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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: 32573

FusionGeneSummary for SAMD12_RTN1

check button Fusion gene summary
Fusion gene informationFusion gene name: SAMD12_RTN1
Fusion gene ID: 32573
HgeneTgene
Gene symbol

SAMD12

RTN1

Gene ID

401474

6252

Gene namesterile alpha motif domain containing 12reticulon 1
Synonyms-NSP
Cytomap

8q24.11-q24.12

14q23.1

Type of geneprotein-codingprotein-coding
Descriptionsterile alpha motif domain-containing protein 12SAM domain-containing protein 12reticulon-1neuroendocrine-specific protein
Modification date2018052120180522
UniProtAcc

Q8N8I0

Q16799

Ensembl transtripts involved in fusion geneENST00000409003, ENST00000314727, 
ENST00000527515, 
ENST00000267484, 
ENST00000395090, ENST00000342503, 
ENST00000557422, 
Fusion gene scores* DoF score13 X 6 X 6=4684 X 3 X 4=48
# samples 144
** MAII scorelog2(14/468*10)=-1.74108170263844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SAMD12 [Title/Abstract] AND RTN1 [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

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
TCGARVLUSCTCGA-22-4594-01ASAMD12chr8

119634043

-RTN1chr14

60074210

-
* 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-shitENST00000409003ENST00000267484SAMD12chr8

119634043

-RTN1chr14

60074210

-
Frame-shitENST00000409003ENST00000395090SAMD12chr8

119634043

-RTN1chr14

60074210

-
Frame-shitENST00000409003ENST00000342503SAMD12chr8

119634043

-RTN1chr14

60074210

-
5CDS-5UTRENST00000409003ENST00000557422SAMD12chr8

119634043

-RTN1chr14

60074210

-
Frame-shitENST00000314727ENST00000267484SAMD12chr8

119634043

-RTN1chr14

60074210

-
Frame-shitENST00000314727ENST00000395090SAMD12chr8

119634043

-RTN1chr14

60074210

-
Frame-shitENST00000314727ENST00000342503SAMD12chr8

119634043

-RTN1chr14

60074210

-
5CDS-5UTRENST00000314727ENST00000557422SAMD12chr8

119634043

-RTN1chr14

60074210

-
intron-3CDSENST00000527515ENST00000267484SAMD12chr8

119634043

-RTN1chr14

60074210

-
intron-3CDSENST00000527515ENST00000395090SAMD12chr8

119634043

-RTN1chr14

60074210

-
intron-3CDSENST00000527515ENST00000342503SAMD12chr8

119634043

-RTN1chr14

60074210

-
intron-5UTRENST00000527515ENST00000557422SAMD12chr8

119634043

-RTN1chr14

60074210

-

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FusionProtFeatures for SAMD12_RTN1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SAMD12

Q8N8I0

RTN1

Q16799

May be involved in neuroendocrine secretion or inmembrane trafficking in neuroendocrine cells.

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 SAMD12_RTN1


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 SAMD12_RTN1


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
SAMD12RTN1BCL2L1, UGCG, FAM160A2, PLEKHF2, HDAC8, SDCBP, RTN4, FGFR1, DYRK2, RTN2, PLSCR1, FAM210B, METTL7A, C4orf32, GYPB, SERPINE2, CYB5R3, TMEM43, TMEM70, SIGMAR1, SLC7A3, TMEM120B, TYMS, ARL6IP5, DERL2, NRAS, FAM213A, LMNA


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 SAMD12_RTN1


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 SAMD12_RTN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRTN1C0151744Myocardial Ischemia1CTD_human