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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SMG1-LRRK1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SMG1-LRRK1
FusionPDB ID: 84070
FusionGDB2.0 ID: 84070
HgeneTgene
Gene symbol

SMG1

LRRK1

Gene ID

23049

79705

Gene nameSMG1 nonsense mediated mRNA decay associated PI3K related kinaseleucine rich repeat kinase 1
Synonyms61E3.4|ATX|LIPRIPK6|Roco1
Cytomap

16p12.3

15q26.3

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase SMG1PI-3-kinase-related kinase SMG-1SMG1 phosphatidylinositol 3-kinase-related kinaselambda-interacting proteinlambda/iota protein kinase C-interacting proteinsmg-1 homolog, phosphatidylinositol 3-kinase-related kinaseleucine-rich repeat serine/threonine-protein kinase 1
Modification date2020031320200313
UniProtAcc.

Q38SD2

Ensembl transtripts involved in fusion geneENST idsENST00000389467, ENST00000446231, 
ENST00000565224, ENST00000567737, 
ENST00000532145, ENST00000284395, 
ENST00000388948, ENST00000532029, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score28 X 23 X 9=57964 X 4 X 4=64
# samples 314
** MAII scorelog2(31/5796*10)=-4.22471747428269
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/64*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: SMG1 [Title/Abstract] AND LRRK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SMG1(18907374)-LRRK1(101528839), # samples:1
Anticipated loss of major functional domain due to fusion event.SMG1-LRRK1 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.
SMG1-LRRK1 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.
SMG1-LRRK1 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.
SMG1-LRRK1 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSMG1

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

11544179

HgeneSMG1

GO:0018105

peptidyl-serine phosphorylation

11544179|15175154

HgeneSMG1

GO:0046777

protein autophosphorylation

11331269|11544179

HgeneSMG1

GO:0046854

phosphatidylinositol phosphorylation

11331269

HgeneSMG1

GO:2001020

regulation of response to DNA damage stimulus

15175154


check buttonFusion gene breakpoints across SMG1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across LRRK1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4OVTCGA-29-1711-01ASMG1chr16

18907374

-LRRK1chr15

101528839

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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000389467SMG1chr1618907374-ENST00000388948LRRK1chr15101528839+765477515363892078
ENST00000389467SMG1chr1618907374-ENST00000284395LRRK1chr15101528839+765177579763881863
ENST00000389467SMG1chr1618907374-ENST00000532029LRRK1chr15101528839+13547751531136327
ENST00000446231SMG1chr1618907374-ENST00000388948LRRK1chr15101528839+770482520364392078
ENST00000446231SMG1chr1618907374-ENST00000284395LRRK1chr15101528839+770182584764381863
ENST00000446231SMG1chr1618907374-ENST00000532029LRRK1chr15101528839+14048252031186327
ENST00000565224SMG1chr1618907374-ENST00000388948LRRK1chr15101528839+72573784459921982
ENST00000565224SMG1chr1618907374-ENST00000284395LRRK1chr15101528839+725437840059911863
ENST00000565224SMG1chr1618907374-ENST00000532029LRRK1chr15101528839+95737844739231

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
ENST00000389467ENST00000388948SMG1chr1618907374-LRRK1chr15101528839+0.0018806350.9981193
ENST00000389467ENST00000284395SMG1chr1618907374-LRRK1chr15101528839+0.002730170.9972698
ENST00000389467ENST00000532029SMG1chr1618907374-LRRK1chr15101528839+0.0077711770.9922288
ENST00000446231ENST00000388948SMG1chr1618907374-LRRK1chr15101528839+0.0020021230.9979978
ENST00000446231ENST00000284395SMG1chr1618907374-LRRK1chr15101528839+0.0029056030.9970944
ENST00000446231ENST00000532029SMG1chr1618907374-LRRK1chr15101528839+0.0075642430.99243575
ENST00000565224ENST00000388948SMG1chr1618907374-LRRK1chr15101528839+0.0012120010.99878806
ENST00000565224ENST00000284395SMG1chr1618907374-LRRK1chr15101528839+0.0017311160.99826884
ENST00000565224ENST00000532029SMG1chr1618907374-LRRK1chr15101528839+0.0036119870.9963881

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Fusion Amino Acid Sequences


check button 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

>84070_84070_1_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000389467_LRRK1_chr15_101528839_ENST00000284395_length(amino acids)=1863AA_BP=
MNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIE
ASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWGLINLRKLNLSDNHLGELPGVQSSDEIICSRLL
EIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDISDNKLTELPALFLHSFKSLNSLNVSRNNLKVFPDP
WACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMFLRLQGNQLAALPPQEKWTCRQLKTLDLSRNQLGKN
EDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSLSELYLGNNPGLRELPPELGQLGNLWQLDT
EDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEILQTGRAPQVVHGEATIRTTKWELQRPAGSRAKVES
VEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKAPNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALC
RSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQRLAGRLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTD
RQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVGTG
FTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRVFKMSFVPVGFWQRFIARMLISLAEMDLQLFENKKN
TKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVNWKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLID
QWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTAIERDFISCPRHPDLPVPLQELVPELFMTDFPARLF
LENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADTMLRHLRATDAMKNFSEFRQEASMLHALQHPCIVAL
IGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYLHKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGI
SRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGHHQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMMEC
WDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKEESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQR
SLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGLADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIA
DEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVVCSSEGRGEEVVWCLDDKANSLVMYHSTTYQLC
ARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQILIHQESLTDYCSMSSYSSSPPRQAARSPSSLPSS
PASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRDLIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARE

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>84070_84070_2_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000389467_LRRK1_chr15_101528839_ENST00000388948_length(amino acids)=2078AA_BP=207
MRCGLRRNPERPSSSPALRRLLLLLLLLLLLLLGFLLSPGPERGVGGGRFGRRLALLWAAALGHVVSGKVMSRRAPGSRLSSGGGGGGTK
YPRSWNDWQPRTDSASADPDNLKYSSSRDRGGSSSYGLQPSNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRV
NNVTSPEFTSVQHGSRALATKDMRKSQGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNE
DIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIEASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVI
PWGLINLRKLNLSDNHLGELPGVQSSDEIICSRLLEIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDI
SDNKLTELPALFLHSFKSLNSLNVSRNNLKVFPDPWACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMF
LRLQGNQLAALPPQEKWTCRQLKTLDLSRNQLGKNEDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSV
CLLKSLSELYLGNNPGLRELPPELGQLGNLWQLDTEDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEI
LQTGRAPQVVHGEATIRTTKWELQRPAGSRAKVESVEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKA
PNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALCRSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQR
LAGRLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTDRQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWL
SECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVGTGFTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRV
FKMSFVPVGFWQRFIARMLISLAEMDLQLFENKKNTKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVN
WKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLIDQWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTA
IERDFISCPRHPDLPVPLQELVPELFMTDFPARLFLENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADT
MLRHLRATDAMKNFSEFRQEASMLHALQHPCIVALIGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYL
HKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGISRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGH
HQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMMECWDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKE
ESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQRSLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGL
ADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIADEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVT
SVVCSSEGRGEEVVWCLDDKANSLVMYHSTTYQLCARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQ
ILIHQESLTDYCSMSSYSSSPPRQAARSPSSLPSSPASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRD
LIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARELTPHGVLVDAAVVAKDTVVCTFENENTEWCLAVWRGWGAREFDIFYQSYEELGRL

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>84070_84070_3_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000389467_LRRK1_chr15_101528839_ENST00000532029_length(amino acids)=327AA_BP=207
MRCGLRRNPERPSSSPALRRLLLLLLLLLLLLLGFLLSPGPERGVGGGRFGRRLALLWAAALGHVVSGKVMSRRAPGSRLSSGGGGGGTK
YPRSWNDWQPRTDSASADPDNLKYSSSRDRGGSSSYGLQPSNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRV
NNVTSPEFTSVQHGSRALATKDMRKSQGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNE

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>84070_84070_4_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000446231_LRRK1_chr15_101528839_ENST00000284395_length(amino acids)=1863AA_BP=
MNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIE
ASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWGLINLRKLNLSDNHLGELPGVQSSDEIICSRLL
EIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDISDNKLTELPALFLHSFKSLNSLNVSRNNLKVFPDP
WACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMFLRLQGNQLAALPPQEKWTCRQLKTLDLSRNQLGKN
EDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSLSELYLGNNPGLRELPPELGQLGNLWQLDT
EDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEILQTGRAPQVVHGEATIRTTKWELQRPAGSRAKVES
VEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKAPNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALC
RSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQRLAGRLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTD
RQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVGTG
FTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRVFKMSFVPVGFWQRFIARMLISLAEMDLQLFENKKN
TKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVNWKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLID
QWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTAIERDFISCPRHPDLPVPLQELVPELFMTDFPARLF
LENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADTMLRHLRATDAMKNFSEFRQEASMLHALQHPCIVAL
IGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYLHKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGI
SRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGHHQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMMEC
WDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKEESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQR
SLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGLADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIA
DEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVVCSSEGRGEEVVWCLDDKANSLVMYHSTTYQLC
ARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQILIHQESLTDYCSMSSYSSSPPRQAARSPSSLPSS
PASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRDLIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARE

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>84070_84070_5_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000446231_LRRK1_chr15_101528839_ENST00000388948_length(amino acids)=2078AA_BP=207
MRCGLRRNPERPSSSPALRRLLLLLLLLLLLLLGFLLSPGPERGVGGGRFGRRLALLWAAALGHVVSGKVMSRRAPGSRLSSGGGGGGTK
YPRSWNDWQPRTDSASADPDNLKYSSSRDRGGSSSYGLQPSNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRV
NNVTSPEFTSVQHGSRALATKDMRKSQGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNE
DIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIEASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVI
PWGLINLRKLNLSDNHLGELPGVQSSDEIICSRLLEIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDI
SDNKLTELPALFLHSFKSLNSLNVSRNNLKVFPDPWACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMF
LRLQGNQLAALPPQEKWTCRQLKTLDLSRNQLGKNEDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSV
CLLKSLSELYLGNNPGLRELPPELGQLGNLWQLDTEDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEI
LQTGRAPQVVHGEATIRTTKWELQRPAGSRAKVESVEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKA
PNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALCRSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQR
LAGRLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTDRQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWL
SECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVGTGFTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRV
FKMSFVPVGFWQRFIARMLISLAEMDLQLFENKKNTKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVN
WKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLIDQWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTA
IERDFISCPRHPDLPVPLQELVPELFMTDFPARLFLENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADT
MLRHLRATDAMKNFSEFRQEASMLHALQHPCIVALIGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYL
HKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGISRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGH
HQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMMECWDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKE
ESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQRSLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGL
ADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIADEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVT
SVVCSSEGRGEEVVWCLDDKANSLVMYHSTTYQLCARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQ
ILIHQESLTDYCSMSSYSSSPPRQAARSPSSLPSSPASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRD
LIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARELTPHGVLVDAAVVAKDTVVCTFENENTEWCLAVWRGWGAREFDIFYQSYEELGRL

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>84070_84070_6_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000446231_LRRK1_chr15_101528839_ENST00000532029_length(amino acids)=327AA_BP=207
MRCGLRRNPERPSSSPALRRLLLLLLLLLLLLLGFLLSPGPERGVGGGRFGRRLALLWAAALGHVVSGKVMSRRAPGSRLSSGGGGGGTK
YPRSWNDWQPRTDSASADPDNLKYSSSRDRGGSSSYGLQPSNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRV
NNVTSPEFTSVQHGSRALATKDMRKSQGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNE

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

>84070_84070_7_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000565224_LRRK1_chr15_101528839_ENST00000284395_length(amino acids)=1863AA_BP=
MNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIE
ASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWGLINLRKLNLSDNHLGELPGVQSSDEIICSRLL
EIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDISDNKLTELPALFLHSFKSLNSLNVSRNNLKVFPDP
WACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMFLRLQGNQLAALPPQEKWTCRQLKTLDLSRNQLGKN
EDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSLSELYLGNNPGLRELPPELGQLGNLWQLDT
EDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEILQTGRAPQVVHGEATIRTTKWELQRPAGSRAKVES
VEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKAPNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALC
RSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQRLAGRLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTD
RQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVGTG
FTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRVFKMSFVPVGFWQRFIARMLISLAEMDLQLFENKKN
TKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVNWKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLID
QWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTAIERDFISCPRHPDLPVPLQELVPELFMTDFPARLF
LENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADTMLRHLRATDAMKNFSEFRQEASMLHALQHPCIVAL
IGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYLHKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGI
SRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGHHQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMMEC
WDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKEESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQR
SLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGLADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIA
DEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVVCSSEGRGEEVVWCLDDKANSLVMYHSTTYQLC
ARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQILIHQESLTDYCSMSSYSSSPPRQAARSPSSLPSS
PASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRDLIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARE

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

>84070_84070_8_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000565224_LRRK1_chr15_101528839_ENST00000388948_length(amino acids)=1982AA_BP=111
MRFLRTDSASADPDNLKYSSSRDRGGSSSYGLQPSNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRVNNVTSP
EFTSVQHGSRALATKDMRKSQGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFL
LRHGAYFCSYILLDSPDPSKHLLRKYFIEASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWGLIN
LRKLNLSDNHLGELPGVQSSDEIICSRLLEIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDISDNKLT
ELPALFLHSFKSLNSLNVSRNNLKVFPDPWACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMFLRLQGN
QLAALPPQEKWTCRQLKTLDLSRNQLGKNEDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSL
SELYLGNNPGLRELPPELGQLGNLWQLDTEDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEILQTGRA
PQVVHGEATIRTTKWELQRPAGSRAKVESVEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKAPNAVVL
VVGTHLDLIEAKFRVERIATLRAYVLALCRSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQRLAGRLI
PRSYLSLQEAVLAEQQRRSRDDDVQYLTDRQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWLSECLQR
IFNIKGSRSVAKNGVIRAEDLRMLLVGTGFTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRVFKMSFV
PVGFWQRFIARMLISLAEMDLQLFENKKNTKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVNWKKKKS
GGMKIVCQSEVRDFSAMAFITDHVNSLIDQWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTAIERDFI
SCPRHPDLPVPLQELVPELFMTDFPARLFLENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADTMLRHLR
ATDAMKNFSEFRQEASMLHALQHPCIVALIGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYLHKKNII
FCDLKSDNILVWSLDVKEHINIKLSDYGISRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGHHQLQIA
KKLSKGIRPVLGQPEEVQFRRLQALMMECWDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKEESRNYT
VVNTEKGLMEVQRMCCPGMKVSCQLQVQRSLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGLADGLVA
VFPVVRGTPKDSCSYLCSHTANRSKFSIADEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVVCSS
EGRGEEVVWCLDDKANSLVMYHSTTYQLCARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQILIHQE
SLTDYCSMSSYSSSPPRQAARSPSSLPSSPASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRDLIWVPR
RGGDVIVIGLEKDSGAQRGRVIAVLKARELTPHGVLVDAAVVAKDTVVCTFENENTEWCLAVWRGWGAREFDIFYQSYEELGRLEACTRK

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

>84070_84070_9_SMG1-LRRK1_SMG1_chr16_18907374_ENST00000565224_LRRK1_chr15_101528839_ENST00000532029_length(amino acids)=231AA_BP=111
MRFLRTDSASADPDNLKYSSSRDRGGSSSYGLQPSNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRVNNVTSP
EFTSVQHGSRALATKDMRKSQGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFL

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Fusion Protein Functional Features


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/chr16:18907374/chr15:101528839)
- 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
.LRRK1

Q38SD2

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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneLRRK1chr16:18907374chr15:101528839ENST000003889483341242_1525144.333333333333342016.0DomainProtein kinase
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334632_826144.333333333333342016.0DomainRoc
TgeneLRRK1chr16:18907374chr15:101528839ENST00000532029361242_1525144.33333333333334265.0DomainProtein kinase
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936632_826144.33333333333334265.0DomainRoc
TgeneLRRK1chr16:18907374chr15:101528839ENST000003889483341248_1256144.333333333333342016.0Nucleotide bindingATP
TgeneLRRK1chr16:18907374chr15:101528839ENST00000532029361248_1256144.33333333333334265.0Nucleotide bindingATP
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334152_182144.333333333333342016.0RepeatNote=ANK 3
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334193_222144.333333333333342016.0RepeatNote=ANK 4
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334279_300144.333333333333342016.0RepeatNote=LRR 1
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334303_324144.333333333333342016.0RepeatNote=LRR 2
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334330_351144.333333333333342016.0RepeatNote=LRR 3
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334353_374144.333333333333342016.0RepeatNote=LRR 4
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334381_402144.333333333333342016.0RepeatNote=LRR 5
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334405_426144.333333333333342016.0RepeatNote=LRR 6
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334427_447144.333333333333342016.0RepeatNote=LRR 7
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334451_472144.333333333333342016.0RepeatNote=LRR 8
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334474_495144.333333333333342016.0RepeatNote=LRR 9
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334498_519144.333333333333342016.0RepeatNote=LRR 10
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334549_570144.333333333333342016.0RepeatNote=LRR 11
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334572_594144.333333333333342016.0RepeatNote=LRR 12
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334596_617144.333333333333342016.0RepeatNote=LRR 13
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936152_182144.33333333333334265.0RepeatNote=ANK 3
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936193_222144.33333333333334265.0RepeatNote=ANK 4
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936279_300144.33333333333334265.0RepeatNote=LRR 1
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936303_324144.33333333333334265.0RepeatNote=LRR 2
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936330_351144.33333333333334265.0RepeatNote=LRR 3
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936353_374144.33333333333334265.0RepeatNote=LRR 4
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936381_402144.33333333333334265.0RepeatNote=LRR 5
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936405_426144.33333333333334265.0RepeatNote=LRR 6
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936427_447144.33333333333334265.0RepeatNote=LRR 7
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936451_472144.33333333333334265.0RepeatNote=LRR 8
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936474_495144.33333333333334265.0RepeatNote=LRR 9
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936498_519144.33333333333334265.0RepeatNote=LRR 10
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936549_570144.33333333333334265.0RepeatNote=LRR 11
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936572_594144.33333333333334265.0RepeatNote=LRR 12
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936596_617144.33333333333334265.0RepeatNote=LRR 13

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMG1chr16:18907374chr15:101528839ENST00000446231-3631283_1866137.333333333333343662.0DomainFAT
HgeneSMG1chr16:18907374chr15:101528839ENST00000446231-3632150_2478137.333333333333343662.0DomainPI3K/PI4K
HgeneSMG1chr16:18907374chr15:101528839ENST00000446231-3633629_3661137.333333333333343662.0DomainFATC
HgeneSMG1chr16:18907374chr15:101528839ENST00000446231-3631817_1852137.333333333333343662.0RepeatNote=HEAT
TgeneLRRK1chr16:18907374chr15:101528839ENST00000388948334119_148144.333333333333342016.0RepeatNote=ANK 2
TgeneLRRK1chr16:18907374chr15:101528839ENST0000038894833486_116144.333333333333342016.0RepeatNote=ANK 1
TgeneLRRK1chr16:18907374chr15:101528839ENST0000053202936119_148144.33333333333334265.0RepeatNote=ANK 2
TgeneLRRK1chr16:18907374chr15:101528839ENST000005320293686_116144.33333333333334265.0RepeatNote=ANK 1


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SMG1
LRRK1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneSMG1chr16:18907374chr15:101528839ENST00000446231-3631_1977137.333333333333343662.0SMG8 and SMG9


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Related Drugs to SMG1-LRRK1


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

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Related Diseases to SMG1-LRRK1


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

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