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

Gene ID: 361341, updated on 4-Jan-2025

Summary

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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, Jan 2025]
Expression
Biased expression in Adrenal (RPKM 60.0), Lung (RPKM 44.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Ccbe1 in Genome Data Viewer
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_086036.1Genomic Context describing neighboring genes Neighboring gene complexin 4 Neighboring gene lectin, mannose-binding, 1 Neighboring gene uncharacterized LOC108348805 Neighboring gene thioredoxin-like 4A, pseudogene 9

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans. Alders M, et al. Nat Genet, 2009 Dec. PMID 19935664
  2. CCBE1 enhances lymphangiogenesis via A disintegrin and metalloprotease with thrombospondin motifs-3-mediated vascular endothelial growth factor-C activation. Jeltsch M, et al. Circulation, 2014 May 13. PMID 24552833
  3. CCBE1 is essential for mammalian lymphatic vascular development and enhances the lymphangiogenic effect of vascular endothelial growth factor-C in vivo. Bos FL, et al. Circ Res, 2011 Aug 19. PMID 21778431
  4. Lymphatic function is required prenatally for lung inflation at birth. Jakus Z, et al. J Exp Med, 2014 May 5. PMID 24733830, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

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

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Preferred Names
collagen and calcium-binding EGF domain-containing protein 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)

  1. 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

  1. NC_086036.1 Reference GRCr8

    Range
    61849821..62093876 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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
Nucleotide Protein Strain
Heading Accession and Version

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