9992374

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Fusion Genomic Features for LSM3-MRPL22

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)
LSM3	chr3	14225532	+	MRPL22	chr5	154335930	+	1.65E-10	1
LSM3	chr3	14225532	+	MRPL22	chr5	154335930	+	1.65E-10	1

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 LSM3-MRPL22

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:14225532/chr5:154335931)
- 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
LSM3 P62310	MRPL22 Q9NWU5
FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320). {ECO:0000269\|PubMed:10523320, ECO:0000269\|PubMed:28781166}.

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

Tgene

MRPL22

chr3:14225532

chr5:154335931

ENST00000265229

176_183

127.0

Compositional bias

Note=Poly-Pro

Tgene

MRPL22

chr3:14225532

chr5:154335931

ENST00000523037

176_183

207.0

Compositional bias

Note=Poly-Pro

- 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 LSM3-MRPL22

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.

>50210_50210_1_LSM3-MRPL22_LSM3_chr3_14225532_ENST00000306024_MRPL22_chr5_154335931_ENST00000523037_length(transcript)=3671nt_BP=731nt
GCGCAGCAACCTCCACCAGGCCTCCGCGTCTGGACTCCCGCCCTGCCTCTGGGCCTCCTCCGCCCACCGGCGGCGTCTCCCGCGAAGCCC
GCTGGGCCTCGCTCTCACCCTCCTCCTCCTCCTCACGCCGGGCCTTGCTCTTGGCCTTGGATTTCTGGCTGCGCAGTTCGCGTCCCCGCG
GCTCCCCGCCGGCCGCGCGTTTCCGAGCCATGTTGCTTGTCTGGGCAAATTCCACTTCGCGAGTGACGCACCCGGCCGCGATGCGCTAGA
ACGCCGGCCCCGCCCCGAGGCGGTGCGCTTGGCCACGCCCCTTCGTTGGAGGCCTAGTCACGCCCCTAAAGGAAGCTCCACCCCATACCC
GTGGCCACTAAAAAACTGCGGGAAGCAGGAAAGAGCACAACAGGTTTCTCTCTATTTCCGGTGTATTGTATCCTCACGTTTCCGGAGATT
GACGTTGCTCTTGTGTTCTCGCGAGAGGCGGGAAAGGGCGCAGGGTTTGAAACATGGCGGACGACGTAGACCAGCAACAAACTACCAACA
CTGTAGAGGAGCCCCTGGATCTTATCAGGCTCAGCCTAGATGAGCGAATTTATGTGAAAATGAGAAATGACCGAGAGCTTCGAGGCAGAT
TACATGCTTATGATCAACATTTAAATATGATCTTGGGAGATGTGGAAGAAACTGTGACTACTATAGAAATTGATGAAGAAACATATGAAG
AGATATATAAAGAAATCTACCACTGTCGAAGACAAATAAAATATAGCAAAGACAAGATGTGGTATTTGGCAAAATTGATACGAGGAATGT
CTATTGACCAGGCTTTGGCTCAGTTGGAATTCAATGACAAAAAAGGGGCCAAAATAATTAAAGAGGTTCTCTTAGAAGCACAAGATATGG
CAGTGAGAGACCATAACGTGGAATTCAGGTCCAATTTATATATAGCTGAGTCCACCTCAGGACGAGGCCAGTGCCTGAAACGCATCCGCT
ACCATGGCAGAGGTCGCTTTGGGATCATGGAGAAGGTTTATTGCCATTATTTTGTGAAGTTGGTGGAAGGGCCCCCACCTCCACCTGAGC
CACCAAAGACGGCAGTTGCCCATGCCAAAGAGTATATTCAGCAGCTTCGCAGCCGGACCATCGTTCACACTCTATGATGAGGAGATTCAG
ACTCCACAGTGTATATATTTTGCCATTTATTTTCTAAAAATAAACAAAAATTGAAGGCAAATGCTTTTTATGATTTCTCATTGAATTATT
GAAACAGTGTATAACTGCTAGTTGTAAATGAATATTTATAAGGCTTTGCCCATTTCTTTTGAGCCTCTGGGCATATTTGTATGCATTTGC
GACTTGGAAGGGGAAATCAGCTTTAAACATAGTAACAGACTATATTTCAAAAGGCTTTTGGAGTAACTTTGAAAGGGAATGTTAACTTTC
CAACTAGTGTCCTGCAGGTGGCTGTTTTGATACTGGACTTGAATACAGTGTTATGAGGTAAGAAAATTGCTTTTATTTCACTTAATTTTC
TCTTGGGACCATGGGAAGTTAGAGTGGCTGCATGTTGTTTCATTACAGTATTTTAGGGTGTTCAGTGGTACCGTTTTTCCTTTCACTGTT
GGCACAGGCCAGTGAGTCAAAAATTATATTTTCCTTTACTGTTTTAGCAGTAACTCGAAACTACAGGAGTTTATTAGATATACGAATCTA
AAACTCCAAAAACCTTTAACTTTGAAAATTTTCTTTTGGTTAAGCAAAGCCTGTTTTTATTTCTTCTTCCAACAGTGCTTTATATTGTTT
GGATATCTTGTTTAGGATTGATTTATTTTTCAGGGTAAATTCAATTACTGAGAGAGGAATTGAACCAATCTCAGCATTGCATTCTAAAAT
GGGGCAGTAGGTGGCACTCAACCTTTTATTAGCAGAAAATTGTTAGTTTCAAATTAGAGTGTTCAACACTGCTTCCCTCTCATTCATACA
CGTCTTCATTAAGAAGAAGTACTCTTTGTCTACAGCCCTAGTCCAACTTTTGCATGCAAAAGAAGAATCGAGGATGCTTGCTTGTTAATG
CAGACTTCTGGGCCCCACCCCAATGATTCAATTCACTAGGTCTTATGGGGGGCTGGTTTCAGAAATCTATGTTTTAAACAAACACTTCCA
GGTAATTCTGTTGTAGGGGACTACGCTTTGAGAATACGGCTTTAGGAGAATGAAAAAATGTAGTTTTATTGCCATGTTTTAAGATGGCAT
TAATAATAGTTACTGTTTACTGGGAACTTGTTATTTGCAAGCTCTGTGCTAGTATTTTACATAATTCTTCACAACATCCTGAAAATGTAG
CTTTTGTTTTACCACTTTACAAAGGAATAAACCGAAGCACACAGAATTCAAATAACTATCACAAGTCACACAGCATGTAAATATTGGGGC
TATGATTGAAAGGTTTCTAAAGTAGCTGGTTCTGCATACCTTTTGAGTATACAGCTGGGTTTTTGTGTCTCTCCAGTTAACCTAATGCAT
GGGTAAAAAGACATCAGGGGTCAGTGGAATAAACCAAGGTGTAGGACAGATTCATTCTGGGTCCTAAGCTGTTGTAGCATGGAGTCAGGG
AAATAACACTGGAATATTAAAAGGTAACCTTCATTCTAGTCTGTGCATTCTCATTAGCCAGAAAGAAGACTGGATAGGTCTCTTCCCTTG
CTGGCCTCCATTTCATTCATTTATGAAACAAGAGACTCAATGTTCTCTGTAGAAAACCTTTTTTAGAATCACTTGAAGAATTTGTTTAAA
AATGCAAATTCCTGGGCTCTACTCTCAGACTAAGTGAATCAGAAGCTTTGGTGTGGGAGACCATGGAACCTGCAGTTTTAATAAATGCCC
CAGTGATTTGCATGTTGGAGAATTATCACACCAGGTCACTGTGCTCTCATGTGGTGGGGATGCTCCACGATTGCTCTTGGAGTTGTGACT
TCCTTGGGTGTGACTAAAGCCAGGTGGTGCCATGGACATCATAAATATAAATTATGTAAGTGAAGGCACTGCTTCAGTCAGGCTGTAAAA
GCTATTTTGAAAGTGGTAAGGAAAAAGTAGGATTGTAATGAAGAAAATTTCCTTCCCAGGTTAAGCCTTCATTTGGAACTGCTTCCAGTA
CGTTACAAAAAGTAATAATAGCTAACCTGTGTCACTGACTGTATCTGGTACTATTTTAAGCACTATATATACATTATCTCAATGAATCTT
TCCCATTGTGACATCCGGCTAGTTTTCGTGGCTAAGAGTGTACTTTCTAACATCCATGAACATTGTGGTCCCCACCTGAAGTTTCACTTT
GCATGTTCAGTGATATGGTTTGGCTCTGTGTTCCCACCCAATCTTATCTCAAATTGTAATCCCCATGTGTCCAGGGAGGGACCTGTAATC
CCCACCTAGTGACGGAGGGAGGTGATTGATGATGGGTGTGGTGTACCCCATGCTGTTCTCGTGATAGTGAGTGGGTTCTCATGAGATCTG
ATGGTTTTATAAGTGTTTGAAAGTTCCCTCTTCACTCGCTGTCTTGCCTGCTGCCATGTAAAATGTGCCTACTTCACCCTCTGCCATGAT

>50210_50210_1_LSM3-MRPL22_LSM3_chr3_14225532_ENST00000306024_MRPL22_chr5_154335931_ENST00000523037_length(amino acids)=217AA_BP=73
MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKEIYHCRRQIKYSKD
KMWYLAKLIRGMSIDQALAQLEFNDKKGAKIIKEVLLEAQDMAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIMEKVYCHYF

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

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Fusion Gene PPI Analysis for LSM3-MRPL22

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 LSM3-MRPL22

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 LSM3-MRPL22

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source