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

Summary

Official Symbol: Efemp1provided by RGD
Official Full Name: EGF containing fibulin extracellular matrix protein 1provided by RGD
Primary source: RGD:1308528
See related: Ensembl: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

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_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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
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?

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.
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.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH128749 (e-PCR)
- UniSTS:212057

AU049307 (e-PCR)
- UniSTS:145755

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 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 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)

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

ENSRNOP00000004764.5, ENSRNOT00000004764.8

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

NC_086032.1 Reference GRCr8

Range

106811769..106890961

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Related

ENSRNOP00000088163.1

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
XM_063273283.1 → XP_063129353.1 EGF-containing fibulin-like extracellular matrix protein 1 isoform X2
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
XM_039092117.2 → XP_038948045.1 EGF-containing fibulin-like extracellular matrix protein 1 isoform X2

UniProtKB/Swiss-Prot

O35568

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

UniProtKB/TrEMBL

D4A080, Q6AXN2
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