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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 31314

FusionGeneSummary for RMDN3_SKA2

check button Fusion gene summary
Fusion gene informationFusion gene name: RMDN3_SKA2
Fusion gene ID: 31314
HgeneTgene
Gene symbol

RMDN3

SKA2

Gene ID

55177

348235

Gene nameregulator of microtubule dynamics 3spindle and kinetochore associated complex subunit 2
SynonymsFAM82A2|FAM82C|RMD-3|RMD3|ptpip51FAM33A
Cytomap

15q15.1

17q22

Type of geneprotein-codingprotein-coding
Descriptionregulator of microtubule dynamics protein 3TCPTP-interacting protein 51cerebral protein 10family with sequence similarity 82, member A2family with sequence similarity 82, member Cmicrotubule-associated proteinprotein tyrosine phosphatase-interactingspindle and kinetochore-associated protein 2family with sequence similarity 33, member Aspindle and KT (kinetochore) associated 2
Modification date2018052220180522
UniProtAcc

Q96TC7

Q8WVK7

Ensembl transtripts involved in fusion geneENST00000260385, ENST00000338376, 
ENST00000558560, 
ENST00000330137, 
ENST00000580541, ENST00000578105, 
ENST00000583927, ENST00000581068, 
ENST00000437036, ENST00000583380, 
Fusion gene scores* DoF score4 X 3 X 3=363 X 2 X 2=12
# samples 43
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RMDN3 [Title/Abstract] AND SKA2 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
TgeneSKA2

GO:0031110

regulation of microtubule polymerization or depolymerization

19289083


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDBRCATCGA-C8-A1HI-01ARMDN3chr15

41043624

-SKA2chr17

57189706

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shiftENST00000260385ENST00000330137RMDN3chr15

41043624

-SKA2chr17

57189706

-
Frame-shiftENST00000260385ENST00000580541RMDN3chr15

41043624

-SKA2chr17

57189706

-
Frame-shiftENST00000260385ENST00000578105RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000260385ENST00000583927RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000260385ENST00000581068RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000260385ENST00000437036RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000260385ENST00000583380RMDN3chr15

41043624

-SKA2chr17

57189706

-
Frame-shiftENST00000338376ENST00000330137RMDN3chr15

41043624

-SKA2chr17

57189706

-
Frame-shiftENST00000338376ENST00000580541RMDN3chr15

41043624

-SKA2chr17

57189706

-
In-frameENST00000338376ENST00000578105RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000338376ENST00000583927RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000338376ENST00000581068RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000338376ENST00000437036RMDN3chr15

41043624

-SKA2chr17

57189706

-
5CDS-5UTRENST00000338376ENST00000583380RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-3CDSENST00000558560ENST00000330137RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-3CDSENST00000558560ENST00000580541RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-3CDSENST00000558560ENST00000578105RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-5UTRENST00000558560ENST00000583927RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-5UTRENST00000558560ENST00000581068RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-5UTRENST00000558560ENST00000437036RMDN3chr15

41043624

-SKA2chr17

57189706

-
5UTR-5UTRENST00000558560ENST00000583380RMDN3chr15

41043624

-SKA2chr17

57189706

-

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FusionProtFeatures for RMDN3_SKA2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RMDN3

Q96TC7

SKA2

Q8WVK7

Involved in cellular calcium homeostasis regulation. Mayparticipate in differentiation and apoptosis of keratinocytes.Overexpression induces apoptosis. {ECO:0000269|PubMed:16820967,ECO:0000269|PubMed:22131369}. Component of the SKA1 complex, a microtubule-bindingsubcomplex of the outer kinetochore that is essential for properchromosome segregation (PubMed:17093495, PubMed:19289083,PubMed:23085020). Required for timely anaphase onset duringmitosis, when chromosomes undergo bipolar attachment on spindlemicrotubules leading to silencing of the spindle checkpoint(PubMed:17093495). The SKA1 complex is a direct component of thekinetochore-microtubule interface and directly associates withmicrotubules as oligomeric assemblies (PubMed:19289083). Thecomplex facilitates the processive movement of microspheres alonga microtubule in a depolymerization-coupled manner(PubMed:17093495, PubMed:19289083). In the complex, it is requiredfor SKA1 localization (PubMed:19289083). Affinity for microtubulesis synergistically enhanced in the presence of the ndc-80 complexand may allow the ndc-80 complex to track depolymerizingmicrotubules (PubMed:23085020). {ECO:0000269|PubMed:17093495,ECO:0000269|PubMed:19289083, ECO:0000269|PubMed:23085020}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for RMDN3_SKA2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_RMDN3_ENST00000338376_chr15_41043624_-_SKA2_ENST00000578105_chr17_57189706_-_197aa
MSRLGALGGARAGLGLLLGTAAGLGFLCLLYSQRWKRTQRHGRSQSLPNSLDYTQTSDPGRHVMLLRAVPGGAGDASVLPSLPREGQEKV
LDRLDFVLTSLVALRREVEELRSSLRGLAGEIVGEVRCHMEENQRVARRRRFPFVRERSDSTGSSSVYFTASSGATFTDAESEGGCHHXL


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_RMDN3_ENST00000338376_chr15_41043624_-_SKA2_ENST00000578105_chr17_57189706_-_593nt
ATGTCTAGACTGGGAGCCCTGGGTGGTGCCCGTGCCGGGCTGGGACTGTTGCTGGGTACCGCCGCCGGCCTTGGATTCCTGTGCCTCCTT
TACAGCCAGCGATGGAAACGGACCCAGCGTCATGGCCGCAGCCAGAGCCTGCCCAACTCCCTGGACTATACGCAGACTTCAGATCCCGGA
CGCCACGTGATGCTCCTGCGGGCTGTCCCAGGTGGGGCTGGAGATGCCTCAGTGCTGCCCAGCCTTCCACGGGAAGGACAGGAGAAGGTG
CTGGACCGCCTGGACTTTGTGCTGACCAGCCTTGTGGCGCTGCGGCGGGAGGTGGAGGAGCTGAGAAGCAGCCTGCGAGGGCTTGCGGGG
GAGATTGTTGGGGAGGTCCGATGCCACATGGAAGAGAACCAGAGAGTGGCTCGGCGGCGAAGGTTTCCGTTTGTCCGGGAGAGGAGTGAC
TCCACTGGCTCCAGCTCTGTCTACTTCACGGCCTCCTCGGGAGCCACGTTCACAGATGCTGAGAGTGAAGGGGGCTGTCACCACTGACTA


* Fusion transcript sequences (Full-length transcript).
>In-frame_RMDN3_ENST00000338376_chr15_41043624_-_SKA2_ENST00000578105_chr17_57189706_-_1167nt
GACGTCACGGTCACTGACAGCGTGAGCCCGCGGCGGCTGCTGCCATGGTGGCTGGCGGCCGGGTAAGGGTCTGAGTGGATCTCCTGCCAG
GCCAGAGCGCCTTCGGGGGCCGCGGCGGAAGGCCAGGAGTTTGCAGCCAGGGCGCCGGGTTTGTGGTCTGCAGTGTCGTGAGGCTGAGGT
GCAGCATGTCTAGACTGGGAGCCCTGGGTGGTGCCCGTGCCGGGCTGGGACTGTTGCTGGGTACCGCCGCCGGCCTTGGATTCCTGTGCC
TCCTTTACAGCCAGCGATGGAAACGGACCCAGCGTCATGGCCGCAGCCAGAGCCTGCCCAACTCCCTGGACTATACGCAGACTTCAGATC
CCGGACGCCACGTGATGCTCCTGCGGGCTGTCCCAGGTGGGGCTGGAGATGCCTCAGTGCTGCCCAGCCTTCCACGGGAAGGACAGGAGA
AGGTGCTGGACCGCCTGGACTTTGTGCTGACCAGCCTTGTGGCGCTGCGGCGGGAGGTGGAGGAGCTGAGAAGCAGCCTGCGAGGGCTTG
CGGGGGAGATTGTTGGGGAGGTCCGATGCCACATGGAAGAGAACCAGAGAGTGGCTCGGCGGCGAAGGTTTCCGTTTGTCCGGGAGAGGA
GTGACTCCACTGGCTCCAGCTCTGTCTACTTCACGGCCTCCTCGGGAGCCACGTTCACAGATGCTGAGAGTGAAGGGGGCTGTCACCACT
GACTAAAGAAGAGAAAACTGCGGCAGAGCAATTCAAATTTCACATGCCAGATTTATGAAGAAATGGACTTGGAAAGGAAATTCTAACAGA
GAAGAGCTTAATTCCGGAGAAATTTAGGAAGATGTCTTGTTAACCCTTGATGTCTAGAGATTGGGGGCTGGTGAAGGGGGTTTGGCTTCA
ATGACTGGATAATGATATCTTTCATGAGAGAGATTATAAGAAGAAGGGCAGATAATATATGAATAAAGTTCAGCCAAAAGGATCAAATGA
GAATAAAACGATTTAAATATATGTACACACGCATGCACACACACACTTAGTCTTGTAATTTCAGGCCAGAAATTCTCAACACTATTTTGC


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FusionGenePPI for RMDN3_SKA2


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
RMDN3YWHAB, YWHAG, YWHAZ, VAPA, PSEN1, FAM3C, ATP6V1H, ATP6V1A, HNRNPD, HNRNPDL, FAM162A, ELAVL1, ILF3, TOMM40, HSPA5, GORASP2, TIMM17B, CYSRT1, MDC1, YWHAQ, EGFL8, HLA-DPA1, GPM6A, RMDN2, VAPB, PFKFB2, RAB5C, FOXA3, FOXL1, APOOL, NEUROG3, RAF1, MAPK1, PTPN1SKA2PPP2R2B, SKA1, DSN1, SPC24, HMOX2, PRKD3, RALYL, KIAA0753, SPICE1, DCTN1, SKA3, HAUS1


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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RelatedDrugs for RMDN3_SKA2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RMDN3_SKA2


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