Col2a1 collagen type II alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col2a1provided by RGD
Official Full Name: collagen type II alpha 1 chainprovided by RGD
Primary source: RGD:2375
See related: Ensembl:ENSRNOG00000058560 AllianceGenome:RGD:2375
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: CG2A1A; COLLII
Summary: Predicted to enable several functions, including MHC class II protein binding activity; identical protein binding activity; and platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent. Involved in several processes, including cartilage development; cellular response to hormone stimulus; and cellular response to mechanical stimulus. Located in collagen-containing extracellular matrix and cytoplasm. Used to study degenerative disc disease; hypothyroidism; and osteoarthritis. Biomarker of degenerative disc disease and osteonecrosis. Human ortholog(s) of this gene implicated in Stickler syndrome (multiple); bone disease (multiple); cleft palate; eye disease (multiple); and multiple epiphyseal dysplasia with myopia and deafness. Orthologous to human COL2A1 (collagen type II alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 27.9), Lung (RPKM 21.2) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q36

Exon count:: 54

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (130977561..131006627, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (129098489..129127560, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (139454945..139484403, complement)

Chromosome 7 - NC_086025.1 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?

Gene expression of type II collagen is regulated by direct interaction with Kruppel-like factor 4 and AT-rich interactive domain 5B.
Title: Gene expression of type II collagen is regulated by direct interaction with Kruppel-like factor 4 and AT-rich interactive domain 5B.
Induction of OA caused downregulation of Col2a1. Expression of Col2a1 showed upregulation in therapeutic group with separate administration chondroitin sulfate or a probiotic diet and the cumulative effects in case of co-administration.
Title: The influence of probiotic diet and chondroitin sulfate administration on Ptgs2, Tgfb1 and Col2a1 expression in rat knee cartilage during monoiodoacetate-induced osteoarthritis.
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.
These findings suggest a novel mechanism of action of SOX5/6; namely, the SOX9/5/6 combination enhances Col2a1 transcription through a novel enhancer in intron 6 together with the enhancer in intron 1.
Title: A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-dependent Enhancer in Intron 6.
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.
Local adipose tissue stem cells protected the bronchial stump after pneumonectomy and induced local changes in Col2a1 gene expression.
Title: Stem cells protect the bronchial stump in rat, increasing Sox6, Col2a1, and Agc1 expression.
Rat collagen II citrullination decreased the adhesion of human synovial fibroblasts and rat mesenchymal stem cells by decreasing the binding of integrins alpha10beta1 and alpha11beta1 (but not alpha1beta1 and alpha2beta1)to Arg-containing motifs. It decreased MSC survival.
Title: Citrullination of collagen II affects integrin-mediated cell adhesion in a receptor-specific manner.
Screening of the Col2a1 gene, and enhancer domain, for the sequence encoded regulation of its expression.
Title: A newly identified enhancer element responsible for type II collagen gene expression.
While urinary C-telopeptide of type II collagen was significantly increased during the experimental periods, serum type II procollagen-C-peptide was significantly decreased at the early phase.
Title: Skeletal unloading induces a full-thickness patellar cartilage defect with increase of urinary collagen II CTx degradation marker in growing rats.
immunohistochemical findings are consistent with the concept that the major source of serum c-telopeptide type Ii is the damaged articular cartilage in collagen-induced arthritis.
Title: Early elevation in circulating levels of C-telopeptides of type II collagen predicts structural damage in articular cartilage in the rodent model of collagen-induced arthritis.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH142189 (e-PCR)
- UniSTS:231439

UniSTS:464658 (e-PCR)
- UniSTS:464658

Col2a1 (e-PCR), detects polymorphism
- UniSTS:464658

Col2a1 (e-PCR), detects polymorphism
- UniSTS:508440

RH137074 (e-PCR)
- UniSTS:219162

PMC156609P2 (e-PCR)
- UniSTS:271414

RH94387 (e-PCR)
- UniSTS:119635

Col2a1 (e-PCR), detects polymorphism
- UniSTS:259692

COL2A1 (e-PCR)
- UniSTS:503994

RH128349 (e-PCR)
- UniSTS:211657

GDB:177260 (e-PCR)
- UniSTS:154850

COL2A1 (e-PCR)
- UniSTS:258280

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables MHC class II protein binding	IEA Inferred from Electronic Annotation more info
enables MHC class II protein binding	ISO Inferred from Sequence Orthology more info
enables extracellular matrix structural constituent	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor binding	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables proteoglycan binding	IEA Inferred from Electronic Annotation more info
enables proteoglycan binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in anterior head development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior head development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
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 cartilage development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cartilage development	ISO Inferred from Sequence Orthology more info
involved_in cartilage development involved in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cartilage development involved in endochondral bone morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to BMP stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to BMP stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to insulin-like growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to nicotine	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to parathyroid hormone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to peptide hormone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to tumor necrosis factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to vitamin E	IEP Inferred from Expression Pattern more info	PubMed
involved_in central nervous system development	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in chondrocyte differentiation	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in chondrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor 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 collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in embryonic skeletal joint morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic skeletal joint morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endochondral ossification	ISO Inferred from Sequence Orthology more info
involved_in extrinsic apoptotic signaling pathway in absence of ligand	IEA Inferred from Electronic Annotation more info
acts_upstream_of extrinsic apoptotic signaling pathway in absence of ligand	ISO Inferred from Sequence Orthology more info
involved_in growth plate cartilage development	IEP Inferred from Expression Pattern more info	PubMed
involved_in heart morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear development	ISO Inferred from Sequence Orthology more info
involved_in inner ear morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in limb bud formation	IEA Inferred from Electronic Annotation more info
involved_in limb bud formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of extrinsic apoptotic signaling pathway in absence of ligand	ISO Inferred from Sequence Orthology more info
involved_in notochord development	IBA Inferred from Biological aspect of Ancestor more info
involved_in notochord development	IEA Inferred from Electronic Annotation more info
involved_in notochord development	ISO Inferred from Sequence Orthology more info
involved_in ossification	ISO Inferred from Sequence Orthology more info
involved_in otic vesicle development	IEA Inferred from Electronic Annotation more info
involved_in otic vesicle development	ISO Inferred from Sequence Orthology more info
involved_in proteoglycan metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within proteoglycan metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in response to X-ray	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to fibroblast growth factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in roof of mouth development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within roof of mouth development	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in tissue homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within tissue homeostasis	ISO Inferred from Sequence Orthology more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info
involved_in visual perception	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen trimer	ISO Inferred from Sequence Orthology more info
part_of collagen type II trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type II trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type II trimer	ISO Inferred from Sequence Orthology more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	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	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: collagen alpha-1(II) chain

Names: Procollagen II alpha 1; alpha-1 type II collagen; collagen type II (Col2A1) gene, enhancer region; collagen, type II, alpha 1; procollagen, type II, alpha 1

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.