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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: 32904

FusionGeneSummary for SCYL1_COL1A1

check button Fusion gene summary
Fusion gene informationFusion gene name: SCYL1_COL1A1
Fusion gene ID: 32904
HgeneTgene
Gene symbol

SCYL1

COL1A1

Gene ID

57410

1277

Gene nameSCY1 like pseudokinase 1collagen type I alpha 1 chain
SynonymsGKLP|HT019|NKTL|NTKL|P105|SCAR21|TAPK|TEIF|TRAPEDSARTH1|EDSC|OI1|OI2|OI3|OI4
Cytomap

11q13.1

17q21.33

Type of geneprotein-codingprotein-coding
DescriptionN-terminal kinase-like proteinSCY1-like protein 1SCY1-like, kinase-like 1coated vesicle-associated kinase of 90 kDalikely ortholog of mouse N-terminal kinase-like proteintelomerase regulation-associated proteintelomerase transcriptional elements-intcollagen alpha-1(I) chainalpha-1 type I collagenalpha1(I) procollagencollagen alpha 1 chain type Icollagen alpha-1(I) chain preproproteincollagen of skin, tendon and bone, alpha-1 chaincollagen, type I, alpha 1pro-alpha-1 collagen type 1type I pro
Modification date2018052220180527
UniProtAcc

Q96KG9

P02452

Ensembl transtripts involved in fusion geneENST00000525364, ENST00000270176, 
ENST00000420247, ENST00000533862, 
ENST00000279270, ENST00000524944, 
ENST00000527009, ENST00000534462, 
ENST00000225964, 
Fusion gene scores* DoF score4 X 4 X 6=9625 X 35 X 6=5250
# samples 839
** MAII scorelog2(8/96*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(39/5250*10)=-3.75077139369124
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SCYL1 [Title/Abstract] AND COL1A1 [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
HgeneSCYL1

GO:0006890

retrograde vesicle-mediated transport, Golgi to ER

18556652

TgeneCOL1A1

GO:0010718

positive regulation of epithelial to mesenchymal transition

20018240

TgeneCOL1A1

GO:0030335

positive regulation of cell migration

20018240

TgeneCOL1A1

GO:0034504

protein localization to nucleus

20018240

TgeneCOL1A1

GO:0045893

positive regulation of transcription, DNA-templated

20018240

TgeneCOL1A1

GO:0090263

positive regulation of canonical Wnt signaling pathway

20018240


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
ChiTaRS3.1BF926669SCYL1chr11

65300218

+COL1A1chr17

48268274

-
ChiTaRS3.1CV337912SCYL1chr11

65300218

+COL1A1chr17

48268274

-
* 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
In-frameENST00000525364ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
In-frameENST00000270176ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
In-frameENST00000420247ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
In-frameENST00000533862ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
In-frameENST00000279270ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
In-frameENST00000524944ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
In-frameENST00000527009ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-
intron-3CDSENST00000534462ENST00000225964SCYL1chr11

65300218

+COL1A1chr17

48268274

-

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FusionProtFeatures for SCYL1_COL1A1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SCYL1

Q96KG9

COL1A1

P02452

Regulates COPI-mediated retrograde protein traffic atthe interface between the Golgi apparatus and the endoplasmicreticulum (PubMed:18556652). Involved in the maintenance of theGolgi apparatus morphology (PubMed:26581903). Has no detectablekinase activity in vitro (PubMed:18556652).{ECO:0000269|PubMed:18556652, ECO:0000269|PubMed:26581903}. Isoform 6 acts as transcriptional activator. It binds tothree different types of GC-rich DNA binding sites (box-A, -B and-C) in the beta-polymerase promoter region. It also binds to theTERT promoter region. {ECO:0000269|PubMed:18556652}.

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 SCYL1_COL1A1


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_SCYL1_ENST00000525364_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000270176_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000420247_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000533862_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000279270_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000524944_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000527009_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000525364_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000270176_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000420247_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000533862_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000279270_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000524944_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa

>In-frame_SCYL1_ENST00000527009_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0aa


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_SCYL1_ENST00000525364_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000270176_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000420247_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000533862_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000279270_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000524944_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000527009_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000525364_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000270176_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000420247_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000533862_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000279270_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000524944_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000527009_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt


* Fusion transcript sequences (Full-length transcript).
>In-frame_SCYL1_ENST00000525364_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000270176_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000420247_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000533862_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000279270_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000524944_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000527009_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000525364_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000270176_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000420247_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000533862_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000279270_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000524944_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt

>In-frame_SCYL1_ENST00000527009_chr11_65300218_+_COL1A1_ENST00000225964_chr17_48268274_-_0nt


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FusionGenePPI for SCYL1_COL1A1


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 SCYL1_COL1A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCOL1A1P02452DB00048Collagenase clostridium histolyticumCollagen alpha-1(I) chainbiotechapproved|investigational
TgeneCOL1A1P02452DB13133Von Willebrand Factor HumanCollagen alpha-1(I) chainbiotechapproved|investigational

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RelatedDiseases for SCYL1_COL1A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCOL1A1C0268358Osteogenesis imperfecta, dominant perinatal lethal39CTD_human;ORPHANET;UNIPROT
TgeneCOL1A1C0268362Osteogenesis imperfecta type III (disorder)18CTD_human;ORPHANET;UNIPROT
TgeneCOL1A1C0268363Osteogenesis imperfecta type IV (disorder)14CTD_human;ORPHANET;UNIPROT
TgeneCOL1A1C0023931Lobstein's Disease12ORPHANET;UNIPROT
TgeneCOL1A1C0023890Liver Cirrhosis4CTD_human
TgeneCOL1A1C0023893Liver Cirrhosis, Experimental3CTD_human
TgeneCOL1A1C4225429Ehlers-Danlos syndrome classic type2UNIPROT
TgeneCOL1A1C0000786Spontaneous abortion1CTD_human
TgeneCOL1A1C0002949Aneurysm, Dissecting1CTD_human
TgeneCOL1A1C0003504Aortic Valve Insufficiency1CTD_human
TgeneCOL1A1C0004364Autoimmune Diseases1CTD_human
TgeneCOL1A1C0006663Calcinosis1CTD_human
TgeneCOL1A1C0008311Cholangitis1CTD_human
TgeneCOL1A1C0016059Fibrosis1CTD_human
TgeneCOL1A1C0018824Heart valve disease1CTD_human
TgeneCOL1A1C0020497Cortical Congenital Hyperostosis1CTD_human;ORPHANET;UNIPROT
TgeneCOL1A1C0020538Hypertensive disease1CTD_human
TgeneCOL1A1C0022548Keloid1CTD_human
TgeneCOL1A1C0027726Nephrotic Syndrome1CTD_human
TgeneCOL1A1C0029172Oral Submucous Fibrosis1CTD_human
TgeneCOL1A1C0029434Osteogenesis Imperfecta1CTD_human
TgeneCOL1A1C0149721Left Ventricular Hypertrophy1CTD_human
TgeneCOL1A1C1619692Nephrogenic Fibrosing Dermopathy1CTD_human