Scube3 signal peptide, CUB domain, EGF-like 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scube3provided by MGI
Official Full Name: signal peptide, CUB domain, EGF-like 3provided by MGI
Primary source: MGI:MGI:3045253
See related: Ensembl:ENSMUSG00000038677 AllianceGenome:MGI:3045253
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: CEGF3; D030038I21Rik
Summary: Predicted to enable BMP binding activity; BMP receptor binding activity; and identical protein binding activity. Involved in positive regulation of osteoblast differentiation. Acts upstream of or within positive regulation of smoothened signaling pathway. Predicted to be located in plasma membrane. Predicted to be active in cell surface and extracellular space. Is expressed in several structures, including embryo ectoderm; embryo mesenchyme; integumental system; jaw; and sensory organ. Human ortholog(s) of this gene implicated in short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2. Orthologous to human SCUBE3 (signal peptide, CUB domain and EGF like domain containing 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in limb E14.5 (RPKM 8.4), CNS E11.5 (RPKM 7.4) and 14 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 A3.3; 17 14.63 cM

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (28361074..28393825)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (28142100..28174851)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epithelium-derived SCUBE3 promotes polarized odontoblastic differentiation of dental mesenchymal stem cells and pulp regeneration.
Title: Epithelium-derived SCUBE3 promotes polarized odontoblastic differentiation of dental mesenchymal stem cells and pulp regeneration.
These findings correlate with characteristics of the rare metabolic bone disorder Paget disease of bone (PDB), associated with the chromosomal region of human SCUBE3 In addition, alterations in energy metabolism, behavior, and neurological functions were detected in Scube3(N294K/N294K) mice. The Scube3(N294K/N294K) mutant mouse line may serve as a new model for further studying the effect of impaired SCUBE3 gene function.
Title: The First Scube3 Mutant Mouse Line with Pleiotropic Phenotypic Alterations.
Scube3 may be a critical upstream regulator of fast fiber myogenesis by modulating fgf8 signaling during zebrafish embryogenesis
Title: SCUBE3 (signal peptide-CUB-EGF domain-containing protein 3) modulates fibroblast growth factor signaling during fast muscle development.
Scube3 is expressed in multiple tissues during development but is dispensable for embryonic survival in the mouse.
Title: Scube3 is expressed in multiple tissues during development but is dispensable for embryonic survival in the mouse.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (2)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables BMP binding	ISO Inferred from Sequence Orthology more info
enables BMP receptor binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in positive regulation of BMP signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of BMP signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of smoothened signaling pathway	IDA Inferred from Direct Assay 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	ISO Inferred from Sequence Orthology more info
located_in cell surface	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001004366.2 → NP_001004366.1 signal peptide, CUB and EGF-like domain-containing protein 3 isoform 1 precursor

See identical proteins and their annotated locations for NP_001004366.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC126937

Consensus CDS

CCDS37527.1

UniProtKB/Swiss-Prot

B2KF22, Q66PY1, Q68FG9

UniProtKB/TrEMBL

A0A3B2W867

Related

ENSMUSP00000038366.4, ENSMUST00000043503.11

Conserved Domains (6) summary

smart00179
Location:357 → 398

EGF_CA; Calcium-binding EGF-like domain

cd00041
Location:804 → 915

CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

pfam07699
Location:696 → 743

GCC2_GCC3; GCC2 and GCC3

pfam12947
Location:33 → 68

EGF_3; EGF domain

pfam14670
Location:240 → 275

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:313 → 349

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 ...
NM_001368734.1 → NP_001355663.1 signal peptide, CUB and EGF-like domain-containing protein 3 isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC126937

Conserved Domains (3) summary

pfam12947
Location:33 → 68

EGF_3; EGF domain

pfam12662
Location:93 → 115

cEGF; Complement Clr-like EGF-like

cl00057
Location:110 → 150

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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

28361074..28393825

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006524323.4 → XP_006524386.1 signal peptide, CUB and EGF-like domain-containing protein 3 isoform X1

See identical proteins and their annotated locations for XP_006524386.1

UniProtKB/TrEMBL

A0A3B2W867, A0A3B2WCG9

Related

ENSMUSP00000156515.2, ENSMUST00000137147.9

Conserved Domains (5) summary

smart00179
Location:334 → 363

EGF_CA; Calcium-binding EGF-like domain

cd00041
Location:820 → 931

CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

pfam07699
Location:712 → 759

Ephrin_rec_like; Putative ephrin-receptor like

pfam12947
Location:33 → 68

EGF_3; EGF domain

pfam14670
Location:256 → 291

FXa_inhibition; Coagulation Factor Xa inhibitory site
XM_006524324.3 → XP_006524387.1 signal peptide, CUB and EGF-like domain-containing protein 3 isoform X2

See identical proteins and their annotated locations for XP_006524387.1

UniProtKB/TrEMBL

A0A3B2W867

Conserved Domains (5) summary

smart00179
Location:334 → 363

EGF_CA; Calcium-binding EGF-like domain

cd00041
Location:766 → 877

CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

pfam07699
Location:658 → 705

Ephrin_rec_like; Putative ephrin-receptor like

pfam12947
Location:33 → 68

EGF_3; EGF domain

pfam14670
Location:256 → 291

FXa_inhibition; Coagulation Factor Xa inhibitory site
XM_030249829.1 → XP_030105689.1 signal peptide, CUB and EGF-like domain-containing protein 3 isoform X3

UniProtKB/TrEMBL

A0A3B2W867

Related

ENSMUSP00000117490.3, ENSMUST00000132670.3

Conserved Domains (5) summary

smart00179
Location:318 → 347

EGF_CA; Calcium-binding EGF-like domain

cd00041
Location:750 → 861

CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

pfam07699
Location:642 → 689

Ephrin_rec_like; Putative ephrin-receptor like

pfam12947
Location:33 → 68

EGF_3; EGF domain

pfam14670
Location:240 → 275

FXa_inhibition; Coagulation Factor Xa inhibitory site