Ccbe1 collagen and calcium binding EGF domains 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ccbe1provided by RGD
Full Name: collagen and calcium binding EGF domains 1provided by RGD
Primary source: RGD:1307670
See related: EnsemblRapid:ENSRNOG00000062986 AllianceGenome:RGD:1307670
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: RGD1307670
Summary: Predicted to enable collagen binding activity and protease binding activity. Predicted to be involved in several processes, including positive regulation of gene expression; positive regulation of lymphangiogenesis; and positive regulation of vascular endothelial growth factor signaling pathway. Predicted to act upstream of or within several processes, including lymphangiogenesis; positive regulation of endothelial cell migration; and respiratory system process. Predicted to be located in extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Hennekam syndrome. Orthologous to human CCBE1 (collagen and calcium binding EGF domains 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Adrenal (RPKM 60.0), Lung (RPKM 44.1) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 18q12.1

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (61849821..62093876, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (59579851..59823977, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (61758754..62013194, complement)

Chromosome 18 - NC_086036.1 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
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?

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

RH144242 (e-PCR)
- UniSTS:233487

D18Wox16 (e-PCR)
- UniSTS:118074

MHAa74a6.seq (e-PCR)
- UniSTS:125303

D18MGH2 (e-PCR)
- UniSTS:120221

AFMa341xb5 (e-PCR)
- UniSTS:13479

AI709546 (e-PCR)
- UniSTS:245983

D18Mit8 (e-PCR), detects polymorphism
- UniSTS:119536

AU048444 (e-PCR)
- UniSTS:144894

Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
acts_upstream_of endothelial cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymph vessel development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymphangiogenesis	ISO Inferred from Sequence Orthology more info
involved_in lymphangiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of lymphatic endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of lymphangiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein processing	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular endothelial growth factor production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular endothelial growth factor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within respiratory gaseous exchange by respiratory system	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within respiratory system process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in extracellular matrix	ISO Inferred from Sequence Orthology 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: collagen and calcium-binding EGF domain-containing protein 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_001432454.1 → NP_001419383.1 collagen and calcium-binding EGF domain-containing protein 1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000018

UniProtKB/TrEMBL

A0A8I6AR48, A6IXS6, A6IXS7

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_086036.1 Reference GRCr8

Range

61849821..62093876 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017601124.3 → XP_017456613.1 collagen and calcium-binding EGF domain-containing protein 1 isoform X1

Related

ENSRNOP00000094341.1, ENSRNOT00000116155.2

Conserved Domains (1) summary

smart00179
Location:135 → 176

EGF_CA; Calcium-binding EGF-like domain
XM_039097364.2 → XP_038953292.1 collagen and calcium-binding EGF domain-containing protein 1 isoform X2

Conserved Domains (1) summary

smart00179
Location:135 → 176

EGF_CA; Calcium-binding EGF-like domain