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

Gene ID: 222663, updated on 1-Jun-2020

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
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
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

Genomic context

See SCUBE3 in Genome Data Viewer
Location:
6p21.31
Exon count:
24
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (35213956..35253079)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35181824..35220856)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene t-complex 11 Neighboring gene uncharacterized LOC112267955 Neighboring gene uncharacterized LOC101929285 Neighboring gene zinc finger protein 76 Neighboring gene Sharpr-MPRA regulatory region 9100 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34743, DKFZp686B1223, DKFZp686B09105, DKFZp686D20108

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
extracellular matrix disassembly TAS
Traceable Author Statement
more info
 
positive regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
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)

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

    See identical proteins and their annotated locations for NP_001290065.1

    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

    See identical proteins and their annotated locations for NP_689966.2

    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
    Q8IX30
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_005249000.1

    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_005248947.1XP_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_011514404.2XP_011512706.1  signal peptide, CUB and EGF-like domain-containing protein 3 isoform X2

    Conserved Domains (6) summary
    smart00179
    Location:365406
    EGF_CA; Calcium-binding EGF-like domain
    cd00041
    Location:812923
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam07699
    Location:704751
    GCC2_GCC3; GCC2 and GCC3
    pfam12947
    Location:2560
    EGF_3; EGF domain
    pfam14670
    Location:248283
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl00057
    Location:321357
    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 ...
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