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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: 7953

FusionGeneSummary for COL4A1_SMIM4

check button Fusion gene summary
Fusion gene informationFusion gene name: COL4A1_SMIM4
Fusion gene ID: 7953
HgeneTgene
Gene symbol

COL4A1

SMIM4

Gene ID

1282

440957

Gene namecollagen type IV alpha 1 chainsmall integral membrane protein 4
SynonymsBSVD|RATORC3orf78
Cytomap

13q34

3p21.1

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(IV) chainCOL4A1 NC1 domainarrestencollagen IV, alpha-1 polypeptidecollagen of basement membrane, alpha-1 chainsmall integral membrane protein 4UPF0640 protein C3orf78
Modification date2018052720180329
UniProtAcc

P02462

Q8WVI0

Ensembl transtripts involved in fusion geneENST00000375820, ENST00000543140, 
ENST00000467182, 
ENST00000482728, 
ENST00000307106, ENST00000477703, 
ENST00000476842, 
Fusion gene scores* DoF score7 X 9 X 5=3153 X 3 X 3=27
# samples 93
** MAII scorelog2(9/315*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: COL4A1 [Title/Abstract] AND SMIM4 [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
ChiTaRS3.1AK000903COL4A1chr13

110885115

-SMIM4chr3

52570821

+
* 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-intronENST00000375820ENST00000482728COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000375820ENST00000307106COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000375820ENST00000477703COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000375820ENST00000476842COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000543140ENST00000482728COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000543140ENST00000307106COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000543140ENST00000477703COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000543140ENST00000476842COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000467182ENST00000482728COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000467182ENST00000307106COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000467182ENST00000477703COL4A1chr13

110885115

-SMIM4chr3

52570821

+
intron-intronENST00000467182ENST00000476842COL4A1chr13

110885115

-SMIM4chr3

52570821

+

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FusionProtFeatures for COL4A1_SMIM4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL4A1

P02462

SMIM4

Q8WVI0


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 COL4A1_SMIM4


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 COL4A1_SMIM4


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 COL4A1_SMIM4


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 COL4A1_SMIM4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL4A1C4013035BRAIN SMALL VESSEL DISEASE WITH OR WITHOUT OCULAR ANOMALIES8ORPHANET;UNIPROT
HgeneCOL4A1C1867983PORENCEPHALY, FAMILIAL3ORPHANET;UNIPROT
HgeneCOL4A1C2673195Angiopathy, Hereditary, With Nephropathy, Aneurysms, And Muscle Cramps3CTD_human;ORPHANET;UNIPROT
HgeneCOL4A1C0017668Focal glomerulosclerosis2CTD_human
HgeneCOL4A1C0011881Diabetic Nephropathy1CTD_human
HgeneCOL4A1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCOL4A1C0027726Nephrotic Syndrome1CTD_human
HgeneCOL4A1C0266484Schizencephaly1HPO;ORPHANET;UNIPROT
HgeneCOL4A1C3281105HEMORRHAGE, INTRACEREBRAL, SUSCEPTIBILITY TO1UNIPROT