Agrn agrin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Agrnprovided by RGD
Official Full Name: agrinprovided by RGD
Primary source: RGD:2067
See related: EnsemblRapid:ENSRNOG00000020205 AllianceGenome:RGD:2067
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: AGR
Summary: Enables calcium ion binding activity; cytokine binding activity; and dystroglycan binding activity. Involved in several processes, including positive regulation of macromolecule metabolic process; regulation of plasma membrane bounded cell projection organization; and synapse organization. Acts upstream of or within receptor clustering. Located in axonal growth cone; basement membrane; and synapse. Is active in glutamatergic synapse. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 8. Orthologous to human AGRN (agrin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 245.6), Kidney (RPKM 170.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (172031528..172064429, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (166749306..166782212, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (173589910..173622813, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Agrin plays a major role in the coalescence of the aquaporin-4 clusters induced by gamma-1-containing laminin.
Title: Agrin plays a major role in the coalescence of the aquaporin-4 clusters induced by gamma-1-containing laminin.
Study in rat sepsis model demonstrates that agrin/MuSK pathway is associated with neuromuscular dysfunction and reexpression of gamma- and alpha7-nAChR caused by sepsis.
Title: Alleviating Sepsis-Induced Neuromuscular Dysfunction Linked With Acetylcholine Receptors by Agrin.
compared expression of agrin isoforms with the expression of AChE-T and ColQ in the developing spinal cord at the stages before and after the formation of NMJ basal lamina
Title: Acetylcholinesterase and agrin: different functions, similar expression patterns, multiple roles.
present the first crystal structure of an agrin-LRP4 complex which is essential for neuronal agrin-induced acetylcholine receptor (AChR) clustering
Title: Structural basis of agrin-LRP4-MuSK signaling.
agrin modulates neuropathic pain through NR1 phosphorylation in GABA neurons
Title: Agrin downregulation induced by nerve injury contributes to neuropathic pain.
a model wherein the z8 insert is a Ca(2+)-responsive allosteric element that is essential in forming an active conformation in neuronal a
Title: Asparagine of z8 insert is critical for the affinity, conformation, and acetylcholine receptor-clustering activity of neural agrin.
Agrin binds BMP2, BMP4 and TGFbeta1 with relatively high affinity.
Title: Agrin binds BMP2, BMP4 and TGFbeta1.
different regions within the agrin protein are responsible for synapse formation at the neuromuscular junction and for process formation in central nervous system neurons
Title: The process-inducing activity of transmembrane agrin requires follistatin-like domains.
The results suggest a physiological role for Tm-agrin in the maturation of hippocampal neurons involving positive regulation of dendritic filopodia and promotion of synaptogenesis, but also suggest a role for axonal agrin in synaptogenesis.
Title: Transmembrane agrin regulates dendritic filopodia and synapse formation in mature hippocampal neuron cultures.
transient post-ischemic hypothermia stabilizes brain vessels and reduces blood brain barrier disruption in part by preventing proteolytic degradation of regulatory basement membrane constituents, SPARC and agrin
Title: Post-ischemic hypothermia attenuates loss of the vascular basement membrane proteins, agrin and SPARC, and the blood-brain barrier disruption after global cerebral ischemia.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH94447 (e-PCR)
- UniSTS:119695

RH127796 (e-PCR)
- UniSTS:211106

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATPase inhibitor activity	ISO Inferred from Sequence Orthology more info
enables BMP binding	IPI Inferred from Physical Interaction more info	PubMed
enables acetylcholine receptor regulator activity	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables chondroitin sulfate binding	ISO Inferred from Sequence Orthology more info
enables chondroitin sulfate binding	ISS Inferred from Sequence or Structural Similarity more info
enables dystroglycan binding	IDA Inferred from Direct Assay more info	PubMed
enables heparan sulfate proteoglycan binding	ISO Inferred from Sequence Orthology more info
enables heparan sulfate proteoglycan binding	ISS Inferred from Sequence or Structural Similarity more info
enables laminin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables receptor ligand activity	ISO Inferred from Sequence Orthology more info
enables sialic acid binding	ISS Inferred from Sequence or Structural Similarity more info
enables transforming growth factor beta binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane transporter binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chemical synaptic transmission	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in enzyme-linked receptor protein signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of motor neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of P-type sodium:potassium-exchanging transporter activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of sodium ion export across plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular junction development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuromuscular junction development	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular junction development	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within plasma membrane organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of GTPase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of Rac protein signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of filopodium assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of motor neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein geranylgeranylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein tyrosine kinase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of skeletal muscle acetylcholine-gated channel clustering	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic assembly at neuromuscular junction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic assembly at neuromuscular junction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein transport	ISO Inferred from Sequence Orthology more info
involved_in receptor clustering	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within receptor clustering	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor clustering	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within receptor clustering	ISO Inferred from Sequence Orthology more info
involved_in receptor clustering	ISO Inferred from Sequence Orthology more info
involved_in receptor clustering	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of axon guidance	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cardiac muscle cell membrane potential	ISO Inferred from Sequence Orthology more info
involved_in regulation of cardiac muscle contraction	ISO Inferred from Sequence Orthology more info
involved_in regulation of microtubule cytoskeleton organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of synaptic activity	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic assembly at neuromuscular junction	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle acetylcholine-gated channel clustering	IDA Inferred from Direct Assay more info	PubMed
involved_in skeletal muscle acetylcholine-gated channel clustering	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axonal growth cone	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in basement membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in collagen-containing extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info
located_in synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	ISO Inferred from Sequence Orthology more info
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: agrin

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_001429555.1 → NP_001416484.1 agrin isoform 1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6IUW3, F1LPF2
NM_175754.3 → NP_786930.2 agrin isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6IUW3

Related

ENSRNOP00000108828.1, ENSRNOT00000154534.1

Conserved Domains (7) summary

smart00280
Location:384 → 429

KAZAL; Kazal type serine protease inhibitors

smart00200
Location:1023 → 1147

SEA; Domain found in sea urchin sperm protein, enterokinase, agrin

cd00054
Location:1716 → 1748

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 ...

cd00104
Location:316 → 356

KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...

pfam00053
Location:688 → 730

Laminin_EGF; Laminin EGF domain

pfam00054
Location:1291 → 1422

Laminin_G_1; Laminin G domain

cl00097
Location:244 → 284

KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves 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_086023.1 Reference GRCr8

Range

172031528..172064429 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287202.1 → XP_063143272.1 agrin isoform X7

UniProtKB/TrEMBL

A6IUW3
XM_017593169.3 → XP_017448658.1 agrin isoform X4

UniProtKB/Swiss-Prot

P25304, Q63034
XM_006239542.5 → XP_006239604.1 agrin isoform X6

Related

ENSRNOP00000103040.1, ENSRNOT00000126412.1

Conserved Domains (8) summary

smart00280
Location:491 → 536

KAZAL; Kazal type serine protease inhibitors

smart00200
Location:1130 → 1254

SEA; Domain found in sea urchin sperm protein, enterokinase, agrin

cd00054
Location:1819 → 1851

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 ...

cd00104
Location:423 → 463

KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...

pfam00050
Location:351 → 391

Kazal_1; Kazal-type serine protease inhibitor domain

pfam00053
Location:795 → 837

Laminin_EGF; Laminin EGF domain

pfam00054
Location:1398 → 1529

Laminin_G_1; Laminin G domain

pfam03146
Location:46 → 148

NtA; Agrin NtA domain
XM_017593167.3 → XP_017448656.1 agrin isoform X2

UniProtKB/Swiss-Prot

P25304, Q63034
XM_006239541.5 → XP_006239603.1 agrin isoform X5

UniProtKB/TrEMBL

A6IUW3, D4A2F1

Related

ENSRNOP00000040828.4, ENSRNOT00000047854.5

Conserved Domains (8) summary

smart00280
Location:491 → 536

KAZAL; Kazal type serine protease inhibitors

smart00200
Location:1130 → 1254

SEA; Domain found in sea urchin sperm protein, enterokinase, agrin

cd00054
Location:1823 → 1855

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 ...

cd00104
Location:423 → 463

KAZAL_FS; Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the ...

pfam00050
Location:351 → 391

Kazal_1; Kazal-type serine protease inhibitor domain

pfam00053
Location:795 → 837

Laminin_EGF; Laminin EGF domain

pfam00054
Location:1398 → 1529

Laminin_G_1; Laminin G domain

pfam03146
Location:46 → 148

NtA; Agrin NtA domain
XM_017593168.3 → XP_017448657.1 agrin isoform X3

UniProtKB/Swiss-Prot

P25304, Q63034
XM_017593166.3 → XP_017448655.1 agrin isoform X1

UniProtKB/Swiss-Prot

P25304, Q63034

Related

ENSRNOP00000050623.6, ENSRNOT00000045678.7
XM_017593170.3 → XP_017448659.1 agrin isoform X8

UniProtKB/Swiss-Prot

P25304, Q63034

Related

ENSRNOP00000105718.1, ENSRNOT00000150948.1
XM_039109320.2 → XP_038965248.1 agrin isoform X9

Conserved Domains (6) summary

smart00280
Location:37 → 82

KAZAL; Kazal type serine protease inhibitors

smart00200
Location:611 → 735

SEA; Domain found in sea urchin sperm protein, enterokinase, agrin

cd00054
Location:1304 → 1336

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 ...

pfam00008
Location:812 → 843

EGF; EGF-like domain

pfam00053
Location:276 → 318

Laminin_EGF; Laminin EGF domain

pfam00054
Location:879 → 1010

Laminin_G_1; Laminin G domain