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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:COL1A1-COL3A1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: COL1A1-COL3A1
FusionPDB ID: 18113
FusionGDB2.0 ID: 18113
HgeneTgene
Gene symbol

COL1A1

COL3A1

Gene ID

1277

1281

Gene namecollagen type I alpha 1 chaincollagen type III alpha 1 chain
SynonymsCAFYD|EDSARTH1|EDSC|OI1|OI2|OI3|OI4EDS4A|EDSVASC|PMGEDSV
Cytomap

17q21.33

2q32.2

Type of geneprotein-codingprotein-coding
Descriptioncollagen 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 procollagen alpha-1(III) chainEhlers-Danlos syndrome type IV, autosomal dominantalpha-1 type III collagenalpha1 (III) collagencollagen, fetalcollagen, type III, alpha 1
Modification date2020032220200313
UniProtAcc

P02452

P02461

Ensembl transtripts involved in fusion geneENST idsENST00000225964, ENST00000304636, 
ENST00000317840, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score56 X 95 X 16=8512034 X 39 X 8=10608
# samples 8643
** MAII scorelog2(86/85120*10)=-6.62901768079909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(43/10608*10)=-4.62467221052313
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: COL1A1 [Title/Abstract] AND COL3A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)COL1A1(48269148)-COL3A1(189864010), # samples:1
COL3A1(189863444)-COL1A1(48268851), # samples:1
Anticipated loss of major functional domain due to fusion event.COL1A1-COL3A1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
COL1A1-COL3A1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
COL1A1-COL3A1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
COL1A1-COL3A1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
COL3A1-COL1A1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
COL3A1-COL1A1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* 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
HgeneCOL1A1

GO:0010718

positive regulation of epithelial to mesenchymal transition

20018240

HgeneCOL1A1

GO:0030335

positive regulation of cell migration

20018240

HgeneCOL1A1

GO:0034504

protein localization to nucleus

20018240

HgeneCOL1A1

GO:0045893

positive regulation of transcription, DNA-templated

20018240

HgeneCOL1A1

GO:0090263

positive regulation of canonical Wnt signaling pathway

20018240

TgeneCOL3A1

GO:0007160

cell-matrix adhesion

16912226

TgeneCOL3A1

GO:0007179

transforming growth factor beta receptor signaling pathway

16360482

TgeneCOL3A1

GO:0009314

response to radiation

14736764

TgeneCOL3A1

GO:0018149

peptide cross-linking

16754721

TgeneCOL3A1

GO:0034097

response to cytokine

9076960|16360482

TgeneCOL3A1

GO:0042060

wound healing

1466622


check buttonFusion gene breakpoints across COL1A1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across COL3A1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4Non-Cancer149NCOL1A1chr17

48269148

-COL3A1chr2

189864010

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000225964COL1A1chr1748269148-ENST00000304636COL3A1chr2189864010+5597224611946241501
ENST00000225964COL1A1chr1748269148-ENST00000317840COL3A1chr2189864010+4688224611937151198

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000225964ENST00000304636COL1A1chr1748269148-COL3A1chr2189864010+0.0013071950.9986928
ENST00000225964ENST00000317840COL1A1chr1748269148-COL3A1chr2189864010+0.0008402460.9991598

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>18113_18113_1_COL1A1-COL3A1_COL1A1_chr17_48269148_ENST00000225964_COL3A1_chr2_189864010_ENST00000304636_length(amino acids)=1501AA_BP=109
MFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLCDDVICDETKNCPGAEVPEGE
CCPVCPDGSESPTDQETTGVEGPKGDTGPRGPRGPAGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGGISVPGP
MGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGF
SGLDGAKGDAGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGAPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVGAKGEAGPQGP
RGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPGGPPGPKGNSGEPGAPGSKGDTGAKGE
PGPVGVQGPPGPAGEEGKRGARGEPGPTGLPGPPGERGGPGSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGL
TGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGPPGPAGPAGE
RGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGANGAPGNDGAKGDAGAPGERGP
PGLAGAPGLRGGAGPPGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPPGPAGQ
PGDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGPAGPPGPQGVKGERGS
PGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPGKDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITGA
RGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGA
PGHPGPPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGP
AGPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGVGAAAIAGIGGEKAGGFAPYYGDEPM
DFKINTDEIMTSLKSVNGQIESLISPDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHW
WTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVLDVHLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEFKAEGN

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>18113_18113_2_COL1A1-COL3A1_COL1A1_chr17_48269148_ENST00000225964_COL3A1_chr2_189864010_ENST00000317840_length(amino acids)=1198AA_BP=111
MFSFVDLRLLLLLAATALLTHGQEEGQVEGQDEDIPPITCVQNGLRYHDRDVWKPEPCRICVCDNGKVLCDDVICDETKNCPGAEVPEGE
CCPVCPDGSESPTDQETTGVEGPKGDTGPRGPRGPAGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGGISVPGP
MGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGF
SGLDGAKGDAGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGAPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVGAKGEAGPQGP
RGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPGGPPGPKGNSGEPGAPGSKGDTGAKGE
PGPVGVQGPPGPAGEEGKRGARGEPGPTGLPGPPGERGGPGSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGL
TGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGPPGPAGPAGE
RGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGANGAPGNDGAKGDAGAPGERGP
PGLAGAPGLRGGAGPPGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPPGPAGQ
PGDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGLFGPPGKDGTSGHPGPIGPPGPRGN
RGERGSEGSPGHPGQPGPPGPPGAPGPCCGGVGAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNP
ARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPED
VLDVHLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVR

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:48269148/chr2:189864010)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL1A1

P02452

COL3A1

P02461

FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen).FUNCTION: Collagen type III occurs in most soft connective tissues along with type I collagen. Involved in regulation of cortical development. Is the major ligand of ADGRG1 in the developing brain and binding to ADGRG1 inhibits neuronal migration and activates the RhoA pathway by coupling ADGRG1 to GNA13 and possibly GNA12.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-315138_96709.01465.0DomainVWFC
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-3151162_178709.01465.0RegionNote=Nonhelical region (N-terminal)
TgeneCOL3A1chr17:48269148chr2:189864010ENST0000030463628511232_1466674.01467.0DomainFibrillar collagen NC1
TgeneCOL3A1chr17:48269148chr2:189864010ENST0000030463628511197_1205674.01467.0RegionNote=Nonhelical region (C-terminal)

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-31511229_1464709.01465.0DomainFibrillar collagen NC1
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-31511093_1095709.01465.0MotifCell attachment site
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-3151745_747709.01465.0MotifCell attachment site
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-31511193_1218709.01465.0RegionNote=Nonhelical region (C-terminal)
HgeneCOL1A1chr17:48269148chr2:189864010ENST00000225964-3151179_1192709.01465.0RegionNote=Triple-helical region
TgeneCOL3A1chr17:48269148chr2:189864010ENST00000304636285130_89674.01467.0DomainVWFC
TgeneCOL3A1chr17:48269148chr2:189864010ENST000003046362851149_167674.01467.0RegionNote=Nonhelical region (N-terminal)
TgeneCOL3A1chr17:48269148chr2:189864010ENST000003046362851168_1196674.01467.0RegionNote=Triple-helical region


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
COL1A1IGFBP3, TXN, ITGA2, ITGB1, NID1, Nid1, NID2, SPARC, PRELP, PKD1, VWF, THBS1, MMP2, COL7A1, MATN2, MAG, ELAVL1, ATP13A2, C12orf57, RNH1, BARD1, BRCA1, UBC, CAPN1, COL1A1, COL1A2, PDGFA, PDGFB, GIPC2, UBXN11, DNM3, CD200R1, TMTC4, ERAL1, CAMKMT, TMEM180, OTUB1, EGFR, COLGALT2, P4HA2, PLOD1, LIN9, TIMM44, RASGEF1B, TLE3, YAF2, LPAR1, CYLD, MCPH1, HEXIM1, PPP1CC, KEAP1, PINK1, CDC42, NMRAL1, PAX3, NTPCR, FOXO1, IGLC1, DDX58, YIPF1, LAIR2, LAT, KIAA1191, SLC25A40, CTNND1, FOXD3, CHMP3, ZNF645, CD247, RANBP6, TRIM41, TNFRSF10D, KIR3DS1, SMDT1, PPIA, PEG10, TMEM44, RNF144A, VCP, TESPA1, ABHD14A, TADA1, ST3GAL3, KLF15, BGN, TGM2, COL18A1, NLRP7,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
COL1A1all structure
COL3A1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to COL1A1-COL3A1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to COL1A1-COL3A1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL1A1C0268358Osteogenesis imperfecta, dominant perinatal lethal38CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0268362Osteogenesis imperfecta type III (disorder)17CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0023931Lobstein Disease15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0268363Osteogenesis imperfecta type IV (disorder)12GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0023890Liver Cirrhosis4CTD_human
HgeneCOL1A1C0239946Fibrosis, Liver4CTD_human
HgeneCOL1A1C4551623EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE, 14CTD_human;GENOMICS_ENGLAND
HgeneCOL1A1C4552122EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 14GENOMICS_ENGLAND;UNIPROT
HgeneCOL1A1C0020497Cortical Congenital Hyperostosis3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL1A1C0023893Liver Cirrhosis, Experimental3CTD_human
HgeneCOL1A1C0268345EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE2ORPHANET
HgeneCOL1A1C0000786Spontaneous abortion1CTD_human
HgeneCOL1A1C0000822Abortion, Tubal1CTD_human
HgeneCOL1A1C0002949Aneurysm, Dissecting1CTD_human
HgeneCOL1A1C0003504Aortic Valve Insufficiency1CTD_human
HgeneCOL1A1C0004364Autoimmune Diseases1CTD_human
HgeneCOL1A1C0005398Cholestasis, Extrahepatic1CTD_human
HgeneCOL1A1C0005779Blood Coagulation Disorders1GENOMICS_ENGLAND
HgeneCOL1A1C0006663Calcinosis1CTD_human
HgeneCOL1A1C0008311Cholangitis1CTD_human
HgeneCOL1A1C0013720Ehlers-Danlos Syndrome1GENOMICS_ENGLAND
HgeneCOL1A1C0016059Fibrosis1CTD_human
HgeneCOL1A1C0018824Heart valve disease1CTD_human
HgeneCOL1A1C0020538Hypertensive disease1CTD_human
HgeneCOL1A1C0022548Keloid1CTD_human
HgeneCOL1A1C0027719Nephrosclerosis1CTD_human
HgeneCOL1A1C0027726Nephrotic Syndrome1CTD_human
HgeneCOL1A1C0029172Oral Submucous Fibrosis1CTD_human
HgeneCOL1A1C0029434Osteogenesis Imperfecta1CTD_human;GENOMICS_ENGLAND
HgeneCOL1A1C0149721Left Ventricular Hypertrophy1CTD_human
HgeneCOL1A1C0220679Ehlers-Danlos Syndrome, Autosomal Dominant, Type Unspecified1ORPHANET
HgeneCOL1A1C0263628Tumoral calcinosis1CTD_human
HgeneCOL1A1C0340643Dissection of aorta1CTD_human
HgeneCOL1A1C0521174Microcalcification1CTD_human
HgeneCOL1A1C1458140Bleeding tendency1GENOMICS_ENGLAND
HgeneCOL1A1C1619692Nephrogenic Fibrosing Dermopathy1CTD_human
HgeneCOL1A1C1623038Cirrhosis1CTD_human
HgeneCOL1A1C1846545Autoimmune Lymphoproliferative Syndrome Type 2B1GENOMICS_ENGLAND
HgeneCOL1A1C3830362Early Pregnancy Loss1CTD_human
HgeneCOL1A1C4277533Dissection, Blood Vessel1CTD_human
HgeneCOL1A1C4552766Miscarriage1CTD_human