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Aliases for SCUBE1 Gene

Aliases for SCUBE1 Gene

  • Signal Peptide, CUB Domain And EGF Like Domain Containing 1 2 3 5
  • Signal Peptide, CUB Domain, EGF-Like 1 2

External Ids for SCUBE1 Gene

Previous GeneCards Identifiers for SCUBE1 Gene

  • GC22U990211
  • GC22M040206
  • GC22M041830
  • GC22M041924
  • GC22M043599
  • GC22M026558

Summaries for SCUBE1 Gene

Entrez Gene Summary for SCUBE1 Gene

  • This gene encodes a cell surface glycoprotein that is a member of the SCUBE (signal peptide, CUB domain, EGF (epidermal growth factor)-like protein) family. Family members have an amino-terminal signal peptide, nine copies of EGF-like repeats and a CUB domain at the carboxyl terminus. This protein is expressed in platelets and endothelial cells and may play an important role in vascular biology. [provided by RefSeq, Oct 2011]

GeneCards Summary for SCUBE1 Gene

SCUBE1 (Signal Peptide, CUB Domain And EGF Like Domain Containing 1) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding and protein heterodimerization activity. An important paralog of this gene is SCUBE3.

UniProtKB/Swiss-Prot for SCUBE1 Gene

  • Could function as an adhesive molecule and its matrix bound and soluble fragments may play a critical role in vascular biology.

Additional gene information for SCUBE1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCUBE1 Gene

Genomics for SCUBE1 Gene

Regulatory Elements for SCUBE1 Gene

Enhancers for SCUBE1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22H043292 1.5 Ensembl ENCODE dbSUPER 16.4 +49.9 49894 2.8 PKNOX1 ATF1 FOXA2 ARID4B FEZF1 FOS ATF7 SP5 ZNF488 ZNF592 SCUBE1 GC22M043280 GC22M043296
GH22H043240 1.4 FANTOM5 ENCODE dbSUPER 11.9 +102.3 102296 0.8 FOXA2 MLX ARID4B DNMT3B RARA SLC30A9 EGR2 KLF11 HMG20B SP5 LOC101927447 SCUBE1 TTLL12 TTLL1 GC22P043247 ENSG00000234892
GH22H043376 1.2 Ensembl ENCODE 12.5 -34.5 -34537 2.2 PKNOX1 TBL1XR1 MLX NFIB BATF RARA YY1 RUNX3 CREM IKZF2 SCUBE1 LOC101927447 MPPED1 ENSG00000234892 MCAT LOC105373053
GH22H043300 0.7 ENCODE dbSUPER 18.1 +41.5 41538 2.1 ZFHX2 EGR2 SCUBE1 LOC101927447 GC22M043280 GC22M043296
GH22H043257 1 FANTOM5 ENCODE dbSUPER 11.9 +85.9 85866 0.9 PRDM10 ATF7 EGR2 SCUBE1 GC22M043260 GC22M043246
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCUBE1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SCUBE1 Gene

Genomic Locations for SCUBE1 Gene
146,106 bases
Minus strand

Genomic View for SCUBE1 Gene

Genes around SCUBE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCUBE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCUBE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCUBE1 Gene

Proteins for SCUBE1 Gene

  • Protein details for SCUBE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Signal peptide, CUB and EGF-like domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • Q5R336

    Protein attributes for SCUBE1 Gene

    988 amino acids
    Molecular mass:
    107910 Da
    Quaternary structure:
    • Forms homooligomers and heterooligomers with SCUBE2 and SCUBE3.

neXtProt entry for SCUBE1 Gene

Post-translational modifications for SCUBE1 Gene

  • Could be proteolytically cleaved to release a smaller active fragment.
  • N-glycosylated.
  • Glycosylation at isoforms=370, isoforms=466, Asn679, isoforms=750, isoforms=779, and isoforms=789
  • Modification sites at PhosphoSitePlus

Other Protein References for SCUBE1 Gene

No data available for DME Specific Peptides for SCUBE1 Gene

Domains & Families for SCUBE1 Gene

Gene Families for SCUBE1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCUBE1: view

No data available for UniProtKB/Swiss-Prot for SCUBE1 Gene

Function for SCUBE1 Gene

Molecular function for SCUBE1 Gene

UniProtKB/Swiss-Prot Function:
Could function as an adhesive molecule and its matrix bound and soluble fragments may play a critical role in vascular biology.
UniProtKB/Swiss-Prot Induction:
Down-regulated by inflammatory cytokines.

Phenotypes From GWAS Catalog for SCUBE1 Gene

Gene Ontology (GO) - Molecular Function for SCUBE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding TAS 12270931
GO:0042802 identical protein binding IDA 12270931
GO:0046982 protein heterodimerization activity IDA 12270931
genes like me logo Genes that share ontologies with SCUBE1: view
genes like me logo Genes that share phenotypes with SCUBE1: view

Animal Models for SCUBE1 Gene

MGI Knock Outs for SCUBE1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCUBE1 Gene

Localization for SCUBE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCUBE1 Gene

Secreted. Cell membrane; Peripheral membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCUBE1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SCUBE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IDA 12270931
GO:0005886 plasma membrane TAS --
GO:0009897 external side of plasma membrane IDA 12270931
GO:0009986 cell surface IDA 12270931
genes like me logo Genes that share ontologies with SCUBE1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCUBE1 Gene

Pathways & Interactions for SCUBE1 Gene

SuperPathways for SCUBE1 Gene

No Data Available

Interacting Proteins for SCUBE1 Gene

Gene Ontology (GO) - Biological Process for SCUBE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006954 inflammatory response NAS 12270931
GO:0007165 signal transduction IBA --
GO:0007512 adult heart development NAS 12270931
GO:0007596 blood coagulation NAS 12270931
GO:0009791 post-embryonic development NAS 12270931
genes like me logo Genes that share ontologies with SCUBE1: view

No data available for Pathways by source and SIGNOR curated interactions for SCUBE1 Gene

Drugs & Compounds for SCUBE1 Gene

No Compound Related Data Available

Transcripts for SCUBE1 Gene

Unigene Clusters for SCUBE1 Gene

Signal peptide, CUB domain, EGF-like 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCUBE1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - -
SP2: - - - - - - -

ExUns: 22 ^ 23a · 23b

Relevant External Links for SCUBE1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCUBE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCUBE1 Gene

mRNA differential expression in normal tissues according to GTEx for SCUBE1 Gene

This gene is overexpressed in Esophagus - Gastroesophageal Junction (x10.9), Esophagus - Muscularis (x9.0), Nerve - Tibial (x6.5), and Ovary (x5.5).

Protein differential expression in normal tissues from HIPED for SCUBE1 Gene

This gene is overexpressed in Fetal testis (28.8), Spinal cord (11.7), Ovary (10.9), and Testis (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCUBE1 Gene

Protein tissue co-expression partners for SCUBE1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCUBE1 Gene:


SOURCE GeneReport for Unigene cluster for SCUBE1 Gene:


mRNA Expression by UniProt/SwissProt for SCUBE1 Gene:

Tissue specificity: Detected in endothelial cells. Highly expressed in platelets. Stored in platelet alpha granules, and transferred to the cell surface upon activation and aggregation. A smaller form, probably produced by limited proteolysis, after being released from the storage granules, is associated with thrombus and localized with the subendothelial matrices in atherosclerotic plaques.
genes like me logo Genes that share expression patterns with SCUBE1: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCUBE1 Gene

Orthologs for SCUBE1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCUBE1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCUBE1 33
  • 94.87 (n)
(Bos Taurus)
Mammalia SCUBE1 33 34
  • 90.06 (n)
(Canis familiaris)
Mammalia SCUBE1 33 34
  • 89.54 (n)
(Rattus norvegicus)
Mammalia Scube1 33
  • 88.33 (n)
(Mus musculus)
Mammalia Scube1 33 16 34
  • 88.02 (n)
(Monodelphis domestica)
Mammalia SCUBE1 34
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia SCUBE1 34
  • 75 (a)
(Gallus gallus)
Aves SCUBE1 33 34
  • 74.86 (n)
(Anolis carolinensis)
Reptilia SCUBE1 34
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia scube1 33
  • 75.91 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15105 33
(Danio rerio)
Actinopterygii scube1 33
  • 71.41 (n)
zgc:158328 34
  • 24 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG32373 34
  • 23 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
Species where no ortholog for SCUBE1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCUBE1 Gene

Gene Tree for SCUBE1 (if available)
Gene Tree for SCUBE1 (if available)

Paralogs for SCUBE1 Gene

Paralogs for SCUBE1 Gene

(11) SIMAP similar genes for SCUBE1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with SCUBE1: view

Variants for SCUBE1 Gene

Sequence variations from dbSNP and Humsavar for SCUBE1 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000004043 -- 43,223,836(+) AGCCT(C/T)GCACT intron-variant
rs1000031673 -- 43,229,741(+) AATGT(C/G)AAATG intron-variant
rs1000067867 -- 43,223,586(+) GGGGG(-/T)ATCGC intron-variant
rs1000080343 -- 43,229,345(+) GACTC(C/T)TTGCT intron-variant
rs1000100475 -- 43,294,637(+) GTGGG(C/T)GATGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SCUBE1 Gene

Variant ID Type Subtype PubMed ID
nsv955167 CNV deletion 24416366
nsv955166 CNV deletion 24416366
nsv834216 CNV loss 17160897
nsv834214 CNV gain 17160897
nsv821331 CNV deletion 20802225
nsv589097 CNV loss 21841781
nsv589094 CNV loss 21841781
nsv589090 CNV loss 21841781
nsv589089 CNV gain 21841781
nsv589088 CNV loss 21841781
nsv520927 CNV loss 19592680
nsv474133 CNV novel sequence insertion 20440878
nsv471202 CNV gain 18288195
nsv471201 CNV loss 18288195
nsv459891 CNV gain 19166990
nsv191393 CNV insertion 16902084
nsv1122056 CNV deletion 24896259
nsv1072642 CNV deletion 25765185
nsv1056118 CNV gain 25217958
esv5307 CNV loss 18987735
esv3647862 CNV loss 21293372
esv3568426 CNV loss 25503493
esv3472 CNV loss 18987735
esv3442804 CNV insertion 20981092
esv3433826 CNV insertion 20981092
esv33816 CNV gain 17666407
esv3355407 CNV insertion 20981092
esv3306011 CNV mobile element insertion 20981092
esv3305111 CNV mobile element insertion 20981092
esv29705 CNV gain 19812545
esv2724305 CNV deletion 23290073
esv2724303 CNV deletion 23290073
esv2724302 CNV deletion 23290073
esv2724301 CNV deletion 23290073
esv2677156 CNV deletion 23128226
esv2676917 CNV deletion 23128226
esv2665956 CNV deletion 23128226
esv2660751 CNV deletion 23128226
esv2628998 CNV deletion 19546169
esv2330845 CNV deletion 18987734
esv2215307 CNV deletion 18987734
esv1613247 CNV deletion 17803354
esv1076173 CNV deletion 17803354
esv1000890 CNV deletion 20482838
dgv844e214 CNV gain 21293372
dgv8121n54 CNV loss 21841781
dgv8120n54 CNV loss 21841781
dgv735e201 CNV deletion 23290073

Variation tolerance for SCUBE1 Gene

Residual Variation Intolerance Score: 28.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.85; 91.77% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCUBE1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCUBE1 Gene

Disorders for SCUBE1 Gene

Relevant External Links for SCUBE1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SCUBE1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCUBE1 Gene

Publications for SCUBE1 Gene

  1. Cloning, mapping, and expression analysis of a gene encoding a novel mammalian EGF-related protein (SCUBE1). (PMID: 11087664) Grimmond S … Greenfield A (Genomics 2000) 2 3 22 60
  2. A targeted association study in systemic lupus erythematosus identifies multiple susceptibility alleles. (PMID: 20962850) Budarf ML … Rioux JD (Genes and immunity 2011) 3 45 60
  3. Localization and characterization of a novel secreted protein SCUBE1 in human platelets. (PMID: 16753137) Tu CF … Yang RB (Cardiovascular research 2006) 3 4 60
  4. Identification of a novel family of cell-surface proteins expressed in human vascular endothelium. (PMID: 12270931) Yang RB … Topper JN (The Journal of biological chemistry 2002) 3 4 60
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4 60

Products for SCUBE1 Gene

Sources for SCUBE1 Gene

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