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Aliases for SCUBE3 Gene

Aliases for SCUBE3 Gene

  • Signal Peptide, CUB Domain And EGF Like Domain Containing 3 2 3 5
  • CUB Domain And EGF-Like Repeat Containing 3 2 3
  • CEGF3 3 4
  • Signal Peptide, CUB And EGF-Like Domain-Containing Protein 3 3
  • Signal Peptide, CUB Domain, EGF-Like 3 2

External Ids for SCUBE3 Gene

Previous HGNC Symbols for SCUBE3 Gene

  • CEGF3

Previous GeneCards Identifiers for SCUBE3 Gene

  • GC06P035231
  • GC06P035290
  • GC06P034902
  • GC06P035182
  • GC06P035282
  • GC06P035532
  • GC06P037760
  • GC06P038384

Summaries for SCUBE3 Gene

Entrez Gene Summary for SCUBE3 Gene

  • This gene encodes a member of the signal peptide, complement subcomponents C1r/C1s, Uegf, bone morphogenetic protein-1 and epidermal growth factor-like domain containing protein family. Overexpression of this gene in human embryonic kidney cells results in secretion of a glycosylated form of the protein that forms oligomers and tethers to the cell surface. This gene is upregulated in lung cancer tumor tissue compared to healthy tissue and is associated with loss of the epithelial marker E-cadherin and with increased expression of vimentin, a mesenchymal marker. In addition, the protein encoded by this gene is a transforming growth factor beta receptor ligand, and when secreted by cancer cells, it can be cleaved in vitro to release the N-terminal epidermal growth factor-like repeat domain and the C-terminal complement subcomponents C1r/C1s domain. Both the full length protein and C-terminal fragment can bind to the transforming growth factor beta type II receptor to promote the epithelial-mesenchymal transition and tumor angiogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneCards Summary for SCUBE3 Gene

SCUBE3 (Signal Peptide, CUB Domain And EGF Like Domain Containing 3) is a Protein Coding gene. Diseases associated with SCUBE3 include Lung Cancer. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is SCUBE1.

UniProtKB/Swiss-Prot for SCUBE3 Gene

  • Binds to TGFBR2 and activates TGFB signaling. In lung cancer cells, could serve as an endogenous autocrine and paracrine ligand of TGFBR2, which could regulate TGFBR2 signaling and hence modulate epithelial-mesenchymal transition and cancer progression.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCUBE3 Gene

Genomics for SCUBE3 Gene

Regulatory Elements for SCUBE3 Gene

Enhancers for SCUBE3 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
GH06F035152 1.1 Ensembl ENCODE 25.8 -61.3 -61320 0.7 MAFG BACH1 ARID1B ZNF316 ATF3 PBX2 NFE2L1 NFE2 KDM1A ZNF548 SCUBE3 TCP11 DEF6 GC06P040017
GH06F035164 0.5 Ensembl ENCODE 18 -48.3 -48285 2.1 SOX13 ELF3 TFAP4 SAP130 ZMYM3 CEBPG YY1 GATA3 CREM MIXL1 SCUBE3 C6orf106 TCP11 GC06P040017
GH06F034990 1.1 ENCODE 15.4 -222.1 -222053 3.0 ZNF316 JUND TRIM24 NR2F2 UHRF1BP1 SCUBE3 TAF11 ANKS1A PIR39158 PIR43947 GC06P039566
GH06F035141 0.2 Ensembl 13.6 -73.1 -73080 1.5 CBX3 ARID4B THRB ZBTB40 RAD21 ZNF143 KLF7 MIXL1 KLF11 ZNF654 TCP11 SCUBE3 UHRF1BP1 GC06M037205
GH06F035237 1.2 Ensembl ENCODE 11.8 +24.7 24706 2.3 CTCF TEAD4 BMI1 CEBPG ZNF2 RAD21 TEAD3 POLR2A ZNF143 ZNF207 ZNF76 TCP11 UHRF1BP1 SCUBE3 DEF6 GC06M037522 PIR55616
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SCUBE3 on UCSC Golden Path with GeneCards custom track

Promoters for SCUBE3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001215123 353 1601 KLF17 FEZF1 ZNF2 KAT2B ZNF335 GLIS2 ZNF366 SCRT2 FOS EGR2

Genomic Location for SCUBE3 Gene

Chromosome:
6
Start:
35,214,047 bp from pter
End:
35,253,079 bp from pter
Size:
39,033 bases
Orientation:
Plus strand

Genomic View for SCUBE3 Gene

Genes around SCUBE3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCUBE3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCUBE3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCUBE3 Gene

Proteins for SCUBE3 Gene

  • Protein details for SCUBE3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IX30-SCUB3_HUMAN
    Recommended name:
    Signal peptide, CUB and EGF-like domain-containing protein 3
    Protein Accession:
    Q8IX30
    Secondary Accessions:
    • A8K5A3
    • Q5CZB3
    • Q86UZ9
    • Q8NAU9

    Protein attributes for SCUBE3 Gene

    Size:
    993 amino acids
    Molecular mass:
    D Da
    Quaternary structure:
    • Forms homooligomers and heterooligomers with SCUBE1. Interacts with TGFBR2 through the CUB domain; this interaction does not affect TGFB1-binding to TGFBR2.

    Alternative splice isoforms for SCUBE3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCUBE3 Gene

Post-translational modifications for SCUBE3 Gene

  • N-glycosylated.
  • Proteolytic cleavage produces a CUB-containing C-terminal fragment that retains.
  • Glycosylation at Asn 417, Asn 464, Asn 685, Asn 756, and Asn 785
  • Modification sites at PhosphoSitePlus

Other Protein References for SCUBE3 Gene

Antibody Products

  • Cloud-Clone Corp. Antibodies for SCUBE3

No data available for DME Specific Peptides for SCUBE3 Gene

Domains & Families for SCUBE3 Gene

Suggested Antigen Peptide Sequences for SCUBE3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCUBE3: view

No data available for Gene Families and UniProtKB/Swiss-Prot for SCUBE3 Gene

Function for SCUBE3 Gene

Molecular function for SCUBE3 Gene

UniProtKB/Swiss-Prot Function:
Binds to TGFBR2 and activates TGFB signaling. In lung cancer cells, could serve as an endogenous autocrine and paracrine ligand of TGFBR2, which could regulate TGFBR2 signaling and hence modulate epithelial-mesenchymal transition and cancer progression.

Gene Ontology (GO) - Molecular Function for SCUBE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 15234972
genes like me logo Genes that share ontologies with SCUBE3: view
genes like me logo Genes that share phenotypes with SCUBE3: view

Animal Models for SCUBE3 Gene

MGI Knock Outs for SCUBE3:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCUBE3

miRNA for SCUBE3 Gene

miRTarBase miRNAs that target SCUBE3

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCUBE3 Gene

Localization for SCUBE3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCUBE3 Gene

Secreted. Cell surface.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SCUBE3 Gene COMPARTMENTS Subcellular localization image for SCUBE3 gene
Compartment Confidence
extracellular 5
plasma membrane 3
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SCUBE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0009986 cell surface IEA,IDA 15234972
genes like me logo Genes that share ontologies with SCUBE3: view

Pathways & Interactions for SCUBE3 Gene

SuperPathways for SCUBE3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCUBE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045880 positive regulation of smoothened signaling pathway IEA --
GO:0051260 protein homooligomerization IDA 15234972
GO:0051291 protein heterooligomerization IPI 15234972
genes like me logo Genes that share ontologies with SCUBE3: view

No data available for Pathways by source and SIGNOR curated interactions for SCUBE3 Gene

Transcripts for SCUBE3 Gene

Unigene Clusters for SCUBE3 Gene

Signal peptide, CUB domain, EGF-like 3:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCUBE3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b ·
SP1: -
SP2: - -
SP3: - - -

ExUns: 24c
SP1:
SP2:
SP3:

Relevant External Links for SCUBE3 Gene

GeneLoc Exon Structure for
SCUBE3
ECgene alternative splicing isoforms for
SCUBE3

Expression for SCUBE3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCUBE3 Gene

mRNA differential expression in normal tissues according to GTEx for SCUBE3 Gene

This gene is overexpressed in Artery - Aorta (x15.0), Thyroid (x10.1), and Artery - Tibial (x8.5).

Protein differential expression in normal tissues from HIPED for SCUBE3 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (68.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SCUBE3 Gene



Protein tissue co-expression partners for SCUBE3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCUBE3 Gene:

SCUBE3

SOURCE GeneReport for Unigene cluster for SCUBE3 Gene:

Hs.12923

mRNA Expression by UniProt/SwissProt for SCUBE3 Gene:

Q8IX30-SCUB3_HUMAN
Tissue specificity: Highly expressed in osteoblasts. In normal lung, mainly expressed in bronchial epithelial cells. Tends to be up-regulated in lung cancer cells.
genes like me logo Genes that share expression patterns with SCUBE3: view

Primer Products

Orthologs for SCUBE3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCUBE3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCUBE3 34 35
  • 99.61 (n)
cow
(Bos Taurus)
Mammalia SCUBE3 34 35
  • 93.29 (n)
dog
(Canis familiaris)
Mammalia SCUBE3 34 35
  • 93.15 (n)
oppossum
(Monodelphis domestica)
Mammalia SCUBE3 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Scube3 34 16 35
  • 90.16 (n)
rat
(Rattus norvegicus)
Mammalia Scube3 34
  • 89.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCUBE3 35
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCUBE3 34 35
  • 79.18 (n)
lizard
(Anolis carolinensis)
Reptilia SCUBE3 35
  • 82 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii scube3 34 35
  • 70.91 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32373 35
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 37 (a)
OneToMany
Species where no ortholog for SCUBE3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCUBE3 Gene

ENSEMBL:
Gene Tree for SCUBE3 (if available)
TreeFam:
Gene Tree for SCUBE3 (if available)

Paralogs for SCUBE3 Gene

Paralogs for SCUBE3 Gene

(3) SIMAP similar genes for SCUBE3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SCUBE3: view

Variants for SCUBE3 Gene

Sequence variations from dbSNP and Humsavar for SCUBE3 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs193920941 Uncertain significance 35,245,288(+) CTACC(C/T)GGGCA intron-variant, upstream-variant-2KB, reference, missense
rs1013907 -- 35,234,081(+) TTTAA(C/T)TCCTT intron-variant
rs1034449 -- 35,221,800(+) TAGCA(C/T)ATGAG intron-variant
rs1034450 -- 35,221,913(+) AGTGT(C/T)CCAGC intron-variant
rs1041528 -- 35,222,343(-) TATAA(A/T)ACAAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SCUBE3 Gene

Variant ID Type Subtype PubMed ID
esv2759419 CNV loss 17122850

Variation tolerance for SCUBE3 Gene

Residual Variation Intolerance Score: 8.71% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.18; 51.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCUBE3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCUBE3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCUBE3 Gene

Disorders for SCUBE3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCUBE3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
lung cancer
  • lung cancer, protection against
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SCUBE3

Genetic Association Database (GAD)
SCUBE3
Human Genome Epidemiology (HuGE) Navigator
SCUBE3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SCUBE3
genes like me logo Genes that share disorders with SCUBE3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCUBE3 Gene

Publications for SCUBE3 Gene

  1. SCUBE3 is an endogenous TGF-beta receptor ligand and regulates the epithelial-mesenchymal transition in lung cancer. (PMID: 21441952) Wu Y.Y. … Yang P.C. (Oncogene 2011) 3 4 64
  2. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PMID: 20546612) Zhao J. … Grant S.F. (BMC Med. Genet. 2010) 3 46 64
  3. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson D.F. … Stefansson K. (Nat. Genet. 2008) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. A novel secreted, cell-surface glycoprotein containing multiple epidermal growth factor-like repeats and one CUB domain is highly expressed in primary osteoblasts and bones. (PMID: 15234972) Wu B.-T. … Yang R.-B. (J. Biol. Chem. 2004) 3 4 64

Products for SCUBE3 Gene

Sources for SCUBE3 Gene

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