Efemp2 EGF containing fibulin extracellular matrix protein 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Efemp2provided by RGD
Official Full Name: EGF containing fibulin extracellular matrix protein 2provided by RGD
Primary source: RGD:1359496
See related: EnsemblRapid:ENSRNOG00000020587 AllianceGenome:RGD:1359496
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
Summary: Predicted to enable heparin binding activity and protein homodimerization activity. Predicted to be involved in several processes, including negative regulation of vascular associated smooth muscle cell proliferation; positive regulation of aortic smooth muscle cell differentiation; and vasculature development. Predicted to act upstream of or within artery development and elastic fiber assembly. Predicted to be located in basement membrane; elastic fiber; and microfibril. Biomarker of osteoarthritis. Human ortholog(s) of this gene implicated in aortic aneurysm; arterial tortuosity syndrome; autosomal recessive cutis laxa type IB; endometrial cancer; and osteosarcoma. Orthologous to human EFEMP2 (EGF containing fibulin extracellular matrix protein 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Uterus (RPKM 97.1), Kidney (RPKM 81.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (212211057..212218739)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (202781692..202789784)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (220853695..220861420)

Chromosome 1 - NC_086019.1 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?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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 heparin binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in aorta development	ISO Inferred from Sequence Orthology more info
involved_in aorta smooth muscle tissue morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within artery development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within elastic fiber assembly	ISO Inferred from Sequence Orthology more info
involved_in elastic fiber assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of vascular associated smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of aortic smooth muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of smooth muscle cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
involved_in regulation of collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in vascular associated smooth muscle cell development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in elastic fiber	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in microfibril	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: EGF-containing fibulin-like extracellular matrix protein 2

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_001005907.2 → NP_001005907.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform 2 precursor

See identical proteins and their annotated locations for NP_001005907.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1.

Source sequence(s)

BC083804, CB811907, JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I5ZU12, Q5XI84

Related

ENSRNOP00000072344.3, ENSRNOT00000080520.3

Conserved Domains (3) summary

smart00179
Location:123 → 156

EGF_CA; Calcium-binding EGF-like domain

cl00057
Location:200 → 235

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 ...

cl21504
Location:242 → 269

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
NM_001277341.1 → NP_001264270.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_001264270.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

CB811907, FM037652, JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I5Y8F2

Conserved Domains (4) summary

smart00179
Location:123 → 163

EGF_CA; Calcium-binding EGF-like domain

pfam12662
Location:224 → 246

cEGF; Complement Clr-like EGF-like

cl00057
Location:198 → 238

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 ...

cl21504
Location:283 → 310

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
NM_001277346.1 → NP_001264275.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform 3 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons in the coding region compared to variant 1. It encodes isoform 3 which is shorter compared to isoform 1.

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A0G2KAI7, A0A8I5ZU12

Related

ENSRNOP00000075411.1, ENSRNOT00000078619.3

Conserved Domains (3) summary

smart00179
Location:54 → 87

EGF_CA; Calcium-binding EGF-like domain

cl00057
Location:131 → 166

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 ...

cl21504
Location:173 → 200

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

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_086019.1 Reference GRCr8

Range

212211057..212218739

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006230742.4 → XP_006230804.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform X1

UniProtKB/TrEMBL

A0A8I5Y8F2, A0A8I5ZYG7

Conserved Domains (3) summary

smart00179
Location:151 → 191

EGF_CA; Calcium-binding EGF-like domain

cl00057
Location:269 → 304

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 ...

cl21504
Location:311 → 338

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
XM_006230743.3 → XP_006230805.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform X3

See identical proteins and their annotated locations for XP_006230805.1

UniProtKB/TrEMBL

A0A8I5Y8F2

Related

ENSRNOP00000078095.2, ENSRNOT00000106689.2

Conserved Domains (4) summary

smart00179
Location:123 → 163

EGF_CA; Calcium-binding EGF-like domain

pfam12662
Location:224 → 246

cEGF; Complement Clr-like EGF-like

cl00057
Location:198 → 238

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 ...

cl21504
Location:283 → 310

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
XM_039108373.2 → XP_038964301.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform X2

UniProtKB/TrEMBL

A0A8I5Y8F2

Conserved Domains (4) summary

smart00179
Location:145 → 185

EGF_CA; Calcium-binding EGF-like domain

pfam12662
Location:246 → 268

cEGF; Complement Clr-like EGF-like

cl00057
Location:220 → 260

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 ...

cl21504
Location:305 → 332

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
XM_063286847.1 → XP_063142917.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform X4

UniProtKB/TrEMBL

A0A8I5ZU12
XM_006230744.5 → XP_006230806.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform X3

See identical proteins and their annotated locations for XP_006230806.1

UniProtKB/TrEMBL

A0A8I5Y8F2

Related

ENSRNOP00000040335.3, ENSRNOT00000052315.5

Conserved Domains (4) summary

smart00179
Location:123 → 163

EGF_CA; Calcium-binding EGF-like domain

pfam12662
Location:224 → 246

cEGF; Complement Clr-like EGF-like

cl00057
Location:198 → 238

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 ...

cl21504
Location:283 → 310

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
XM_063286848.1 → XP_063142918.1 EGF-containing fibulin-like extracellular matrix protein 2 isoform X5