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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: 39372

FusionGeneSummary for TRAM1_CLVS1

check button Fusion gene summary
Fusion gene informationFusion gene name: TRAM1_CLVS1
Fusion gene ID: 39372
HgeneTgene
Gene symbol

TRAM1

CLVS1

Gene ID

23471

157807

Gene nametranslocation associated membrane protein 1clavesin 1
SynonymsPNAS8|TRAM|TRAMPC6orf212L|CRALBPL|RLBP1L1
Cytomap

8q13.3

8q12.2-q12.3

Type of geneprotein-codingprotein-coding
Descriptiontranslocating chain-associated membrane protein 1translocating chain-associating membrane proteintranslocation-associating membrane protein 1clavesin-1clathrin vesicle-associated Sec14 protein 1retinaldehyde-binding protein 1-like 1
Modification date2018052320180523
UniProtAcc

Q15629

Q8IUQ0

Ensembl transtripts involved in fusion geneENST00000521425, ENST00000262213, 
ENST00000536748, ENST00000521049, 
ENST00000519846, ENST00000518592, 
ENST00000325897, ENST00000518858, 
Fusion gene scores* DoF score3 X 3 X 2=189 X 7 X 8=504
# samples 39
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(9/504*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TRAM1 [Title/Abstract] AND CLVS1 [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
TCGARVBRCATCGA-C8-A138-01ATRAM1chr8

71512254

-CLVS1chr8

62289164

+
* 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
5UTR-3CDSENST00000521425ENST00000519846TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-5UTRENST00000521425ENST00000518592TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-5UTRENST00000521425ENST00000325897TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-intronENST00000521425ENST00000518858TRAM1chr8

71512254

-CLVS1chr8

62289164

+
Frame-shiftENST00000262213ENST00000519846TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5CDS-5UTRENST00000262213ENST00000518592TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5CDS-5UTRENST00000262213ENST00000325897TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5CDS-intronENST00000262213ENST00000518858TRAM1chr8

71512254

-CLVS1chr8

62289164

+
In-frameENST00000536748ENST00000519846TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5CDS-5UTRENST00000536748ENST00000518592TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5CDS-5UTRENST00000536748ENST00000325897TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5CDS-intronENST00000536748ENST00000518858TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-3CDSENST00000521049ENST00000519846TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-5UTRENST00000521049ENST00000518592TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-5UTRENST00000521049ENST00000325897TRAM1chr8

71512254

-CLVS1chr8

62289164

+
5UTR-intronENST00000521049ENST00000518858TRAM1chr8

71512254

-CLVS1chr8

62289164

+

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FusionProtFeatures for TRAM1_CLVS1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
TRAM1

Q15629

CLVS1

Q8IUQ0

Stimulatory or required for the translocation ofsecretory proteins across the ER membrane. Required for normal morphology of late endosomes and/orlysosomes in neurons (By similarity). Binds phosphatidylinositol3,5-bisphosphate (PtdIns(3,5)P2). {ECO:0000250,ECO:0000269|PubMed:19651769}.

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 TRAM1_CLVS1


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_TRAM1_ENST00000536748_chr8_71512254_-_CLVS1_ENST00000519846_chr8_62289164_+_234aa
MVFLLGLMFEITAKASIIFVTLQYNVTLPATGTPSQTSFVPSCCHWKSXSKIRSFRXMASFXLXTGVIFPSNKPPNXHLQSLNWPLKGCR
TAFLPALEESTLSTSPGTFMPSTHSSSHFLKTRPGNGFSCMETIXTAFTSXYTLNFCPLNLEELFLLMTWELGPGRYSVPTTAMKMTILT


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_TRAM1_ENST00000536748_chr8_71512254_-_CLVS1_ENST00000519846_chr8_62289164_+_704nt
ATGGTCTTCCTGCTGGGGCTCATGTTTGAGATAACGGCAAAAGCTTCTATCATTTTTGTTACTCTTCAGTACAATGTCACCCTCCCAGCA
ACAGGAACTCCTTCACAGACATCCTTCGTGCCATCCTGCTGTCATTGGAAGTCCTAATCGAAGATCCGGAGCTTCAGATAAATGGCTTCA
TTTTAATTATAGACTGGAGTAATTTTTCCTTCAAACAAGCCTCCAAACTGACACCTTCAATCCTTAAACTGGCCATTGAAGGGTTGCAGG
ACAGCTTTCCTGCCCGCTTTGGAGGAGTCCACTTTGTCAACCAGCCCTGGTACATTCATGCCCTCTACACACTCATCAAGCCATTTCTTA
AAGACAAGACCAGGAAACGGATTTTCCTGCATGGAAACAATTTAAACAGCCTTCACCAGCTAATACACCCTGAATTTTTGCCCTCTGAAT
TTGGAGGAACTCTTCCTCCTTATGACATGGGAACTTGGGCCCGGACGTTACTCGGTCCCGACTACAGCGATGAAAATGACTATACTCACA
CATCCTATAATGCAATGCACGTGAAGCATACGTCCTCGAATCTGGAGAGAGAATGCTCACCCAAGCTGATGAAAAGATCTCAGTCTGTGG


* Fusion transcript sequences (Full-length transcript).
>In-frame_TRAM1_ENST00000536748_chr8_71512254_-_CLVS1_ENST00000519846_chr8_62289164_+_2973nt
CCCCCGGGCGGCCCGGCGGCTGCGTACTGGCTGTGGGATGGGAAGTGAAGCCCCAGCGAGCGGCTGCAGCGGGGCCGTGAGGAGCAGCCA
GCGGGAGGCGGCGGCGAGTCGGTGAGCAGCTGGGAAGAGCAGAACCGGGGCGGAGCACCTGCAGAATCACGCGGACATCGTCTCCTGTGT
GGCGATGGTCTTCCTGCTGGGGCTCATGTTTGAGATAACGGCAAAAGCTTCTATCATTTTTGTTACTCTTCAGTACAATGTCACCCTCCC
AGCAACAGGAACTCCTTCACAGACATCCTTCGTGCCATCCTGCTGTCATTGGAAGTCCTAATCGAAGATCCGGAGCTTCAGATAAATGGC
TTCATTTTAATTATAGACTGGAGTAATTTTTCCTTCAAACAAGCCTCCAAACTGACACCTTCAATCCTTAAACTGGCCATTGAAGGGTTG
CAGGACAGCTTTCCTGCCCGCTTTGGAGGAGTCCACTTTGTCAACCAGCCCTGGTACATTCATGCCCTCTACACACTCATCAAGCCATTT
CTTAAAGACAAGACCAGGAAACGGATTTTCCTGCATGGAAACAATTTAAACAGCCTTCACCAGCTAATACACCCTGAATTTTTGCCCTCT
GAATTTGGAGGAACTCTTCCTCCTTATGACATGGGAACTTGGGCCCGGACGTTACTCGGTCCCGACTACAGCGATGAAAATGACTATACT
CACACATCCTATAATGCAATGCACGTGAAGCATACGTCCTCGAATCTGGAGAGAGAATGCTCACCCAAGCTGATGAAAAGATCTCAGTCT
GTGGTAGAAGCTGGGACCCTGAAACATGAGGAGAAGGGAGAGAATGAGAACACCCAGCCACTCCTGGCTCTGGACTGAACCCTGAGTCAC
CCCAATGCTCCTGCACACTGGCCTTCAGTGGTATCAGCCACCCAGGAAGCACATGCACAACTGACCCATGCAGACACGTGTGTTCTGCTT
GACACAAGGTCCTCCACTCCTGAACCCCTGCAGTGACTGTCACCAGCCATCGGTCTGAGCAGCCAAAGTTGGACAAAGACTTGAGAGATG
CTTTTTTTTTCCCCCAGTGAGGGGACTGGAGGATGATGCAAGGCATTTATGTAAAAAAGATTCTCCCTCCTTTCATATTTATTGTAGTAA
ATTGAAAAAATAAAGACTAAATTTGATGGACACACTGCATTAGGACAAGAATTTTTCTGAGGTATCACACAGGGACCCTCTCCAGTTTTT
GAAAATTAAGTGCATTTCCAAGTAAATGTATCAGAGTTAAACTGTACAGACACCACTGTCAAGTTTCATGTAGTACAAAGCCCTGAGACA
ATAGTATCTCCAGTAATTTCCATTCTTACTGAATTATTTCCTTTGACCTCATCACCAGCATCGAATTGTTCAGCCTAAGAGCATGTTCTC
ATAGGTCTGGGTATTTGCAAAGTTTGCTTATTTTGATGATATCCTGCAAAAAATTATTTTGATGTCACATCTCTTGTCAGGTCACTAGCT
GACTGTCATGAGCTGACGTTAAAGGAAGACACATGGACGTGAAATACGATTATTTCATCTGAGCAATGTGAGTTACCACAGGCAGCTCAA
AAGCCCATTAGTGCAGCATGTGTCTGCAGAGGAGATGTCTCATGAAAATCACATGTCAGTGATTAATGAATCCATTCCAGTTGCCTCAAC
TGGGTCACTACAGCAAAGAAAAGTGCTATCAAACCATTTACCCTTGCCCCCACAACCCTCCTGCAACCATTAAAGATGTGGAGAAAGACC
ATGGTTGTTGCTGAGAGGGTAAATATTCAATCATGGAGCATGACCCATATGGATGGCTAAATATGCAAGTACTGAAGTAAGAGAAGACTA
GAAATGCAGGATGAAATGTCAAAGGTCATTTTATTTACCTAGTCTCCTTAGAAATGGAGTCCCCAACTACTCATTCAAAAGAAATCAGAC
ATAAAATAAACAGACATCATATATGATATCCTTACTTGTGCCATGTTTTCCAAGACCAGTGCATATTTTTAGACATCTCTTATTCGCCCA
GCCATCTGCATGACATGGGTATTTATTAGTATTACCAGTTGGTGCTCAAAGTCAAACAAAAATATTTTAGTTAATAATGGGCAGTAAAAT
ATGATTTTACATTATTTTAAATATTTGGGAGAGTTAATTTGTTAGCTAAATAATTCAAGGGAAAGAGATTATTCAACTGGTCATAATCAC
CCCTGATAATATTATTACTAATCTTAATTATTTATTACATCATCTCTTTCTCAATGGATCTAATGTTTTAATTTTTTCCCCTATTGGTAG
AGAACAATAACAGAAGTAATTTTTATATTATACACTTGGAGAAATAAAGTTGAAACAGAATTAAAAATATTTCTCAAACAACTGTATCAC
AATATAAATTAAACTAATTCATTTTTGTGTAGACATACGAAATCACAAAAATAATAACACTGAAATAATTCTACCAATGCAGTGATGGAA
ACACTTTTCTTATGTACCAAGACATAGATAGGTAAGAGAAATAAAGAATTGAAGTGAATTAGAAAATCCATTTTATTGCTTGGGTTTAAA
ATAGTTGTGGGATACAAGTATTTACAATGCTATTGGAGTCAATTATTGACAACACTTTGCAACAGTAATACCATTTCTAGCTTTTCAATT
GGCAATACTTAGAACCTTACTGTAGTGACCTGATTTTAAATACCATATTATATTTACTAAGTTAAGAGCTAGTTTTTACTCTCTTCCATA
ATTTCATTACATGAATGTAAGATGATGGCTCAAAAATGACGACTTATAGTTTGAATTTATGTGTATGCAATATACATATGAGAACCAAAT
TCAACAAGTGACATGAATGTTACTACATGAACATTGAATTGTATTGCCCTTGTCAGTTATTTCCTCTGTTCAATAAATACTGAAGGTCAC


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FusionGenePPI for TRAM1_CLVS1


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
TRAM1ESR1, ESR2, ELAVL1, DERL1, HM13, HLA-A, BCAP31, APP, VKORC1, TCTN3, CREB3, PKN2, MBOAT1, FAF2, TPTE, UBCCLVS1


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 TRAM1_CLVS1


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 TRAM1_CLVS1


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