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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:SRGAP2-COL2A1 (FusionGDB2 ID:85757)

Fusion Gene Summary for SRGAP2-COL2A1

check button Fusion gene summary
Fusion gene informationFusion gene name: SRGAP2-COL2A1
Fusion gene ID: 85757
HgeneTgene
Gene symbol

SRGAP2

COL2A1

Gene ID

23380

1280

Gene nameSLIT-ROBO Rho GTPase activating protein 2collagen type II alpha 1 chain
SynonymsARHGAP34|FNBP2|SRGAP2A|SRGAP3ANFH|AOM|COL11A3|SEDC|STL1
Cytomap

1q32.1

12q13.11

Type of geneprotein-codingprotein-coding
DescriptionSLIT-ROBO Rho GTPase-activating protein 2SLIT-ROBO GAP2formin-binding protein 2rho GTPase-activating protein 34collagen alpha-1(II) chainalpha-1 type II collagenarthroophthalmopathy, progressive (Stickler syndrome)cartilage collagenchondrocalcincollagen II, alpha-1 polypeptidecollagen, type II, alpha 1
Modification date2020031320200328
UniProtAcc.

P02458

Ensembl transtripts involved in fusion geneENST00000414007, ENST00000419187, 
ENST00000471256, 		ENST00000380518, 
ENST00000493991, ENST00000337299, 
Fusion gene scores* DoF score11 X 7 X 7=5398 X 9 X 4=288
# samples 1110
** MAII scorelog2(11/539*10)=-2.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/288*10)=-1.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SRGAP2 [Title/Abstract] AND COL2A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSRGAP2(144014093)-COL2A1(48392214), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneSRGAP2

GO:0043547

positive regulation of GTPase activity

21148482

HgeneSRGAP2

GO:0046847

filopodium assembly

22559944

HgeneSRGAP2

GO:0051014

actin filament severing

21148482

HgeneSRGAP2

GO:0060996

dendritic spine development

22559944

HgeneSRGAP2

GO:2001223

negative regulation of neuron migration

22559944


check buttonFusion gene breakpoints across SRGAP2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across COL2A1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4LIHCTCGA-CC-A8HV-01ASRGAP2chr1

144014093

+COL2A1chr12

48392214

-


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Fusion Gene ORF analysis for SRGAP2-COL2A1

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-3CDSENST00000414007ENST00000380518SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-intronENST00000414007ENST00000493991SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-intronENST00000414007ENST00000337299SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-3CDSENST00000419187ENST00000380518SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-intronENST00000419187ENST00000493991SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-intronENST00000419187ENST00000337299SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-3CDSENST00000471256ENST00000380518SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-intronENST00000471256ENST00000493991SRGAP2chr1

144014093

+COL2A1chr12

48392214

-
intron-intronENST00000471256ENST00000337299SRGAP2chr1

144014093

+COL2A1chr12

48392214

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for SRGAP2-COL2A1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for SRGAP2-COL2A1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.COL2A1

P02458

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces.

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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Fusion Gene Sequence for SRGAP2-COL2A1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for SRGAP2-COL2A1


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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Related Drugs for SRGAP2-COL2A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCOL2A1P02458DB00048Collagenase clostridium histolyticumBinderBiotechApproved|Investigational

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Related Diseases for SRGAP2-COL2A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCOL2A1C0220685Achondrogenesis type 213CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C2745959Spondyloepiphyseal dysplasia, congenita12CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0003865Arthritis, Adjuvant-Induced9CTD_human
TgeneCOL2A1C0265279Kniest dysplasia9CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0971858Arthritis, Collagen-Induced9CTD_human
TgeneCOL2A1C0993582Arthritis, Experimental9CTD_human
TgeneCOL2A1C1836080Stickler Syndrome, Type I, Nonsyndromic Ocular8CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneCOL2A1C1835437Platyspondylic Lethal Skeletal Dysplasia, Torrance Type6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C1836683Czech dysplasia, metatarsal type6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C2020284Stickler syndrome, type 16CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0432214Namaqualand hip dysplasia5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0700635Strudwick syndrome5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C4225273SPONDYLOEPIPHYSEAL DYSPLASIA, STANESCU TYPE5CLINGEN;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0013604Edema4CTD_human
TgeneCOL2A1C0151603Anasarca4CTD_human
TgeneCOL2A1C0796173Spondyloperipheral dysplasia short ulna4CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneCOL2A1C4551562AVASCULAR NECROSIS OF FEMORAL HEAD, PRIMARY, 14GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0003864Arthritis3CTD_human
TgeneCOL2A1C0023234Legg-Calve-Perthes Disease3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0162323Polyarthritis3CTD_human
TgeneCOL2A1C1851536Epiphyseal Dysplasia, Multiple, with Myopia and Conductive Deafness3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL2A1C0003873Rheumatoid Arthritis2CTD_human
TgeneCOL2A1C0008925Cleft Palate2CTD_human;GENOMICS_ENGLAND
TgeneCOL2A1C0021368Inflammation2CTD_human
TgeneCOL2A1C0029408Degenerative polyarthritis2CTD_human
TgeneCOL2A1C0041834Erythema2CTD_human
TgeneCOL2A1C0086743Osteoarthrosis Deformans2CTD_human
TgeneCOL2A1C0376634Craniofacial Abnormalities2CTD_human
TgeneCOL2A1C1262477Weight decreased2CTD_human
TgeneCOL2A1C1852989Vitreoretinopathy with Phalangeal Epiphyseal Dysplasia2GENOMICS_ENGLAND
TgeneCOL2A1C1861481Stickler syndrome, type 32ORPHANET
TgeneCOL2A1C4302548Dysspondyloenchondromatosis2ORPHANET
TgeneCOL2A1C4520892Otospondylomegaepiphyseal dysplasia2CTD_human;GENOMICS_ENGLAND
TgeneCOL2A1C0005974Bone Resorption1CTD_human
TgeneCOL2A1C0007302Cartilage Diseases1CTD_human
TgeneCOL2A1C0008479Chondrosarcoma1CTD_human
TgeneCOL2A1C0013366Dyschondroplasias1CTD_human
TgeneCOL2A1C0015397Disorder of eye1GENOMICS_ENGLAND
TgeneCOL2A1C0018784Sensorineural Hearing Loss (disorder)1CTD_human
TgeneCOL2A1C0020507Hyperplasia1CTD_human
TgeneCOL2A1C0025202melanoma1CTD_human
TgeneCOL2A1C0025237Melnick-Needles Syndrome1CTD_human
TgeneCOL2A1C0026760Multiple Epiphyseal Dysplasia1CTD_human
TgeneCOL2A1C0027092Myopia1CTD_human
TgeneCOL2A1C0029422Osteochondrodysplasias1CTD_human
TgeneCOL2A1C0035305Retinal Detachment1CTD_human
TgeneCOL2A1C0036391Schwartz-Jampel Syndrome1CTD_human
TgeneCOL2A1C0038015Spondyloepiphyseal Dysplasia1CTD_human
TgeneCOL2A1C0039103Synovitis1CTD_human
TgeneCOL2A1C0085700Chondromalacia1CTD_human
TgeneCOL2A1C0086543Cataract1CTD_human
TgeneCOL2A1C0339546Retinal Pigment Epithelial Detachment1CTD_human
TgeneCOL2A1C0410480Avascular Necrosis of Femur Head1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneCOL2A1C0410574Synovial Hypertrophy1CTD_human
TgeneCOL2A1C0432221Spondylometaphyseal dysplasia, 'corner fracture' type1ORPHANET
TgeneCOL2A1C0432272Van Buchem disease1CTD_human
TgeneCOL2A1C0524524Pseudoaphakia1CTD_human
TgeneCOL2A1C0542428Hypochondrogenesis1ORPHANET
TgeneCOL2A1C1510497Lens Opacities1CTD_human
TgeneCOL2A1C1691779Sensory hearing loss1CTD_human
TgeneCOL2A1C1836081RHEGMATOGENOUS RETINAL DETACHMENT, AUTOSOMAL DOMINANT1ORPHANET
TgeneCOL2A1C1837218Cleft palate, isolated1CTD_human
TgeneCOL2A1C1840452Hyaloideoretinal degeneration of Wagner1CTD_human
TgeneCOL2A1C1855310Megaepiphyseal dwarfism1CTD_human
TgeneCOL2A1C1866688Spondylometaphyseal dysplasia, Algerian type1ORPHANET
TgeneCOL2A1C3541456Spondyloepiphyseal Dysplasia Tarda, X-Linked1CTD_human
TgeneCOL2A1C4479260AVASCULAR NECROSIS OF FEMORAL HEAD, PRIMARY, 21ORPHANET
TgeneCOL2A1C4551479Schwartz-Jampel Syndrome, Type 11CTD_human