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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: 7615

FusionGeneSummary for CMTM4_RGMA

check button Fusion gene summary
Fusion gene informationFusion gene name: CMTM4_RGMA
Fusion gene ID: 7615
HgeneTgene
Gene symbol

CMTM4

RGMA

Gene ID

146223

56963

Gene nameCKLF like MARVEL transmembrane domain containing 4repulsive guidance molecule BMP co-receptor a
SynonymsCKLFSF4RGM
Cytomap

16q21-q22.1

15q26.1

Type of geneprotein-codingprotein-coding
DescriptionCKLF-like MARVEL transmembrane domain-containing protein 4chemokine-like factor super family 4chemokine-like factor superfamily member 4repulsive guidance molecule ARGM domain family, member Arepulsive guidance molecule family member a
Modification date2018052320180523
UniProtAcc

Q8IZR5

Q96B86

Ensembl transtripts involved in fusion geneENST00000330687, ENST00000394106, 
ENST00000563952, 
ENST00000425933, 
ENST00000543599, ENST00000329082, 
ENST00000542321, ENST00000538818, 
ENST00000557301, ENST00000557420, 
ENST00000556658, ENST00000556087, 
ENST00000555584, 
Fusion gene scores* DoF score7 X 4 X 5=1403 X 2 X 3=18
# samples 73
** MAII scorelog2(7/140*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CMTM4 [Title/Abstract] AND RGMA [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
TgeneRGMA

GO:0045944

positive regulation of transcription by RNA polymerase II

22728873


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
ChiTaRS3.1BF932730CMTM4chr16

66672250

+RGMAchr15

93588793

+
* 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
intron-3CDSENST00000330687ENST00000425933CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000330687ENST00000543599CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000330687ENST00000329082CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000330687ENST00000542321CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000330687ENST00000538818CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000330687ENST00000557301CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3UTRENST00000330687ENST00000557420CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3UTRENST00000330687ENST00000556658CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-intronENST00000330687ENST00000556087CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-intronENST00000330687ENST00000555584CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000394106ENST00000425933CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000394106ENST00000543599CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000394106ENST00000329082CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000394106ENST00000542321CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000394106ENST00000538818CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000394106ENST00000557301CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3UTRENST00000394106ENST00000557420CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3UTRENST00000394106ENST00000556658CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-intronENST00000394106ENST00000556087CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-intronENST00000394106ENST00000555584CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000563952ENST00000425933CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000563952ENST00000543599CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000563952ENST00000329082CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000563952ENST00000542321CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000563952ENST00000538818CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3CDSENST00000563952ENST00000557301CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3UTRENST00000563952ENST00000557420CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-3UTRENST00000563952ENST00000556658CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-intronENST00000563952ENST00000556087CMTM4chr16

66672250

+RGMAchr15

93588793

+
intron-intronENST00000563952ENST00000555584CMTM4chr16

66672250

+RGMAchr15

93588793

+

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FusionProtFeatures for CMTM4_RGMA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CMTM4

Q8IZR5

RGMA

Q96B86

Acts as a backup for CMTM6 to regulate plasma membraneexpression of PD-L1/CD274, an immune inhibitory ligand criticalfor immune tolerance to self and antitumor immunity. May protectPD-L1/CD274 from being polyubiquitinated and targeted fordegradation. {ECO:0000269|PubMed:28813410}.

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 CMTM4_RGMA


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for CMTM4_RGMA


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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RelatedDrugs for CMTM4_RGMA


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 CMTM4_RGMA


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