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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
  • GC06P038974
  • GC06P039562
  • GC06P040123

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. Gene Ontology (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.

Additional gene information for SCUBE3 Gene

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

Genomics for SCUBE3 Gene

GeneHancer (GH) Regulatory Elements for SCUBE3 Gene

Promoters and enhancers for SCUBE3 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
GH06I035213 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.3 295 1.1 MXI1 ZNF335 POLR2A ZNF366 KLF8 ZBTB20 EGR2 EZH2 MAZ L3MBTL2 SCUBE3 DEF6 GC06M038605
GH06I035215 Enhancer 0.7 Ensembl dbSUPER 550.8 +1.5 1454 0.6 ZNF148 ZNF341 ZNF600 EZH2 SCUBE3 GC06M038605 DEF6
GH06I035214 Enhancer 0.5 ENCODE 550.8 -0.4 -408 0.2 MXI1 RFX3 SIN3A CTBP2 KLF8 EZH2 SCUBE3 DEF6 PIR33203 GC06M038605
GH06I035164 Enhancer 1.2 Ensembl ENCODE dbSUPER 18 -48.3 -48284 2.1 ELF3 FOXA2 YY1 MIXL1 RXRA SP5 ELF1 REST MIER3 CEBPA SCUBE3 C6orf106 TCP11 GC06P042383
GH06I035160 Enhancer 0.7 dbSUPER 29.8 -52.4 -52379 3 BCOR SOX13 ZFP64 ARID4B ZMYM3 ZNF644 RAD21 YY1 GATA3 HNF4G SCUBE3 DEF6 UHRF1BP1 TCP11 GC06P042383
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCUBE3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCUBE3 gene promoter:

Genomic Locations for SCUBE3 Gene

Genomic Locations for SCUBE3 Gene
chr6:35,214,047-35,253,079
(GRCh38/hg38)
Size:
39,033 bases
Orientation:
Plus strand
chr6:35,182,190-35,220,856
(GRCh37/hg19)

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:
    109282 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.
    SequenceCaution:
    • Sequence=BAC03798.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    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 the ability to bind to TGFBR2. This reaction is catalyzed in vitro by MMP2 and, to a lesser extent, by MMP9.
  • Glycosylation at isoforms=2417, posLast=464464, posLast=685685, isoforms=2756, and isoforms=2785

Other Protein References for SCUBE3 Gene

No data available for DME Specific Peptides for SCUBE3 Gene

Domains & Families for SCUBE3 Gene

Gene Families for SCUBE3 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

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 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.

Phenotypes From GWAS Catalog for SCUBE3 Gene

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:

miRNA for SCUBE3 Gene

miRTarBase miRNAs that target SCUBE3

Clone 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
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 SCUBE3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCUBE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA --
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IDA,IEA 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:0007165 signal transduction IBA --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030154 cell differentiation IBA --
GO:0045880 positive regulation of smoothened signaling pathway IEA --
GO:0051260 protein homooligomerization IDA 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

Drugs & Compounds for SCUBE3 Gene

No Compound Related Data Available

Transcripts for SCUBE3 Gene

Unigene Clusters for SCUBE3 Gene

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

Clone 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 CGAP 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

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCUBE3 Gene

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 33 34
  • 99.61 (n)
cow
(Bos Taurus)
Mammalia SCUBE3 33 34
  • 93.29 (n)
dog
(Canis familiaris)
Mammalia SCUBE3 33 34
  • 93.15 (n)
oppossum
(Monodelphis domestica)
Mammalia SCUBE3 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Scube3 33 16 34
  • 90.16 (n)
rat
(Rattus norvegicus)
Mammalia Scube3 33
  • 89.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCUBE3 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCUBE3 33 34
  • 79.18 (n)
lizard
(Anolis carolinensis)
Reptilia SCUBE3 34
  • 82 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii scube3 33 34
  • 70.91 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32373 34
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs193920941 uncertain-significance, Malignant tumor of prostate 35,245,288(+) C/T coding_sequence_variant, missense_variant
rs1000014997 -- 35,228,146(+) C/G intron_variant
rs1000066808 -- 35,214,368(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1000107771 -- 35,248,083(+) A/G intron_variant
rs1000140749 -- 35,235,942(+) T/ 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)

Additional Variant Information 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, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCUBE3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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-β receptor ligand and regulates the epithelial-mesenchymal transition in lung cancer. (PMID: 21441952) Wu YY … Yang PC (Oncogene 2011) 3 4 58
  2. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PMID: 20546612) Zhao J … Grant SF (BMC medical genetics 2010) 3 44 58
  3. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for SCUBE3 Gene

Sources for SCUBE3 Gene

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