Acan aggrecan [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Acanprovided by RGD
Official Full Name: aggrecanprovided by RGD
Primary source: RGD:68358
See related: Ensembl:ENSRNOG00000028992 AllianceGenome:RGD:68358
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: Agc; Agc1
Summary: Enables calcium ion binding activity. Involved in several processes, including chondroblast differentiation; response to acidic pH; and response to glucose. Located in several cellular components, including extracellular space; neuronal cell body; and perineuronal net. Used to study degenerative disc disease. Biomarker of congestive heart failure; degenerative disc disease; osteoarthritis; and status epilepticus. Human ortholog(s) of this gene implicated in spondyloepiphyseal dysplasia Kimberley type. Orthologous to human ACAN (aggrecan). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 13.1), Thymus (RPKM 12.1) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q31

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (142390951..142453779)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (132981582..133044416)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (140762758..140824441)

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?

Brachyury positively regulates extracellular matrix synthesis via directly promoting aggrecan transcription in nucleus pulposus.
Title: Brachyury positively regulates extracellular matrix synthesis via directly promoting aggrecan transcription in nucleus pulposus.
E1 and E2 enhancer activities in type II collagen and aggrecan are regulated through distinct epigenetic modifications by histone deacetylase 10 and sirtuin 6.
Title: Expression of type II collagen and aggrecan genes is regulated through distinct epigenetic modifications of their multiple enhancer elements.
The ERK1/2 and Smad2/3 signaling pathways regulate type II collagen and aggrecan expression in rat chondrocytes.
Title: Transforming growth factor-β1 induces type II collagen and aggrecan expression via activation of extracellular signal-regulated kinase 1/2 and Smad2/3 signaling pathways.
To elucidate the transcriptional mechanism that leads to abundant expression of aggrecan by chondrocytes, it screened for enhancer elements in 130 kb of the aggrecan gene, Agc1, using a reporter assay system that we previously developed.
Title: A candidate enhancer element responsible for high-level expression of the aggrecan gene in chondrocytes.
Local adipose tissue stem cells protected the bronchial stump after pneumonectomy and induced local changes in Agc1 gene expression.
Title: Stem cells protect the bronchial stump in rat, increasing Sox6, Col2a1, and Agc1 expression.
These results support a role for MafB as a regulator of chondrocyte gene expression and matrix formation via control of aggrecan, MMP3 and MMP13 expression, and indicate an important role for RA in the regulation of MafB
Title: Retinoic acid and the transcription factor MafB act together and differentially to regulate aggrecan and matrix metalloproteinase gene expression in neonatal chondrocytes.
Data suggest that expression of aggrecan and matrix metallopeptidase 13 in femur of female neonatal rats is altered by maternal vitamin A status and neonatal diet (i.e., supplementation with vitamin A and retinoic acid).
Title: Perinatal exposure to vitamin A differentially regulates chondrocyte growth and the expression of aggrecan and matrix metalloprotein genes in the femur of neonatal rats.
We suggest that the role of aggrecan is to maintain retinal ganglion cell dendritic structure in the inner plexiform layer and to provide adequate support and flexibility for the photoreceptor outer segments, which is necessary to maintain their function.
Title: Localization and developmental expression patterns of CSPG-cs56 (aggrecan) in normal and dystrophic retinas in two rat strains.
Substate stiffness regulates the gene expression of Col1alpha1, Col2alpha1, aggrecan, MMP-3, MMp-13, and ADAMTS-5 in rat annular (intervertebral disc) cells.
Title: Substrate stiffness regulates apoptosis and the mRNA expression of extracellular matrix regulatory genes in the rat annular cells.
Data show that an increase in collagen-II, aggrecan, and Sox-9 protein expression in NP and AF regions of the disc was detected in the exercised rats.
Title: The effect of running exercise on intervertebral disc extracellular matrix production in a rat model.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Agc1 (e-PCR), detects polymorphism
- UniSTS:259691

Acan (e-PCR), detects polymorphism
- UniSTS:547953

UniSTS:497303 (e-PCR)
- UniSTS:497303

Acan (e-PCR), detects polymorphism
- UniSTS:497303

PMC21264P1 (e-PCR)
- UniSTS:272024

L35593 (e-PCR)
- UniSTS:146611

ODOSTSI (e-PCR)
- UniSTS:146611

RH128365 (e-PCR)
- UniSTS:211673

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables hyaluronic acid binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cartilage condensation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cartilage condensation	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cellular response to growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in chondroblast differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in chondrocyte development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chondrocyte development	ISO Inferred from Sequence Orthology more info
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in glial cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in ossification	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of neuroblast proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteoglycan biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within proteoglycan biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in response to acidic pH	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to glucose	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to gravity	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in spinal cord development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in perineuronal net	IBA Inferred from Biological aspect of Ancestor more info
located_in perineuronal net	IDA Inferred from Direct Assay more info	PubMed
is_active_in perisynaptic extracellular matrix	ISO Inferred from Sequence Orthology more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: aggrecan core protein

Names: CSPCP; aggrecan 1; aggrecan, structural proteoglycan of cartilage; cartilage-specific proteoglycan core protein

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_022190.2 → NP_071526.2 aggrecan core protein precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

D4A7Y1

Related

ENSRNOP00000042691.5, ENSRNOT00000047848.5

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

142390951..142453779

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039101035.2 → XP_038956963.1 aggrecan core protein isoform X1

UniProtKB/TrEMBL

A6JC42, F1LQI4

Related

ENSRNOP00000044130.5

Conserved Domains (8) summary

cd00033
Location:2041 → 2097

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:1914 → 2037

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

PRK15319
Location:1196 → 1597

PRK15319; fibronectin-binding autotransporter adhesin ShdA

PLN02217
Location:1591 → 1753

PLN02217; probable pectinesterase/pectinesterase inhibitor

PHA03307
Location:687 → 998

PHA03307; transcriptional regulator ICP4; Provisional

cd03517
Location:153 → 247

Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. ...

cd03520
Location:254 → 349

Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan ...

cd05900
Location:33 → 155

Ig_Aggrecan; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan