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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:RPH3AL-LRRC37B (FusionGDB2 ID:75737)

Fusion Gene Summary for RPH3AL-LRRC37B

check button Fusion gene summary
Fusion gene informationFusion gene name: RPH3AL-LRRC37B
Fusion gene ID: 75737
HgeneTgene
Gene symbol

RPH3AL

LRRC37B

Gene ID

9501

114659

Gene namerabphilin 3A like (without C2 domains)leucine rich repeat containing 37B
SynonymsNOC2LRRC37
Cytomap

17p13.3

17q11.2

Type of geneprotein-codingprotein-coding
Descriptionrab effector Noc2no C2 domains proteinleucine-rich repeat-containing protein 37BC66 SLIT-like testicular protein
Modification date2020031320200313
UniProtAcc.

Q96QE4

Ensembl transtripts involved in fusion geneENST00000323434, ENST00000331302, 
ENST00000536489, ENST00000576001, 
ENST00000341671, ENST00000394713, 
ENST00000581786, ENST00000584368, 
ENST00000327564, ENST00000543378, 
Fusion gene scores* DoF score8 X 9 X 7=50413 X 14 X 8=1456
# samples 1015
** MAII scorelog2(10/504*10)=-2.33342373372519
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/1456*10)=-3.27897594970282
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPH3AL [Title/Abstract] AND LRRC37B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPH3AL(169210)-LRRC37B(30358396), # samples:1
Anticipated loss of major functional domain due to fusion event.RPH3AL-LRRC37B seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted 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

check buttonFusion gene breakpoints across RPH3AL (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 LRRC37B (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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-85-6560RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+


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Fusion Gene ORF analysis for RPH3AL-LRRC37B

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-intronENST00000323434ENST00000341671RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000323434ENST00000394713RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000323434ENST00000581786RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000323434ENST00000584368RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000331302ENST00000341671RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000331302ENST00000394713RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000331302ENST00000581786RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000331302ENST00000584368RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000536489ENST00000341671RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000536489ENST00000394713RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000536489ENST00000581786RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5CDS-intronENST00000536489ENST00000584368RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5UTR-3CDSENST00000576001ENST00000327564RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5UTR-3CDSENST00000576001ENST00000543378RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5UTR-intronENST00000576001ENST00000341671RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5UTR-intronENST00000576001ENST00000394713RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5UTR-intronENST00000576001ENST00000581786RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
5UTR-intronENST00000576001ENST00000584368RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
Frame-shiftENST00000323434ENST00000327564RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
Frame-shiftENST00000323434ENST00000543378RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
Frame-shiftENST00000331302ENST00000327564RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
Frame-shiftENST00000331302ENST00000543378RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
In-frameENST00000536489ENST00000327564RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+
In-frameENST00000536489ENST00000543378RPH3ALchr17

169210

-LRRC37Bchr17

30358396

+

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)
ENST00000536489RPH3ALchr17169210-ENST00000543378LRRC37Bchr1730358396+16255185221466314
ENST00000536489RPH3ALchr17169210-ENST00000327564LRRC37Bchr1730358396+16435185221466314

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
ENST00000536489ENST00000543378RPH3ALchr17169210-LRRC37Bchr1730358396+0.0016142570.9983858
ENST00000536489ENST00000327564RPH3ALchr17169210-LRRC37Bchr1730358396+0.0015155770.99848443

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Fusion Genomic Features for RPH3AL-LRRC37B


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)
RPH3ALchr17169210-LRRC37Bchr1730358396+0.029418090.9705819
RPH3ALchr17169210-LRRC37Bchr1730358396+0.029418090.9705819

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.
genomic feature

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 RPH3AL-LRRC37B


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/chr17:169210/chr17:30358396)
- 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
.LRRC37B

Q96QE4

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312867_897631948.0Coiled coilOntology_term=ECO:0000255
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312655_676631948.0RepeatNote=LRR 5
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312679_699631948.0RepeatNote=LRR 6
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312927_947631948.0Topological domainCytoplasmic
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312906_926631948.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRPH3ALchr17:169210chr17:30358396ENST00000323434-5941_158117287.0DomainRabBD
HgeneRPH3ALchr17:169210chr17:30358396ENST00000331302-51041_158117316.0DomainRabBD
HgeneRPH3ALchr17:169210chr17:30358396ENST00000536489-4841_158117287.0DomainRabBD
HgeneRPH3ALchr17:169210chr17:30358396ENST00000323434-5989_146117287.0Zinc fingerFYVE-type
HgeneRPH3ALchr17:169210chr17:30358396ENST00000331302-51089_146117316.0Zinc fingerFYVE-type
HgeneRPH3ALchr17:169210chr17:30358396ENST00000536489-4889_146117287.0Zinc fingerFYVE-type
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312556_577631948.0RepeatNote=LRR 1
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312580_601631948.0RepeatNote=LRR 2
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312604_625631948.0RepeatNote=LRR 3
TgeneLRRC37Bchr17:169210chr17:30358396ENST00000341671312628_649631948.0RepeatNote=LRR 4
TgeneLRRC37Bchr17:169210chr17:30358396ENST0000034167131228_905631948.0Topological domainExtracellular


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Fusion Gene Sequence for RPH3AL-LRRC37B


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.
>75737_75737_1_RPH3AL-LRRC37B_RPH3AL_chr17_169210_ENST00000536489_LRRC37B_chr17_30358396_ENST00000327564_length(transcript)=1643nt_BP=518nt
ATTGACTTAAGTCCCAGTGATTCAGCTCCTCATCTGGAACACCTCGGGTCACCCCCGACAACGGTGGTGGGAGGGAGAGCGGCCTCCTCC
TCCCTGGTGGGGCCTGTCTGGGTGAAGCCCCTCTGTTCCCGATGTGACTCCCCACCCCCAGCCGGGTGCTCCGAGCCATGGCCGACACCA
TCTTCGGCAGCGGGAATGATCAGTGGGTTTGCCCCAATGACCGGCAGCTTGCCCTTCGAGCCAAGCTGCAGACGGGCTGGTCCGTGCACA
CCTACCAGACGGAGAAGCAGAGGAGGAAGCAGCACCTCAGCCCGGCGGAGGTGGAGGCCATCCTGCAGGTCATCCAGAGGGCAGAGCGGC
TCGACGTCCTGGAGCAGCAGAGAATCGGGCGGCTGGTGGAGCGGCTGGAGACCATGAGGCGGAATGTGATGGGGAACGGCCTGTCCCAGT
GTCTGCTCTGCGGGGAGGTGCTGGGCTTCCTGGGCAGCTCGTCGGTGTTCTGCAAAGACTGCAGGAAGAAATCTGGGCTGCAATTTAATT
ACAAAACTGAGCCTTGGAACATTTCAGGCCTGGCACGGAATGCAGTTTTTACACAACTTAATTCTCAATCGCAATCCTCTGACTACTGTC
GAAGATCCATATCTCTTTGAACTGCCGGCATTAAAATATCTAGACATGGGAACAACACACATCACACTTACAACACTTAAGAACATTCTC
ACGATGACTGTTGAACTGGAAAAACTGATCTTACCTAGCCATATGGCCTGCTGCCTCTGCCAATTTAAAAATAGCATTGAGGCTGTCTGC
AAGACAGTCAAGCTGCATTGCAACACTGCATGTCTGACTAACAGCATACATTGTCCTGAAGAAGCATCTGTAGGGAATCCAGAAGGAGCG
TTCATGAAGATGTTACAAGCCCGGAAGCAGCACATGAGCACTCAGCTGACTATTGAGTCGGAGGCGCCCTCAGACAGCAGTGGCATCAAC
TTGTCAGGCTTTGGGGGTGATCAGCTTGAAATTCAGCTAACCGAGCAGCTACGGTCCCTCATCCCCAACGAGGATGTGAGAAAGTTCATG
TCTCATGTTATCCGGACCTTGAAAATGGAATGTTCAGAAACACATGTGCAAGGGAGCTGTGCCAAGCTCATGTTGCGAACAGGCCTCCTG
ATGAAGCTTCTCAGCGAGCAGCAGGAAGCAAAGGCATTGAATGTAGAATGGGATACGGACCAACAAAAAACAAATTATATTAATGAGAAC
ATGGAACAGAATGAACAGAAAGAGCAGAAGTCAAGTGAGCTCATGAAAGAAGTTCCAGGAGATGACTATAAGAACAAACTCATCTTCGCA
ATATCTGTGACTGTAATACTAATAATTTTGATTATAATTTTTTGTCTTATAGAGGTGAATTCACATAAAAGGGCATCAGAAAAATACAAA
GACAACCCATCAATATCAGGAGCCTGAGCATGAGTTAAAGCATGTGGATGGCCTGGAGCTATGTTTTTAAAATTGTTATTAAATATTGGT
TTTTTACTTAAATCAATGAAAACTTTCTTTACTTTGTGGTTGTGTTCCTCAAAATGAGAATTTTTAACAATAATAAAAATAAAGCTTGTT

>75737_75737_1_RPH3AL-LRRC37B_RPH3AL_chr17_169210_ENST00000536489_LRRC37B_chr17_30358396_ENST00000327564_length(amino acids)=314AA_BP=1
MGCNLITKLSLGTFQAWHGMQFLHNLILNRNPLTTVEDPYLFELPALKYLDMGTTHITLTTLKNILTMTVELEKLILPSHMACCLCQFKN
SIEAVCKTVKLHCNTACLTNSIHCPEEASVGNPEGAFMKMLQARKQHMSTQLTIESEAPSDSSGINLSGFGGDQLEIQLTEQLRSLIPNE
DVRKFMSHVIRTLKMECSETHVQGSCAKLMLRTGLLMKLLSEQQEAKALNVEWDTDQQKTNYINENMEQNEQKEQKSSELMKEVPGDDYK

--------------------------------------------------------------
>75737_75737_2_RPH3AL-LRRC37B_RPH3AL_chr17_169210_ENST00000536489_LRRC37B_chr17_30358396_ENST00000543378_length(transcript)=1625nt_BP=518nt
ATTGACTTAAGTCCCAGTGATTCAGCTCCTCATCTGGAACACCTCGGGTCACCCCCGACAACGGTGGTGGGAGGGAGAGCGGCCTCCTCC
TCCCTGGTGGGGCCTGTCTGGGTGAAGCCCCTCTGTTCCCGATGTGACTCCCCACCCCCAGCCGGGTGCTCCGAGCCATGGCCGACACCA
TCTTCGGCAGCGGGAATGATCAGTGGGTTTGCCCCAATGACCGGCAGCTTGCCCTTCGAGCCAAGCTGCAGACGGGCTGGTCCGTGCACA
CCTACCAGACGGAGAAGCAGAGGAGGAAGCAGCACCTCAGCCCGGCGGAGGTGGAGGCCATCCTGCAGGTCATCCAGAGGGCAGAGCGGC
TCGACGTCCTGGAGCAGCAGAGAATCGGGCGGCTGGTGGAGCGGCTGGAGACCATGAGGCGGAATGTGATGGGGAACGGCCTGTCCCAGT
GTCTGCTCTGCGGGGAGGTGCTGGGCTTCCTGGGCAGCTCGTCGGTGTTCTGCAAAGACTGCAGGAAGAAATCTGGGCTGCAATTTAATT
ACAAAACTGAGCCTTGGAACATTTCAGGCCTGGCACGGAATGCAGTTTTTACACAACTTAATTCTCAATCGCAATCCTCTGACTACTGTC
GAAGATCCATATCTCTTTGAACTGCCGGCATTAAAATATCTAGACATGGGAACAACACACATCACACTTACAACACTTAAGAACATTCTC
ACGATGACTGTTGAACTGGAAAAACTGATCTTACCTAGCCATATGGCCTGCTGCCTCTGCCAATTTAAAAATAGCATTGAGGCTGTCTGC
AAGACAGTCAAGCTGCATTGCAACACTGCATGTCTGACTAACAGCATACATTGTCCTGAAGAAGCATCTGTAGGGAATCCAGAAGGAGCG
TTCATGAAGATGTTACAAGCCCGGAAGCAGCACATGAGCACTCAGCTGACTATTGAGTCGGAGGCGCCCTCAGACAGCAGTGGCATCAAC
TTGTCAGGCTTTGGGGGTGATCAGCTTGAAATTCAGCTAACCGAGCAGCTACGGTCCCTCATCCCCAACGAGGATGTGAGAAAGTTCATG
TCTCATGTTATCCGGACCTTGAAAATGGAATGTTCAGAAACACATGTGCAAGGGAGCTGTGCCAAGCTCATGTTGCGAACAGGCCTCCTG
ATGAAGCTTCTCAGCGAGCAGCAGGAAGCAAAGGCATTGAATGTAGAATGGGATACGGACCAACAAAAAACAAATTATATTAATGAGAAC
ATGGAACAGAATGAACAGAAAGAGCAGAAGTCAAGTGAGCTCATGAAAGAAGTTCCAGGAGATGACTATAAGAACAAACTCATCTTCGCA
ATATCTGTGACTGTAATACTAATAATTTTGATTATAATTTTTTGTCTTATAGAGGTGAATTCACATAAAAGGGCATCAGAAAAATACAAA
GACAACCCATCAATATCAGGAGCCTGAGCATGAGTTAAAGCATGTGGATGGCCTGGAGCTATGTTTTTAAAATTGTTATTAAATATTGGT
TTTTTACTTAAATCAATGAAAACTTTCTTTACTTTGTGGTTGTGTTCCTCAAAATGAGAATTTTTAACAATAATAAAAATAAAGCTTGTT

>75737_75737_2_RPH3AL-LRRC37B_RPH3AL_chr17_169210_ENST00000536489_LRRC37B_chr17_30358396_ENST00000543378_length(amino acids)=314AA_BP=1
MGCNLITKLSLGTFQAWHGMQFLHNLILNRNPLTTVEDPYLFELPALKYLDMGTTHITLTTLKNILTMTVELEKLILPSHMACCLCQFKN
SIEAVCKTVKLHCNTACLTNSIHCPEEASVGNPEGAFMKMLQARKQHMSTQLTIESEAPSDSSGINLSGFGGDQLEIQLTEQLRSLIPNE
DVRKFMSHVIRTLKMECSETHVQGSCAKLMLRTGLLMKLLSEQQEAKALNVEWDTDQQKTNYINENMEQNEQKEQKSSELMKEVPGDDYK

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Fusion Gene PPI Analysis for RPH3AL-LRRC37B


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 RPH3AL-LRRC37B


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 RPH3AL-LRRC37B


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