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    SCUBE3 signal peptide, CUB domain and EGF like domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 222663, updated on 9-Dec-2024

    Summary

    Official Symbol
    SCUBE3provided by HGNC
    Official Full Name
    signal peptide, CUB domain and EGF like domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:13655
    See related
    Ensembl:ENSG00000146197 MIM:614708; AllianceGenome:HGNC:13655
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CEGF3; SSFSC2
    Summary
    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]
    Expression
    Biased expression in thyroid (RPKM 18.5), adrenal (RPKM 1.4) and 2 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SCUBE3 in Genome Data Viewer
    Location:
    6p21.31
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (35213956..35253079)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (35037034..35076159)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35181733..35220856)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene t-complex 11 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35115441-35116234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35116235-35117028 Neighboring gene MPRA-validated peak5764 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35152333-35152714 Neighboring gene Sharpr-MPRA regulatory region 4993 Neighboring gene uncharacterized LOC112267955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17084 Neighboring gene SCUBE3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 1078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17085 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:35211069-35212268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17087 Neighboring gene zinc finger protein 76 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:35253595-35254794 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35263932-35264096 Neighboring gene Sharpr-MPRA regulatory region 9100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35280323-35280822 Neighboring gene DEF6 guanine nucleotide exchange factor

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2
    MedGen: C5543057 OMIM: 619184 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ34743, DKFZp686B1223, DKFZp686B09105, DKFZp686D20108

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables BMP binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables BMP receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    signal peptide, CUB and EGF-like domain-containing protein 3
    Names
    CUB domain and EGF-like repeat containing 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_050574.1 RefSeqGene

      Range
      4910..44033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001303136.2NP_001290065.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice acceptor compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC052263, CR936873, Z97832
      UniProtKB/Swiss-Prot
      Q8IX30
      Conserved Domains (6) summary
      smart00179
      Location:356397
      EGF_CA; Calcium-binding EGF-like domain
      cd00041
      Location:803914
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam07699
      Location:695742
      GCC2_GCC3; GCC2 and GCC3
      pfam12947
      Location:3368
      EGF_3; EGF domain
      pfam14670
      Location:239274
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00057
      Location:312348
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    2. NM_152753.4NP_689966.2  signal peptide, CUB and EGF-like domain-containing protein 3 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF452494, BC052263, CR936873, Z97832
      Consensus CDS
      CCDS4800.1
      UniProtKB/Swiss-Prot
      A8K5A3, Q5CZB3, Q86UZ9, Q8IX30, Q8NAU9
      Related
      ENSP00000274938.7, ENST00000274938.8
      Conserved Domains (6) summary
      smart00179
      Location:357398
      EGF_CA; Calcium-binding EGF-like domain
      cd00041
      Location:804915
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam07699
      Location:696743
      Ephrin_rec_like; Putative ephrin-receptor like
      pfam12947
      Location:3368
      EGF_3; EGF domain
      pfam14670
      Location:240275
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00057
      Location:313349
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      35213956..35253079
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248943.2XP_005249000.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      Q8IX30
      Conserved Domains (6) summary
      smart00179
      Location:373414
      EGF_CA; Calcium-binding EGF-like domain
      cd00041
      Location:820931
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam07699
      Location:712759
      GCC2_GCC3; GCC2 and GCC3
      pfam12947
      Location:3368
      EGF_3; EGF domain
      pfam14670
      Location:256291
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00057
      Location:329365
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    2. XM_005248947.2XP_005249004.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X3

      Conserved Domains (6) summary
      smart00179
      Location:373414
      EGF_CA; Calcium-binding EGF-like domain
      cd00041
      Location:766877
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam07699
      Location:658705
      GCC2_GCC3; GCC2 and GCC3
      pfam12947
      Location:3368
      EGF_3; EGF domain
      pfam14670
      Location:256291
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00057
      Location:329365
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    3. XM_047418383.1XP_047274339.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X4

    4. XM_047418382.1XP_047274338.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      35037034..35076159
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354663.1XP_054210638.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X1

    2. XM_054354665.1XP_054210640.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X3

    3. XM_054354666.1XP_054210641.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X4

    4. XM_054354664.1XP_054210639.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X2