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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 3
  • Signal Peptide, CUB And EGF-Like Domain-Containing Protein 1 3
  • Signal Peptide-CUB Domain-EGF-Related 1 3

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. Gene Ontology (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

GeneHancer (GH) Regulatory Elements for SCUBE1 Gene

Promoters and enhancers for SCUBE1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J043343 Promoter/Enhancer 1.1 EPDnew ENCODE 650.7 0.0 -45 0.1 MXI1 NFYC ZNF16 ZNF398 ZBTB8A FOXM1 GLIS2 POLR2A NFYB VEZF1 SCUBE1 RPL5P34 RN7SKP80 POLDIP3 LOC105373053
GH22J043292 Enhancer 1.3 Ensembl ENCODE dbSUPER 16.5 +49.9 49893 2.8 PKNOX1 ATF1 FOXA2 ARID4B FEZF1 FOS ATF7 SP5 ZNF488 ZNF592 SCUBE1 GC22M043280 GC22M043296
GH22J043240 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 11.9 +102.3 102295 0.8 FOXA2 MLX ARID4B DNMT3B ZNF48 RARA SLC30A9 EGR2 HMG20B KLF11 LOC101927447 SCUBE1 TTLL12 TTLL1 GC22P043247 ENSG00000234892
GH22J043376 Enhancer 1.1 Ensembl ENCODE 12.5 -34.5 -34536 2.2 PKNOX1 FOXA2 SMAD1 MLX NFIB BATF IRF4 RARA ZNF614 BCLAF1 SCUBE1 LOC101927447 MPPED1 ENSG00000234892 MCAT LOC105373053
GH22J043300 Enhancer 0.6 ENCODE dbSUPER 18.1 +41.5 41538 2.1 ZFHX2 EGR2 SCUBE1 LOC101927447 GC22M043280 GC22M043296
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCUBE1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCUBE1 gene promoter:
  • AREB6
  • HOXA5
  • RREB-1
  • MyoD
  • STAT3
  • HNF-4alpha2
  • Lmo2
  • HNF-4alpha1
  • CBF-B

Genomic Locations for SCUBE1 Gene

Genomic Locations for SCUBE1 Gene
chr22:43,197,283-43,343,388
(GRCh38/hg38)
Size:
146,106 bases
Orientation:
Minus strand
chr22:43,593,289-43,739,394
(GRCh37/hg19)
Size:
146,106 bases
Orientation:
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:
    Q8IWY4-SCUB1_HUMAN
    Recommended name:
    Signal peptide, CUB and EGF-like domain-containing protein 1
    Protein Accession:
    Q8IWY4
    Secondary Accessions:
    • Q5R336

    Protein attributes for SCUBE1 Gene

    Size:
    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

  • N-glycosylated.
  • Could be proteolytically cleaved to release a smaller active fragment.
  • Glycosylation at posLast=789789, isoforms=779, isoforms=750, posLast=679679, isoforms=466, and posLast=370370
  • 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

  • Taconic Biosciences Mouse Models for SCUBE1

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

COMPARTMENTS
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

mRNA/cDNA 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: - - - - - - -
SP3:

ExUns: 22 ^ 23a · 23b
SP1:
SP2:
SP3:

Relevant External Links for SCUBE1 Gene

GeneLoc Exon Structure for
SCUBE1
ECgene alternative splicing isoforms for
SCUBE1

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:

SCUBE1

SOURCE GeneReport for Unigene cluster for SCUBE1 Gene:

Hs.133995

mRNA Expression by UniProt/SwissProt for SCUBE1 Gene:

Q8IWY4-SCUB1_HUMAN
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
chimpanzee
(Pan troglodytes)
Mammalia SCUBE1 33
  • 94.87 (n)
cow
(Bos Taurus)
Mammalia SCUBE1 34 33
  • 90.06 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCUBE1 34 33
  • 89.54 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Scube1 33
  • 88.33 (n)
mouse
(Mus musculus)
Mammalia Scube1 16 34 33
  • 88.02 (n)
oppossum
(Monodelphis domestica)
Mammalia SCUBE1 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCUBE1 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCUBE1 34 33
  • 74.86 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCUBE1 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scube1 33
  • 75.91 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15105 33
zebrafish
(Danio rerio)
Actinopterygii scube1 33
  • 71.41 (n)
zgc:158328 34
  • 24 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CG32373 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToMany
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

ENSEMBL:
Gene Tree for SCUBE1 (if available)
TreeFam:
Gene Tree for SCUBE1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCUBE1: view image

Paralogs for SCUBE1 Gene

Paralogs for SCUBE1 Gene

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

  • SCUB1_HUMAN
  • A0JP65_HUMAN
  • B1AH90_HUMAN
  • H0Y4Y9_HUMAN
  • Q86TI6_HUMAN
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 Variation AA Info Type
rs1000004043 -- 43,223,836(-) C/T intron_variant
rs1000031673 -- 43,229,741(-) G/C intron_variant
rs1000067867 -- 43,223,587(-) /T intron_variant
rs1000080343 -- 43,229,345(-) C/T intron_variant
rs1000100475 -- 43,294,637(-) C/T intron_variant

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

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

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)

Additional Variant Information for SCUBE1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCUBE1

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

Disorders for SCUBE1 Gene

Additional Disease Information for SCUBE1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 58
  2. A targeted association study in systemic lupus erythematosus identifies multiple susceptibility alleles. (PMID: 20962850) Budarf ML … Rioux JD (Genes and immunity 2011) 3 44 58
  3. Localization and characterization of a novel secreted protein SCUBE1 in human platelets. (PMID: 16753137) Tu CF … Yang RB (Cardiovascular research 2006) 3 4 58
  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 58
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4 58

Products for SCUBE1 Gene

Sources for SCUBE1 Gene

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