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Efemp1 EGF containing fibulin extracellular matrix protein 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 305604, updated on 10-Oct-2024

Summary

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Official Symbol
Efemp1provided by RGD
Official Full Name
EGF containing fibulin extracellular matrix protein 1provided by RGD
Primary source
RGD:1308528
See related
EnsemblRapid:ENSRNOG00000003553 AllianceGenome:RGD:1308528
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
Also known as
T16
Summary
Predicted to enable epidermal growth factor receptor binding activity and epidermal growth factor-activated receptor activity. Involved in positive regulation of cell population proliferation; regulation of cell projection organization; and regulation of glial cell migration. Located in basement membrane and cytoplasm. Human ortholog(s) of this gene implicated in Doyne honeycomb retinal dystrophy. Orthologous to human EFEMP1 (EGF containing fibulin extracellular matrix protein 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Lung (RPKM 368.4), Uterus (RPKM 317.1) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Efemp1 in Genome Data Viewer
Location:
14q22
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (106811769..106890961)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (102610813..102690027)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (113202382..113294993)

Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102550402 Neighboring gene uncharacterized LOC102550342 Neighboring gene microRNA 216a Neighboring gene microRNA 217 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene polyribonucleotide nucleotidyltransferase 1

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 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. Hypermethylation of EFEMP1 in the Hippocampus May Be Related to the Deficit in Spatial Memory of Rat Neonates Triggered by Repeated Administration of Propofol. Zhang N, et al. Biomed Res Int, 2020. PMID 33381589, Free PMC Article
  2. Fib3-3 as a Biomarker for Osteoarthritis in a Rat Model with Metabolic Dysregulation. de Visser HM, et al. Cartilage, 2019 Jul. PMID 29366335, Free PMC Article
  3. The glycoprotein fibulin-3 regulates morphology and motility of olfactory ensheathing cells in vitro. Vukovic J, et al. Glia, 2009 Mar. PMID 18803302
  4. Mechanism of action of Profilin-1 and Fibulin-3 in vascular remodeling in hypertensive rats. Chen JM, et al. Eur Rev Med Pharmacol Sci, 2019 Sep. PMID 31599437
  5. A genome-wide association study identifies a susceptibility locus for biliary atresia on 2p16.1 within the gene EFEMP1. Chen Y, et al. PLoS Genet, 2018 Aug. PMID 30102696, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hypermethylation of EFEMP1 in the Hippocampus May Be Related to the Deficit in Spatial Memory of Rat Neonates Triggered by Repeated Administration of Propofol.
    Title: Hypermethylation of EFEMP1 in the Hippocampus May Be Related to the Deficit in Spatial Memory of Rat Neonates Triggered by Repeated Administration of Propofol.
  2. Mechanism of action of Profilin-1 and Fibulin-3 in vascular remodeling in hypertensive rats.
    Title: Mechanism of action of Profilin-1 and Fibulin-3 in vascular remodeling in hypertensive rats.
  3. the study showed that in the rat groove model combined with high-fat diet-induced metabolic dysregulation an increased Fib3-3 concentration was observed systemically, which is associated with local joint degeneration. This suggests that systemic Fib3-3 concentrations can indicate the status of joint degeneration and function as a biomarker in osteoarthritis.
    Title: Fib3-3 as a Biomarker for Osteoarthritis in a Rat Model with Metabolic Dysregulation.
  4. Efemp1 transcripts had higher expression in cholangiocytes and portal fibroblasts as compared with other cell types in normal rat liver.
    Title: A genome-wide association study identifies a susceptibility locus for biliary atresia on 2p16.1 within the gene EFEMP1.
  5. indicated that fibulin3 may reduce the levels of MMP2 and 9 and oxidative stress in hypertensive vascular remodeling.
    Title: Fibulin-3 may improve vascular health through inhibition of MMP-2/9 and oxidative stress in spontaneously hypertensive rats.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

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 epidermal growth factor receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables epidermal growth factor receptor activity ISO
Inferred from Sequence Orthology
more info
  
enables epidermal growth factor receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables epidermal growth factor receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables epidermal growth factor receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables epidermal growth factor receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables growth factor activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in camera-type eye development IEA
Inferred from Electronic Annotation
more info
  
involved_in camera-type eye development ISO
Inferred from Sequence Orthology
more info
  
involved_in embryonic eye morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic eye morphogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in epidermal growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in epidermal growth factor receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in epidermal growth factor receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of chondrocyte differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of neuron projection development IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in peptidyl-tyrosine phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in peptidyl-tyrosine phosphorylation ISO
Inferred from Sequence Orthology
more info
  
involved_in peptidyl-tyrosine phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell projection organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell projection organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in post-embryonic eye morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in post-embryonic eye morphogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of glial cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in basement membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular matrix IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular matrix ISO
Inferred from Sequence Orthology
more info
  
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular space ISO
Inferred from Sequence Orthology
more info
  
located_in extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
EGF-containing fibulin-like extracellular matrix protein 1
Names
FIBL-3
epidermal growth factor-containing fibulin-like extracellular matrix protein 1
fibulin-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)

  1. NM_001012039.1 → NP_001012039.1  EGF-containing fibulin-like extracellular matrix protein 1 precursor

    See identical proteins and their annotated locations for NP_001012039.1

    Status: PROVISIONAL

    Source sequence(s)
    BC079455
    UniProtKB/Swiss-Prot
    O35568
    UniProtKB/TrEMBL
    D4A080, Q6AXN2
    Related
    ENSRNOP00000004764.6, ENSRNOT00000004764.9
    Conserved Domains (3) summary
    smart00179
    Location:214 → 244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173 → 206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:234 → 257
    cEGF; Complement Clr-like EGF-like

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_086032.1 Reference GRCr8

    Range
    106811769..106890961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008770457.4 → XP_008768679.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

    See identical proteins and their annotated locations for XP_008768679.1

    UniProtKB/Swiss-Prot
    O35568
    UniProtKB/TrEMBL
    D4A080, Q6AXN2
    Conserved Domains (3) summary
    smart00179
    Location:214 → 244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173 → 206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:234 → 257
    cEGF; Complement Clr-like EGF-like

  2. XM_063273283.1 → XP_063129353.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X2

  3. XM_008770456.4 → XP_008768678.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

    See identical proteins and their annotated locations for XP_008768678.1

    UniProtKB/Swiss-Prot
    O35568
    UniProtKB/TrEMBL
    D4A080, Q6AXN2
    Conserved Domains (3) summary
    smart00179
    Location:214 → 244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173 → 206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:234 → 257
    cEGF; Complement Clr-like EGF-like

  4. XM_039092117.2 → XP_038948045.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X2

    UniProtKB/Swiss-Prot
    O35568
    Related
    ENSRNOP00000104855.1, ENSRNOT00000157765.1
    Conserved Domains (4) summary
    smart00179
    Location:254 → 293
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173 → 206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:234 → 257
    cEGF; Complement Clr-like EGF-like
    cl00057
    Location:212 → 251
    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 ...

  5. XM_063273282.1 → XP_063129352.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

    UniProtKB/TrEMBL
    D4A080, Q6AXN2
    Related
    ENSRNOP00000111750.1, ENSRNOT00000142978.1

  6. XM_039092115.2 → XP_038948043.1  EGF-containing fibulin-like extracellular matrix protein 1 isoform X1

    UniProtKB/Swiss-Prot
    O35568
    UniProtKB/TrEMBL
    D4A080, Q6AXN2
    Conserved Domains (3) summary
    smart00179
    Location:214 → 244
    EGF_CA; Calcium-binding EGF-like domain
    pfam07645
    Location:173 → 206
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:234 → 257
    cEGF; Complement Clr-like EGF-like
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O35568.1 GenPept UniProtKB/Swiss-Prot:O35568

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