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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:CRIM1-TBC1D25 (FusionGDB2 ID:19445)

Fusion Gene Summary for CRIM1-TBC1D25

check button Fusion gene summary
Fusion gene informationFusion gene name: CRIM1-TBC1D25
Fusion gene ID: 19445
HgeneTgene
Gene symbol

CRIM1

TBC1D25

Gene ID

51232

4943

Gene namecysteine rich transmembrane BMP regulator 1TBC1 domain family member 25
SynonymsCRIM-1|S52MG81|OATL1
Cytomap

2p22.2

Xp11.23

Type of geneprotein-codingprotein-coding
Descriptioncysteine-rich motor neuron 1 proteincysteine rich transmembrane BMP regulator 1 (chordin-like)cysteine-rich repeat-containing protein S52TBC1 domain family member 255SN3 snoRNAornithine aminotransferase-like 1
Modification date2020031320200313
UniProtAcc

Q9NZV1

.
Ensembl transtripts involved in fusion geneENST00000280527, ENST00000473403, 
ENST00000476141, ENST00000537536, 
ENST00000376771, 
Fusion gene scores* DoF score15 X 11 X 8=13201 X 1 X 1=1
# samples 161
** MAII scorelog2(16/1320*10)=-3.04439411935845
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: CRIM1 [Title/Abstract] AND TBC1D25 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCRIM1(36583766)-TBC1D25(48417285), # samples:1
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)

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 CRIM1 (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 TBC1D25 (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
ChimerDB4LUADTCGA-L9-A743-01ACRIM1chr2

36583766

-TBC1D25chrX

48417285

+


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Fusion Gene ORF analysis for CRIM1-TBC1D25

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-3UTRENST00000280527ENST00000476141CRIM1chr2

36583766

-TBC1D25chrX

48417285

+
5CDS-intronENST00000280527ENST00000537536CRIM1chr2

36583766

-TBC1D25chrX

48417285

+
In-frameENST00000280527ENST00000376771CRIM1chr2

36583766

-TBC1D25chrX

48417285

+
intron-3CDSENST00000473403ENST00000376771CRIM1chr2

36583766

-TBC1D25chrX

48417285

+
intron-3UTRENST00000473403ENST00000476141CRIM1chr2

36583766

-TBC1D25chrX

48417285

+
intron-intronENST00000473403ENST00000537536CRIM1chr2

36583766

-TBC1D25chrX

48417285

+

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)
ENST00000280527CRIM1chr236583766-ENST00000376771TBC1D25chrX48417285+40116983672376669

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
ENST00000280527ENST00000376771CRIM1chr236583766-TBC1D25chrX48417285+0.0186879970.981312

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Fusion Genomic Features for CRIM1-TBC1D25


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)

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.

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Fusion Protein Features for CRIM1-TBC1D25


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/chr2:36583766/chrX:48417285)
- 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
CRIM1

Q9NZV1

.
FUNCTION: May play a role in CNS development by interacting with growth factors implicated in motor neuron differentiation and survival. May play a role in capillary formation and maintenance during angiogenesis. Modulates BMP activity by affecting its processing and delivery to the cell surface. {ECO:0000269|PubMed:12464430, ECO:0000269|PubMed:12805376}.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
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-11735_1121101037.0DomainIGFBP N-terminal
TgeneTBC1D25chr2:36583766chrX:48417285ENST0000037677126494_499129689.0Compositional biasNote=Poly-Gly
TgeneTBC1D25chr2:36583766chrX:48417285ENST0000037677126559_564129689.0Compositional biasNote=Poly-Ser
TgeneTBC1D25chr2:36583766chrX:48417285ENST0000037677126228_434129689.0DomainRab-GAP TBC

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117334_3911101037.0DomainVWFC 1
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117401_4571101037.0DomainVWFC 2
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117469_4981101037.0DomainAntistasin-like 1
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117505_5321101037.0DomainAntistasin-like 2
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117539_5641101037.0DomainAntistasin-like 3
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117567_5921101037.0DomainAntistasin-like 4
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117606_6631101037.0DomainVWFC 3
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117677_7351101037.0DomainVWFC 4
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117751_8091101037.0DomainVWFC 5
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117817_8741101037.0DomainVWFC 6
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117314_3161101037.0MotifCell attachment site
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-11735_9391101037.0Topological domainExtracellular
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117961_10361101037.0Topological domainCytoplasmic
HgeneCRIM1chr2:36583766chrX:48417285ENST00000280527-117940_9601101037.0TransmembraneHelical
TgeneTBC1D25chr2:36583766chrX:48417285ENST000003767712622_28129689.0Compositional biasNote=Poly-Ala
TgeneTBC1D25chr2:36583766chrX:48417285ENST000003767712629_34129689.0Compositional biasNote=Poly-Glu


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Fusion Gene Sequence for CRIM1-TBC1D25


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.
>19445_19445_1_CRIM1-TBC1D25_CRIM1_chr2_36583766_ENST00000280527_TBC1D25_chrX_48417285_ENST00000376771_length(transcript)=4011nt_BP=698nt
GCCGCCGGCCCGGGCTGGAGCCGAGCGCAGCAGCCACCGCCGCCGCCGCGCCAGAAGTTTGGGTTGAACCGGAGCTGCCGGGAGGAAACT
TTTTTCTTTTTTCCCCCTCCCTCCCGGGAGGAGGAGGAGGAGGAGGAGGGGAAGCTGCCGCCGGCGCCAAGGCTCGTGGGCTCGGGGTCG
GCGCGGCCCGCAGAAGGGGCGGGGGCCTCGCCCCGCGAGGGGAGGCGCGCCCCGGGGGCCCCGAGAGGGGCGGTGAGGACCGCGGGCTGC
TGGTGCGGCGGCGGCGGCGCGTGTGCCCCGCGCAGGGGAGGGCGCCCGCCCCGCTCCCGGCCCGGCTGCGAGGAGGAGGCGGCGGCGGCG
CAGGAGGATGTACTTGGTGGCGGGGGACAGGGGGTTGGCCGGCTGCGGGCACCTCCTGGTCTCGCTGCTGGGGCTGCTGCTGCTGCTGGC
GCGCTCCGGCACCCGGGCGCTGGTCTGCCTGCCCTGTGACGAGTCCAAGTGCGAGGAGCCCAGGAACTGCCCGGGGAGCATCGTGCAGGG
CGTCTGCGGCTGCTGCTACACGTGCGCCAGCCAGAGGAACGAGAGCTGCGGCGGCACCTTCGGGATTTACGGAACCTGCGACCGGGGGCT
GCGTTGTGTCATCCGCCCCCCGCTCAATGGCGACTCCCTCACCGAGTACGAAGCGGGCGTTTGCGAAGGCCCATTGCTAGAAGACTGGGA
CATAATCAGCCCCAAAGATGTCATTGGCTCCGACGTGTTGCTGGCTGAGAAACGGTCATCACTGACGACTGCCGCCCTGCCCTTTACACA
GTCCATCCTCACTCAGGTGGGCCGTACCTTGTCTAAGGTCCAACAAGTGCTGAGCTGGTCGTATGGGGAAGATGTCAAGCCCTTCAAGCC
ACCCCTGAGCGATGCTGAGTTTCACACGTACCTGAACCACGAGGGCCAGCTCTCCCGACCCGAGGAGTTGCGCCTGCGGATCTATCATGG
CGGTGTGGAGCCCTCGCTGCGAAAGGTGGTGTGGCGGTACCTGCTGAACGTGTATCCAGATGGACTGACAGGCCGAGAGCGGATGGACTA
CATGAAACGCAAGAGCCGCGAGTATGAGCAGCTCAAGAGCGAGTGGGCCCAGCGAGCGAACCCTGAGGACCTGGAATTCATCCGCAGCAC
GGTCCTCAAGGATGTACTGCGCACTGACCGGGCCCACCCCTACTATGCGGGGCCTGAGGATGGCCCACATCTACGGGCGCTGCACGACCT
GCTCACCACCTATGCCGTTACCCACCCACAGGTGTCCTACTGCCAGGGCATGAGTGACCTTGCCTCACCCATCCTCGCTGTCATGGACCA
TGAGGGCCATGCCTTTGTTTGCTTTTGTGGCATCATGAAACGCCTGGCCGCCAACTTCCACCCTGACGGCCGCGCCATGGCCACCAAGTT
TGCACACTTGAAGCTGTTGCTGCGACACGCTGACCCTGACTTTTATCAATACCTGCAAGAGGCAGGCGCTGATGACCTCTTCTTCTGTTA
CCGCTGGCTGCTGCTGGAACTCAAGCGTGAGTTCGCCTTCGACGATGCCCTCCGCATGCTTGAGGTCACTTGGAGTTCGCTGCCCCCTGA
TCCTCCTGAACATGAGGTAGAGCTGGTTGGACCCCCCAGCCAAGTGGCAGACGCTGGTTTTGGTGGCCACAGGGGGTGGCCCGTGCGACA
GAGGCACATGCTGAGGCCTGCTGGTGGAGGAGGTAGTACCTTTGAAGATGCTGTTGACCACCTGGCCACAGCCAGTCAGGGGCCTGGTGG
TGGGGGGCGTCTCCTGAGACAGGCCAGCTTGGATGGCCTCCAGCAACTCAGGGATAACATGGGCTCCAGGAGGGACCCTCTGGTCCAGCT
GCCCCACCCAGCTGCCCTTATCAGCTCCAAGTCCCTCTCTGAGCCTTTATTGAACTCCCCAGACCCACTGCTCTCCTCCTTTTCCCACCC
TGATTCCCCATCTTCCTCATCTCCACCATCCACCCAGGAGGCCTCTCCCACTGGTGATATGGCTGTAGGATCCCCCTTGATGCAAGAGGT
AGGCTCCCCGAAAGACCCTGGAAAGTCCCTGCCACCTGTACCACCAATGGGCCTGCCCCCACCCCAGGAGTTTGGCCGGGGGAACCCATT
CATGCTGTTCCTCTGCCTGGCCATCCTGCTGGAGCACCGCGACCACATCATGCGCAATGGGCTGGATTATAATGAGCTGGCCATGCACTT
TGACCGCCTTGTGCGAAAACACCACCTGGGGCGCGTCCTGCGCCGGGCTAGGGCTCTCTTTGCTGATTACCTGCAGTCAGAGGTGTGGGA
CTCAGAGGAGGGGGCTGAGGCCACAGCCGCATCTTGATCAGGCTTTCTCAAGCCCTCCATCGGCCCCACCAGATCTCCATTCTTTGCCAT
GAGGGCCAACACATGAGACCCCACCTCCCTCCCTGCCTGCCAGCCCTAGACTTGTTGGAGCATAGAGCCCTTCCTCCCCAGGCCTAAGTA
TGTGGAGCTCTGCTTTGGCACTGCCCCGCAGAGGCCACGCCTATTTATTCTGTTTCTGTTGTTTTGTTTTTAACAACTATACTTTGCACA
CATGAAGGTCACTGTGGTTTGTGTGTTTCTCTGCCTCCTCCCTGGGTTTTGCTGTAGATGGAGTCCTCAGGGGCCCTTTACCTGATGGAG
GGGAAATACTTCACTTGGTGGAGAGAGGCTCCAGCTTCCCCCTTGTGATGGGGAGAGTGGATGCTGACAATCAGTTCCCAAAGGTGAGCC
CAGGTGGAGCACTGCTTGAGGAAGGCCTGAGTCTGTTTTTTTGGTACATCCATCGGCCTGTAAGGGTCTGTATTATGGCTGTGAATATAT
GTTTTCAGGACAGCCCCCTGGATGAGAGATAAGAGAGTTCCTGGCTCAAAAAAGGACAAGATTCTTTACTGAGATTGGGAAGTATGGGCT
ACTTAGAAACGTTGGAGCAGCCACCCCTGGCATTCCACATGTCACCATTTCTAGGATCTTGGCCTCTCTGTGAGGTTTATGCACCAATGC
TGGCAGCCCTGGGCAGGGGCCTCGGCCTCCTTTTTGTTTTCCACTTCAGACAGGTACCGTGCAGATGTTAACAAGGTTTGAGCGAGGTGC
ATCTCACACAAGTGTGAAAGCCCAATCATCACATTGTTGAATTACAAAAGGATCTAGGGCTCCTATTCTTGTCACTTGCTTTGGAGCCAG
TTTGAAAGACTGGCCTAGCCCATGCCTAGCGGCCCTAAACTGGGATTCCAGCTCACAGCACCTGTCTTAACCATTTCAGCAGTAGAAACC
ACTTATTTACCTTCTCCATCTCACTAATATGGACAAACAACAAGCACTGATAAAACGCAGGCCCTAATAGAATTCACTTCGTTATTTGGA
GGATAATGATCAAAAAAAGGTCCTTTTTCCCACTGACATGCTCAGAGGGTGGGATTCTCTCACAGGCCAGGTGCTGTCATCCACAAAGGA
TGGGTGAAATAACTGGGGTCCTCAGGTCACGGTCTAGCCACACCAGCTTCTCCCAAGTACTAACCAGGCTTGACCCTGCTTAGCTTCAGA
GGTCAGACAAGATCTGGCATGTTCAGGATGGTATGGCTGTAGACCAGGCTGGGTTCTGGCCAGAGCTGTTGCACTAGGCAATGCTGCCAG
AGATGAGGAGGCATCAGGGCAGTCATCCCTTCTGCTGTTTGCCCCAAGAATGCCATACAAACCTGGGGATGACCCTTAAAAGTCTCCCGT
CACCCCCAGTATTGGGGGGAAGCTGACTATTCCTCAGATGATAGCCCAGTCACTTGAAGAACAGGACAAGACTATTCTGTGTCTAGGGGG
CTCAAGCACTGTGTGTGGGTCTAACGAATGCATTTTGTGGAAATGGGCTCAGACTCCCCAAAGGGCCATCCAACCTATGGGAGTGTCTGG

>19445_19445_1_CRIM1-TBC1D25_CRIM1_chr2_36583766_ENST00000280527_TBC1D25_chrX_48417285_ENST00000376771_length(amino acids)=669AA_BP=107
MYLVAGDRGLAGCGHLLVSLLGLLLLLARSGTRALVCLPCDESKCEEPRNCPGSIVQGVCGCCYTCASQRNESCGGTFGIYGTCDRGLRC
VIRPPLNGDSLTEYEAGVCEGPLLEDWDIISPKDVIGSDVLLAEKRSSLTTAALPFTQSILTQVGRTLSKVQQVLSWSYGEDVKPFKPPL
SDAEFHTYLNHEGQLSRPEELRLRIYHGGVEPSLRKVVWRYLLNVYPDGLTGRERMDYMKRKSREYEQLKSEWAQRANPEDLEFIRSTVL
KDVLRTDRAHPYYAGPEDGPHLRALHDLLTTYAVTHPQVSYCQGMSDLASPILAVMDHEGHAFVCFCGIMKRLAANFHPDGRAMATKFAH
LKLLLRHADPDFYQYLQEAGADDLFFCYRWLLLELKREFAFDDALRMLEVTWSSLPPDPPEHEVELVGPPSQVADAGFGGHRGWPVRQRH
MLRPAGGGGSTFEDAVDHLATASQGPGGGGRLLRQASLDGLQQLRDNMGSRRDPLVQLPHPAALISSKSLSEPLLNSPDPLLSSFSHPDS
PSSSSPPSTQEASPTGDMAVGSPLMQEVGSPKDPGKSLPPVPPMGLPPPQEFGRGNPFMLFLCLAILLEHRDHIMRNGLDYNELAMHFDR

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Fusion Gene PPI Analysis for CRIM1-TBC1D25


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 CRIM1-TBC1D25


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 CRIM1-TBC1D25


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