Scube1 signal peptide, CUB domain and EGF like domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scube1provided by RGD
Official Full Name: signal peptide, CUB domain and EGF like domain containing 1provided by RGD
Primary source: RGD:1309015
See related: EnsemblRapid:ENSRNOG00000010617 AllianceGenome:RGD:1309015
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable identical protein binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within positive regulation of smoothened signaling pathway. Predicted to be located in external side of plasma membrane. Predicted to be active in cell surface and extracellular space. Orthologous to human SCUBE1 (signal peptide, CUB domain and EGF like domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Uterus (RPKM 34.5), Lung (RPKM 30.9) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q34

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (116639027..116760986, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (114759016..114880995, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (124501988..124620755, complement)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A pronounced rise in SCUBE-1 levels was determined with 6-hour acute mesenteric ischemia in rats.
Title: The value of signal peptide-CUB-EGF domain-containing protein 1 and oxidative stress parameters in the diagnosis of acute mesenteric ischemia.
Scube1 encodes a novel stromal molecule that is involved in prostate development and tumorigenesis.
Title: Transcriptional profiling of inductive mesenchyme to identify molecules involved in prostate development and disease.

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General gene information

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Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
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
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology 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
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 1

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

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_001134884.1 → NP_001128356.1 signal peptide, CUB and EGF-like domain-containing protein 1 precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A0A8I6AMT3, F1M987

Related

ENSRNOP00000017727.5, ENSRNOT00000017727.7

Conserved Domains (5) summary

cd00041
Location:828 → 939

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

pfam07699
Location:776 → 823

GCC2_GCC3; GCC2 and GCC3

pfam12947
Location:37 → 72

EGF_3; EGF domain

pfam14670
Location:275 → 310

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:348 → 384

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086025.1 Reference GRCr8

Range

116639027..116760986 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039079288.2 → XP_038935216.1 signal peptide, CUB and EGF-like domain-containing protein 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AMT3

Conserved Domains (4) summary

pfam07699
Location:776 → 823

Ephrin_rec_like; Putative ephrin-receptor like

pfam12947
Location:37 → 72

EGF_3; EGF domain

pfam14670
Location:275 → 310

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:348 → 384

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_039079290.2 → XP_038935218.1 signal peptide, CUB and EGF-like domain-containing protein 1 isoform X3

UniProtKB/TrEMBL

A0A8I6A5S5, A0A8I6AMT3

Related

ENSRNOP00000088785.1, ENSRNOT00000112140.2

Conserved Domains (5) summary

cd00041
Location:717 → 828

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

pfam07699
Location:665 → 712

Ephrin_rec_like; Putative ephrin-receptor like

pfam12947
Location:37 → 72

EGF_3; EGF domain

pfam14670
Location:164 → 199

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:237 → 273

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_006242092.5 → XP_006242154.1 signal peptide, CUB and EGF-like domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A8I6AMT3

Conserved Domains (5) summary

cd00041
Location:798 → 909

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

pfam07699
Location:746 → 793

GCC2_GCC3; GCC2 and GCC3

pfam12947
Location:37 → 72

EGF_3; EGF domain

pfam14670
Location:245 → 280

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:318 → 354

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_039079292.2 → XP_038935220.1 signal peptide, CUB and EGF-like domain-containing protein 1 isoform X4

Conserved Domains (3) summary

pfam12947
Location:37 → 72

EGF_3; EGF domain

pfam14670
Location:275 → 310

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl00057
Location:348 → 384

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 ...