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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:LARP4B-PAMR1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LARP4B-PAMR1
	FusionPDB ID: 44140
	FusionGDB2.0 ID: 44140
		Hgene	Tgene
	Gene symbol	LARP4B	PAMR1
	Gene ID	23185	25891
	Gene name	La ribonucleoprotein 4B	peptidase domain containing associated with muscle regeneration 1
	Synonyms	KIAA0217\|LARP5	DKFZP586H2123\|FP938\|RAMP
	Cytomap	10p15.3	11p13
	Type of gene	protein-coding	protein-coding
	Description	la-related protein 4BLa ribonucleoprotein domain family member 4BLa ribonucleoprotein domain family, member 5la-related protein 5	inactive serine protease PAMR1peptidase domain-containing protein associated with muscle regeneration 1regeneration associated muscle proteaseregeneration-associated muscle protease homolog
	Modification date	20200313	20200313
	UniProtAcc	Q92615	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000316157, ENST00000469487,	ENST00000532848, ENST00000534803, ENST00000278360, ENST00000378878, ENST00000378880,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 11 X 8=1144	5 X 4 X 4=80
	# samples	14	5
	** MAII score	log2(14/1144*10)=-3.03058831983342 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LARP4B [Title/Abstract] AND PAMR1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LARP4B(909683)-PAMR1(35515820), # samples:1
Anticipated loss of major functional domain due to fusion event.	LARP4B-PAMR1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. LARP4B-PAMR1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. LARP4B-PAMR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. LARP4B-PAMR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* 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

Fusion gene breakpoints across LARP4B (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 PAMR1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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	SKCM	TCGA-FS-A4F4-06A	LARP4B	chr10	909683	-	PAMR1	chr11	35515820	-

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000316157	LARP4B	chr10	909683	-	ENST00000278360	PAMR1	chr11	35515820	-	3146	471	41	2611	856
ENST00000316157	LARP4B	chr10	909683	-	ENST00000378880	PAMR1	chr11	35515820	-	3095	471	41	2560	839
ENST00000316157	LARP4B	chr10	909683	-	ENST00000378878	PAMR1	chr11	35515820	-	2754	471	41	2227	728

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
ENST00000316157	ENST00000278360	LARP4B	chr10	909683	-	PAMR1	chr11	35515820	-	0.004074353	0.99592566
ENST00000316157	ENST00000378880	LARP4B	chr10	909683	-	PAMR1	chr11	35515820	-	0.004455267	0.99554473
ENST00000316157	ENST00000378878	LARP4B	chr10	909683	-	PAMR1	chr11	35515820	-	0.007736863	0.9922631

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>44140_44140_1_LARP4B-PAMR1_LARP4B_chr10_909683_ENST00000316157_PAMR1_chr11_35515820_ENST00000278360_length(amino acids)=856AA_BP=128
MTSDQDAKVVAEPQTQRVQEGKDSAHLMNGPISQTTSQTSSIPPLSQVPATKVSELNPNAEVWGAPVLHLEASSAADGVSAAWEEVAGHH
ADRGPQGSDANGDGDQGHENAALPDPQESDPADMNALALGPSEYDSLPENSETEYTVINEACPGAEWNIMCRECCEYDQIECVCPGKREV
VGYTIPCCRNEENECDSCLIHPGCTIFENCKSCRNGSWGGTLDDFYVKGFYCAECRAGWYGGDCMRCGQVLRAPKGQILLESYPLNAHCE
WTIHAKPGFVIQLRFVMLSLEFDYMCQYDYVEVRDGDNRDGQIIKRVCGNERPAPIQSIGSSLHVLFHSDGSKNFDGFHAIYEEITACSS
SPCFHDGTCVLDKAGSYKCACLAGYTGQRCENLLEAGKSKIKASEDSLSVLEERNCSDPGGPVNGYQKITGGPGLINGRHAKIGTVVSFF
CNNSYVLSGNEKRTCQQNGEWSGKQPICIKACREPKISDLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGYQ
HLHTQLQYECISPFYRRLGSSRRTCLRTGKWSGRAPSCIPICGKIENITAPKTQGLRWPWQAAIYRRTSGVHDGSLHKGAWFLVCSGALV
NERTVVVAAHCVTDLGKVTMIKTADLKVVLGKFYRDDDRDEKTIQSLQISAIILHPNYDPILLDADIAILKLLDKARISTRVQPICLAAS
RDLSTSFQESHITVAGWNVLADVRSPGFKNDTLRSGVVSVVDSLLCEEQHEDHGIPVSVTDNMFCASWEPTAPSDICTAETGGIAAVSFP

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

>44140_44140_2_LARP4B-PAMR1_LARP4B_chr10_909683_ENST00000316157_PAMR1_chr11_35515820_ENST00000378878_length(amino acids)=728AA_BP=128
MTSDQDAKVVAEPQTQRVQEGKDSAHLMNGPISQTTSQTSSIPPLSQVPATKVSELNPNAEVWGAPVLHLEASSAADGVSAAWEEVAGHH
ADRGPQGSDANGDGDQGHENAALPDPQESDPADMNALALGPSEYDSLPENSETEYTVINEACPGAEWNIMCRECCEYDQIECVCPGKREV
VGYTIPCCRNEENECDSCLIHPGCTIFENCKSCRNGSWGGTLDDFYVKGFYCAECRAGWYGGDCMPCSSSPCFHDGTCVLDKAGSYKCAC
LAGYTGQRCENLLEERNCSDPGGPVNGYQKITGGPGLINGRHAKIGTVVSFFCNNSYVLSGNEKRTCQQNGEWSGKQPICIKACREPKIS
DLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGYQHLHTQLQYECISPFYRRLGSSRRTCLRTGKWSGRAPSC
IPICGKIENITAPKTQGLRWPWQAAIYRRTSGVHDGSLHKGAWFLVCSGALVNERTVVVAAHCVTDLGKVTMIKTADLKVVLGKFYRDDD
RDEKTIQSLQISAIILHPNYDPILLDADIAILKLLDKARISTRVQPICLAASRDLSTSFQESHITVAGWNVLADVRSPGFKNDTLRSGVV
SVVDSLLCEEQHEDHGIPVSVTDNMFCASWEPTAPSDICTAETGGIAAVSFPGRASPEPRWHLMGLVSWSYDKTCSHRLSTAFTKVLPFK

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

>44140_44140_3_LARP4B-PAMR1_LARP4B_chr10_909683_ENST00000316157_PAMR1_chr11_35515820_ENST00000378880_length(amino acids)=839AA_BP=128
MTSDQDAKVVAEPQTQRVQEGKDSAHLMNGPISQTTSQTSSIPPLSQVPATKVSELNPNAEVWGAPVLHLEASSAADGVSAAWEEVAGHH
ADRGPQGSDANGDGDQGHENAALPDPQESDPADMNALALGPSEYDSLPENSETEYTVINEACPGAEWNIMCRECCEYDQIECVCPGKREV
VGYTIPCCRNEENECDSCLIHPGCTIFENCKSCRNGSWGGTLDDFYVKGFYCAECRAGWYGGDCMRCGQVLRAPKGQILLESYPLNAHCE
WTIHAKPGFVIQLRFVMLSLEFDYMCQYDYVEVRDGDNRDGQIIKRVCGNERPAPIQSIGSSLHVLFHSDGSKNFDGFHAIYEEITACSS
SPCFHDGTCVLDKAGSYKCACLAGYTGQRCENLLEERNCSDPGGPVNGYQKITGGPGLINGRHAKIGTVVSFFCNNSYVLSGNEKRTCQQ
NGEWSGKQPICIKACREPKISDLVRRRVLPMQVQSRETPLHQLYSAAFSKQKLQSAPTKKPALPFGDLPMGYQHLHTQLQYECISPFYRR
LGSSRRTCLRTGKWSGRAPSCIPICGKIENITAPKTQGLRWPWQAAIYRRTSGVHDGSLHKGAWFLVCSGALVNERTVVVAAHCVTDLGK
VTMIKTADLKVVLGKFYRDDDRDEKTIQSLQISAIILHPNYDPILLDADIAILKLLDKARISTRVQPICLAASRDLSTSFQESHITVAGW
NVLADVRSPGFKNDTLRSGVVSVVDSLLCEEQHEDHGIPVSVTDNMFCASWEPTAPSDICTAETGGIAAVSFPGRASPEPRWHLMGLVSW

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

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr10:909683/chr11:35515820)
- 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
LARP4B Q92615	.
FUNCTION: Stimulates mRNA translation. {ECO:0000269\|PubMed:20573744}.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.

- 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

PAMR1

chr10:909683

chr11:35515820

ENST00000278360

42_94

24.333333333333332

738.0

Compositional bias

Note=Cys-rich

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000378880

42_94

24.333333333333332

721.0

Compositional bias

Note=Cys-rich

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000278360

128_236

24.333333333333332

738.0

Domain

CUB

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000278360

235_272

24.333333333333332

738.0

Domain

EGF-like

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000278360

278_344

24.333333333333332

738.0

Domain

Sushi 1

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000278360

387_444

24.333333333333332

738.0

Domain

Sushi 2

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000278360

445_720

24.333333333333332

738.0

Domain

Peptidase S1

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000378880

128_236

24.333333333333332

721.0

Domain

CUB

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000378880

235_272

24.333333333333332

721.0

Domain

EGF-like

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000378880

278_344

24.333333333333332

721.0

Domain

Sushi 1

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000378880

387_444

24.333333333333332

721.0

Domain

Sushi 2

Tgene

PAMR1

chr10:909683

chr11:35515820

ENST00000378880

445_720

24.333333333333332

721.0

Domain

Peptidase S1

- 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

Hgene

LARP4B

chr10:909683

chr11:35515820

ENST00000316157

150_239

143.33333333333334

739.0

Domain

HTH La-type RNA-binding

Hgene

LARP4B

chr10:909683

chr11:35515820

ENST00000316157

240_307

143.33333333333334

739.0

Domain

Note=RRM

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Fusion Protein-Protein Interaction

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 from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
LARP4B
PAMR1

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to LARP4B-PAMR1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to LARP4B-PAMR1

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source