Scube2 signal peptide, CUB domain and EGF like domain containing 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scube2provided by RGD
Official Full Name: signal peptide, CUB domain and EGF like domain containing 2provided by RGD
Primary source: RGD:1563998
See related: EnsemblRapid:ENSRNOG00000013123 AllianceGenome:RGD:1563998
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1563998; Scube2-ps1
Summary: Predicted to enable hedgehog family protein binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within several processes, including positive regulation of chondrocyte proliferation; positive regulation of osteoblast differentiation; and positive regulation of smoothened signaling pathway. Predicted to be active in cell surface and extracellular space. Orthologous to human SCUBE2 (signal peptide, CUB domain and EGF like domain containing 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 139.9), Muscle (RPKM 21.6) and 3 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 1q33

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (173264862..173341323, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (163831876..163899925, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (174428056..174495356, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Matrix metalloproteinase-9 regulates the blood brain barrier via the hedgehog pathway in a rat model of traumatic brain injury.
Title: Matrix metalloproteinase-9 regulates the blood brain barrier via the hedgehog pathway in a rat model of traumatic brain injury.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables hedgehog family protein binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chondrocyte differentiation involved in endochondral bone morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of chondrocyte proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of ossification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
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
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

Preferred Names: signal peptide, CUB and EGF-like domain-containing protein 2

Names: signal peptide, CUB domain, EGF-like 2, pseudogene 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

mRNA and Protein(s)

NM_001427604.1 → NP_001414533.1 signal peptide, CUB and EGF-like domain-containing protein 2 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

D4AC02

Related

ENSRNOP00000045001.4, ENSRNOT00000052377.6

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

173264862..173341323 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063271300.1 → XP_063127370.1 signal peptide, CUB and EGF-like domain-containing protein 2 isoform X4
XM_006230005.5 → XP_006230067.1 signal peptide, CUB and EGF-like domain-containing protein 2 isoform X1

See identical proteins and their annotated locations for XP_006230067.1

Related

ENSRNOP00000069415.3, ENSRNOT00000086349.3

Conserved Domains (4) summary

cd00041
Location:741 → 852

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

pfam07699
Location:689 → 736

GCC2_GCC3; GCC2 and GCC3

pfam14670
Location:368 → 403

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:273 → 322

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 ...
XM_006230006.5 → XP_006230068.1 signal peptide, CUB and EGF-like domain-containing protein 2 isoform X3

See identical proteins and their annotated locations for XP_006230068.1

UniProtKB/TrEMBL

A0A0G2JVB2

Conserved Domains (5) summary

cd00041
Location:628 → 739

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

pfam07699
Location:576 → 623

GCC2_GCC3; GCC2 and GCC3

pfam12947
Location:51 → 86

EGF_3; EGF domain

pfam14670
Location:409 → 444

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:314 → 363

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 ...
XM_039094567.2 → XP_038950495.1 signal peptide, CUB and EGF-like domain-containing protein 2 isoform X2

Conserved Domains (5) summary

cd00041
Location:782 → 839

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

pfam07699
Location:730 → 777

Ephrin_rec_like; Putative ephrin-receptor like

pfam12947
Location:51 → 86

EGF_3; EGF domain

pfam14670
Location:409 → 444

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:314 → 363

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 ...