Col2a1 (collagen type II alpha 1 chain) - Rat Genome Database

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Gene: Col2a1 (collagen type II alpha 1 chain) Rattus norvegicus
Symbol: Col2a1
Name: collagen type II alpha 1 chain
RGD ID: 2375
Description: Predicted to enable several functions, including MHC class II protein binding activity; platelet-derived growth factor binding activity; and protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in several processes, including cartilage development; cellular response to hormone stimulus; and cellular response to mechanical stimulus. Located in collagen-containing extracellular matrix. 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); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH (R)-carnitine; (R)-pantothenic acid; (S)-magnoflorine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha-1 type II collagen; CG2A1A; collagen alpha-1(II) chain; collagen type II (Col2A1) gene, enhancer region; collagen, type II, alpha 1; COLLII; Procollagen II alpha 1; procollagen, type II, alpha 1
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr87130,977,561 - 131,006,627 (-)NCBIGRCr8
mRatBN7.27129,098,489 - 129,127,560 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7129,098,786 - 129,127,546 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,895,443 - 130,924,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07133,120,981 - 133,149,729 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07133,033,447 - 133,062,197 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07139,454,945 - 139,484,403 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7139,455,242 - 139,483,997 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,646,698 - 139,675,832 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,679,219 - 136,707,976 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17136,755,655 - 136,784,413 (-)NCBI
Celera7125,589,749 - 125,618,504 (-)NCBICelera
RH 3.4 Map71096.2RGD
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Disease Annotations     Click to see Annotation Detail View
achondrogenesis type II  (ISO,ISS)
Animal Disease Models  (ISO)
arthritis  (ISO)
asphyxiating thoracic dystrophy  (ISO)
bone resorption disease  (ISO)
Bronchial Fistula  (IDA)
cartilage disease  (ISO)
cataract  (ISO)
chondrosarcoma  (ISO)
chorioretinitis  (ISO)
cleft palate  (ISO)
Collagenopathy, Type 2 Alpha 1  (ISO)
congenital heart disease  (ISO)
connective tissue disease  (ISO)
Craniofacial Abnormalities  (ISO)
Czech Dysplasia, Metatarsal Type  (ISO)
degenerative disc disease  (IDA,IEP)
developmental dysplasia of the hip  (ISO)
Dwarfism  (ISO)
Edema  (ISO)
Erythema  (ISO)
Experimental Arthritis  (ISO)
eye disease  (ISO)
Femur Head Necrosis  (IEP,ISO)
Fetal Growth Retardation  (IEP)
fundus dystrophy  (ISO)
genetic disease  (ISO)
Hearing Loss  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
High Myopia  (ISO)
Hyaloideoretinal Degeneration of Wagner  (ISO)
Hyperplasia  (ISO)
hypochondrogenesis  (ISO)
hypothyroidism  (IDA)
Inflammation  (ISO)
intellectual disability  (ISO)
Kniest dysplasia  (ISO)
Legg-Calve-Perthes disease  (ISO)
Maffucci syndrome  (ISO)
Marfan syndrome  (ISO)
MASS Syndrome  (ISO)
melanoma  (ISO)
multiple epiphyseal dysplasia with myopia and deafness  (ISO)
myopia  (ISO)
orofacial cleft 1  (ISO)
osteoarthritis  (IDA,ISO)
Osteoarthritis with Mild Chondrodysplasia  (ISO)
osteochondrodysplasia  (ISO)
otospondylomegaepiphyseal dysplasia, autosomal dominant  (ISO)
otospondylomegaepiphyseal dysplasia, autosomal recessive  (ISO)
Prognathism  (ISO)
retinal detachment  (ISO)
retinitis pigmentosa  (ISO)
Rhegmatogenous Retinal Detachment, Autosomal Dominant  (ISO)
rheumatoid arthritis  (ISO)
sensorineural hearing loss  (ISO)
spondyloarthropathy  (ISO)
spondyloepimetaphyseal dysplasia  (ISS)
spondyloepimetaphyseal dysplasia, Strudwick type  (ISO)
spondyloepiphyseal dysplasia congenita  (ISO,ISS)
spondyloepiphyseal dysplasia Stanescu type  (ISO)
spondylometaphyseal dysplasia  (ISO)
spondylometaphyseal dysplasia corner fracture type  (ISO)
spondyloperipheral dysplasia  (ISO)
Stargardt disease  (ISO)
Stickler syndrome  (ISO)
Stickler syndrome 1  (ISO)
Stickler Syndrome, Type I, Nonsyndromic Ocular  (ISO)
synovitis  (ISO)
Torrance type platyspondylic dysplasia  (ISO)
Vitreoretinopathy with Phalangeal Epiphyseal Dysplasia  (ISO)
Weight Loss  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-Tetrandrine  (ISO)
(R)-carnitine  (EXP)
(R)-pantothenic acid  (EXP)
(S)-magnoflorine  (EXP)
(S)-nicotine  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-tribromophenol  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP,ISO)
2-butoxyethanol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-(indol-3-yl)lactic acid  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-pyridoxic acid  (EXP)
5-aza-2'-deoxycytidine  (EXP,ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (EXP)
acetaldehyde  (EXP,ISO)
acetic acid  (ISO)
aldehydo-D-glucosamine  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (ISO)
allantoin  (EXP)
amiloride  (EXP)
amino acid  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
astaxanthin  (EXP)
atrazine  (EXP)
Bavachinin  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
benzoic acid  (EXP)
berberine  (ISO)
beta-D-glucosamine  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
Butylparaben  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
carbamazepine  (ISO)
chlorogenic acid  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
citric acid  (EXP)
corticosterone  (EXP)
creatine  (EXP)
creatinine  (EXP)
crocin-1  (EXP)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (ISO)
dexamethasone  (EXP,ISO)
diethyl malate  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fenvalerate  (EXP)
ferrostatin-1  (EXP)
flavonoids  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
Fulvic acid  (ISO)
furan  (EXP)
gallic acid  (EXP)
Geniposide  (EXP)
genistein  (EXP)
graphite  (EXP)
hyaluronic acid  (ISO)
hydroquinone  (EXP)
immunological adjuvant  (EXP)
Indeno[1,2,3-cd]pyrene  (ISO)
indole-3-carboxylic acid  (EXP)
indometacin  (EXP,ISO)
irigenin  (ISO)
isoprenaline  (ISO)
kaempferol  (ISO)
keto-phenylpyruvic acid  (EXP)
kynurenic acid  (EXP)
L-ascorbic acid  (EXP,ISO)
L-cysteine  (EXP)
L-methionine  (EXP,ISO)
lead diacetate  (EXP,ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
lupeol  (EXP)
LY-2157299  (EXP)
mercaptopurine  (EXP)
methapyrilene  (ISO)
methimazole  (EXP)
methylparaben  (ISO)
mevalonic acid  (EXP)
mifepristone  (EXP,ISO)
Mofezolac (TN)  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
montelukast  (ISO)
morin  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-benzoylglycine  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
nicotine  (EXP)
O-acetyl-L-carnitine  (EXP)
O-palmitoylcarnitine  (EXP)
ochratoxin A  (EXP)
oxaliplatin  (EXP)
p-aminohippuric acid  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
Phellodendrine  (EXP)
phenylacetylglycine  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
propranolol  (ISO)
prostaglandin E2  (EXP,ISO)
prostaglandin F2alpha  (ISO)
Ptaquiloside  (ISO)
purine-6-thiol  (EXP)
quercetin  (ISO)
raloxifene  (EXP)
resveratrol  (ISO)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
simvastatin  (EXP)
sirolimus  (ISO)
sirtinol  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
spermidine  (EXP)
succinic acid  (EXP)
sulfamethoxazole  (EXP)
T-2 toxin  (ISO)
taurine  (EXP)
tetraphene  (ISO)
Theaflavin 3,3'-digallate  (EXP)
thioacetamide  (EXP)
topotecan  (EXP)
tributylstannane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
urethane  (ISO)
uridine  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (EXP,ISO)
xanthurenic acid  (EXP)
yohimbine  (EXP)
zileuton  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (IEA)
anterior head development  (IEA,ISO)
bone development  (ISO)
cartilage condensation  (IEA,ISO)
cartilage development  (IEP,ISO)
cartilage development involved in endochondral bone morphogenesis  (IEA,IEP,ISO)
cellular response to BMP stimulus  (IEA,ISO)
cellular response to insulin-like growth factor stimulus  (IEP)
cellular response to mechanical stimulus  (IEP)
cellular response to nicotine  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
cellular response to peptide hormone stimulus  (IEP)
cellular response to retinoic acid  (IEP)
cellular response to tumor necrosis factor  (IEP)
cellular response to vitamin E  (IEP)
central nervous system development  (IEA,ISO)
chondrocyte differentiation  (IEA,IEP,ISO)
collagen fibril organization  (IBA,IEA,ISO)
embryonic skeletal joint morphogenesis  (IEA,ISO)
endochondral ossification  (IEA,ISO)
extrinsic apoptotic signaling pathway in absence of ligand  (IEA,ISO)
growth plate cartilage development  (IEP)
heart morphogenesis  (IEA,ISO)
inner ear development  (ISO)
inner ear morphogenesis  (IEA,ISO)
limb bud formation  (IEA,ISO)
limb morphogenesis  (ISO)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (IEA,ISO)
notochord development  (IBA,IEA,ISO)
ossification  (ISO)
otic vesicle development  (IEA,ISO)
proteoglycan metabolic process  (IEA,ISO)
regulation of gene expression  (IEA,ISO)
response to fibroblast growth factor  (IEP)
response to mechanical stimulus  (IEP)
response to X-ray  (IEP)
roof of mouth development  (IEA,ISO)
sensory perception of sound  (IEA,ISO)
skeletal system development  (IBA,IEA,ISO)
skeletal system morphogenesis  (ISO)
tissue homeostasis  (IEA,ISO)
visual perception  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype

References - curated
# Reference Title Reference Citation
1. Stickler syndrome. A mutation in the nonhelical 3' end of type II procollagen gene. Ahmad NN, etal., Arch Ophthalmol. 1995 Nov;113(11):1454-7.
2. PCR assay confirms diagnosis in syndrome with variably expressed phenotype: mutation detection in Stickler syndrome. Ahmad NN, etal., J Med Genet. 1996 Aug;33(8):678-81.
3. Stop codon in the procollagen II gene (COL2A1) in a family with the Stickler syndrome (arthro-ophthalmopathy). Ahmad NN, etal., Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6624-7.
4. Age-related changes in gene expression patterns of matrix metalloproteinases and their collagenous substrates in mandibular condylar cartilage in rats. Bae JW, etal., J Anat. 2003 Aug;203(2):235-41.
5. Stickler-like syndrome due to a dominant negative mutation in the COL2A1 gene. Ballo R, etal., Am J Med Genet. 1998 Oct 30;80(1):6-11.
6. Vitamin E protects chondrocytes against hydrogen peroxide-induced oxidative stress in vitro. Bhatti FU, etal., Inflamm Res. 2013 Aug;62(8):781-9. doi: 10.1007/s00011-013-0635-y. Epub 2013 May 31.
7. Novel and recurrent COL2A1 mutations in Chinese patients with spondyloepiphyseal dysplasia. Cao LH, etal., Genet Mol Res. 2012 Dec 3;11(4):4130-7. doi: 10.4238/2012.September.27.1.
8. Precocious osteoarthritis in a family with recurrent COL2A1 mutation. Carlson KM, etal., J Rheumatol. 2006 Jun;33(6):1133-6.
9. Modulated expression of type X collagen in Meckel's cartilage with different developmental fates. Chung KS, etal., Dev Biol 1995 Aug;170(2):387-96.
10. Effect of nicotine on chondrogenic differentiation of rat bone marrow mesenchymal stem cells in alginate bead culture. Deng Y, etal., Biomed Mater Eng. 2012;22(1-3):81-7. doi: 10.3233/BME-2012-0692.
11. [Inhibition effect of osthole on proliferation of rat chondrocytes]. Ding DF, etal., Zhong Xi Yi Jie He Xue Bao. 2012 Dec;10(12):1413-8. doi: 10.3736/jcim20121213.
12. A missense mutation in the mouse Col2a1 gene causes spondyloepiphyseal dysplasia congenita, hearing loss, and retinoschisis. Donahue LR, etal., J Bone Miner Res 2003 Sep;18(9):1612-21.
13. Familial retinal detachment associated with COL2A1 exon 2 and FZD4 mutations. Edwards TL, etal., Clin Experiment Ophthalmol. 2012 Jul;40(5):476-83. doi: 10.1111/j.1442-9071.2012.02804.x. Epub 2012 Jun 19.
14. ENU-induced missense mutation in the C-propeptide coding region of Col2a1 creates a mouse model of platyspondylic lethal skeletal dysplasia, Torrance type. Furuichi T, etal., Mamm Genome. 2011 Jun;22(5-6):318-28. doi: 10.1007/s00335-011-9329-3. Epub 2011 May 3.
15. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. A frame shift mutation in a tissue-specific alternatively spliced exon of collagen 2A1 in Wagner's vitreoretinal degeneration. Gupta SK, etal., Am J Ophthalmol. 2002 Feb;133(2):203-10.
17. A rat tail temporary static compression model reproduces different stages of intervertebral disc degeneration with decreased notochordal cell phenotype. Hirata H, etal., J Orthop Res. 2014 Mar;32(3):455-63. doi: 10.1002/jor.22533. Epub 2013 Nov 28.
18. Stickler syndrome caused by COL2A1 mutations: genotype-phenotype correlation in a series of 100 patients. Hoornaert KP, etal., Eur J Hum Genet. 2010 Aug;18(8):872-80. doi: 10.1038/ejhg.2010.23. Epub 2010 Feb 24.
19. [Preventive and therapeutic effects of Yiqi Huayu Recipe on degeneration of articular cartilage in rats with osteoarthritis]. Hou W, etal., Zhong Xi Yi Jie He Xue Bao. 2009 Feb;7(2):163-8.
20. The chondrogenic transcription factor Sox9 is a target of signaling by the parathyroid hormone-related peptide in the growth plate of endochondral bones. Huang W, etal., Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):160-5.
21. Host genetic and epigenetic factors in toxoplasmosis. Jamieson SE, etal., Mem Inst Oswaldo Cruz. 2009 Mar;104(2):162-9.
22. Genetic and epigenetic factors at COL2A1 and ABCA4 influence clinical outcome in congenital toxoplasmosis. Jamieson SE, etal., PLoS One. 2008 Jun 4;3(6):e2285. doi: 10.1371/journal.pone.0002285.
23. Mechanism of Yiqi Huayu Bushen Recipe in treating cervical syndrome with kidney deficiency in rats Jiang JC, etal., Zhong Xi Yi Jie He Xue Bao. 2008 Dec;6(12):1280-5. doi: 10.3736/jcim200812114.
24. A mouse model for Stickler's syndrome: ocular phenotype of mice carrying a targeted heterozygous inactivation of type II (pro)collagen gene (Col2a1). Kaarniranta K, etal., Exp Eye Res. 2006 Aug;83(2):297-303. Epub 2006 Mar 20.
25. New insights into the pathogenesis of glucocorticoid-induced avascular necrosis: microarray analysis of gene expression in a rat model. Kerachian MA, etal., Arthritis Res Ther. 2010;12(3):R124. doi: 10.1186/ar3062. Epub 2010 Jun 25.
26. Structure of the promoter of the rat type II procollagen gene. Kohno K, etal., J Biol Chem 1985 Apr 10;260(7):4441-7.
27. Mutation in type II procollagen (COL2A1) that substitutes aspartate for glycine alpha 1-67 and that causes cataracts and retinal detachment: evidence for molecular heterogeneity in the Wagner syndrome and the Stickler syndrome (arthro-ophthalmopathy) Korkko J, etal., Am J Hum Genet. 1993 Jul;53(1):55-61.
28. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
29. p38 MAPK mediated in compressive stress-induced chondrogenesis of rat bone marrow MSCs in 3D alginate scaffolds. Li J, etal., J Cell Physiol. 2009 Dec;221(3):609-17. doi: 10.1002/jcp.21890.
30. Endoplasmic reticulum stress-unfolding protein response-apoptosis cascade causes chondrodysplasia in a col2a1 p.Gly1170Ser mutated mouse model. Liang G, etal., PLoS One. 2014 Jan 27;9(1):e86894. doi: 10.1371/journal.pone.0086894. eCollection 2014.
31. Prolonged upright posture induces degenerative changes in intervertebral discs of rat cervical spine. Liang QQ, etal., Spine (Phila Pa 1976). 2011 Jan 1;36(1):E14-9. doi: 10.1097/BRS.0b013e3181d2dec2.
32. Effects of intermittent versus continuous parathyroid hormone administration on condylar chondrocyte proliferation and differentiation. Liu Q, etal., Biochem Biophys Res Commun. 2012 Jul 20;424(1):182-8. doi: 10.1016/j.bbrc.2012.06.106. Epub 2012 Jun 27.
33. Stem cells protect the bronchial stump in rat, increasing sox6, col2a1, and agc1 expression. Llontop P, etal., Lung. 2014 Jun;192(3):441-8. doi: 10.1007/s00408-014-9569-6. Epub 2014 Mar 20.
34. Association of a p.Pro786Leu variant in COL2A1 with mild spondyloepiphyseal dysplasia congenita in a three-generation family. Mark PR, etal., Am J Med Genet A. 2011 Jan;155A(1):174-9. doi: 10.1002/ajmg.a.33762.
35. Endochondral bone formation in toothless (osteopetrotic) rats: failures of chondrocyte patterning and type X collagen expression. Marks SC Jr, etal., Int J Dev Biol 2000 Apr;44(3):309-16.
36. Czech dysplasia occurring in a Japanese family. Matsui Y, etal., Am J Med Genet A. 2009 Oct;149A(10):2285-9. doi: 10.1002/ajmg.a.33010.
37. COL1A1 and COL2A1 genes and myopia susceptibility: evidence of association and suggestive linkage to the COL2A1 locus. Metlapally R, etal., Invest Ophthalmol Vis Sci. 2009 Sep;50(9):4080-6. doi: 10.1167/iovs.08-3346. Epub 2009 Apr 22.
38. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
39. The transcription factor deltaEF1 is inversely expressed with type II collagen mRNA and can repress Col2a1 promoter activity in transfected chondrocytes. Murray D, etal., J Biol Chem 2000 Feb 4;275(5):3610-8.
40. Candidate gene and locus analysis of myopia. Mutti DO, etal., Mol Vis. 2007 Jun 28;13:1012-9.
41. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
42. Genetic variants in COL2A1, COL11A2, and IRF6 contribute risk to nonsyndromic cleft palate. Nikopensius T, etal., Birth Defects Res A Clin Mol Teratol. 2010 Sep;88(9):748-56. doi: 10.1002/bdra.20700.
43. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
44. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
45. Mechanical stimulation alters tissue differentiation and molecular expression during bone healing. Palomares KT, etal., J Orthop Res. 2009 Sep;27(9):1123-32. doi: 10.1002/jor.20863.
46. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
47. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
48. GOA pipeline RGD automated data pipeline
49. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
50. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
51. A novel mutation of COL2A1 resulting in dominantly inherited rhegmatogenous retinal detachment. Richards AJ, etal., Invest Ophthalmol Vis Sci. 2005 Feb;46(2):663-8.
52. Egr-1 inhibits the expression of extracellular matrix genes in chondrocytes by TNFalpha-induced MEK/ERK signalling. Rockel JS, etal., Arthritis Res Ther. 2009;11(1):R8. doi: 10.1186/ar2595. Epub 2009 Jan 14.
53. Development dependent collagen gene expression in the rat cranial base growth plate. Romer P, etal., Ann Anat. 2010 Aug 20;192(4):205-9. doi: 10.1016/j.aanat.2010.05.006. Epub 2010 Jun 11.
54. Localization and thyroid hormone influenced expression of collagen II in ovarian tissue. Saha S, etal., Cell Physiol Biochem. 2007;19(1-4):67-76.
55. A human COL2A1 gene with an Arg519Cys mutation causes osteochondrodysplasia in transgenic mice. Sahlman J, etal., Arthritis Rheum. 2004 Oct;50(10):3153-60.
56. The heterozygous disproportionate micromelia (dmm) mouse: morphological changes in fetal cartilage precede postnatal dwarfism and compared with lethal homozygotes can explain the mild phenotype. Seegmiller RE, etal., J Histochem Cytochem. 2008 Nov;56(11):1003-11. doi: 10.1369/jhc.2008.951673. Epub 2008 Aug 4.
57. Effect of In-Vitro Passaging on the Stem Cell-related Properties of Tendon-Derived Stem Cells (TDSCs) - Implication in Tissue Engineering. Tan Q, etal., Stem Cells Dev. 2011 Jun 1.
58. Caffeine-induced fetal rat over-exposure to maternal glucocorticoid and histone methylation of liver IGF-1 might cause skeletal growth retardation. Tan Y, etal., Toxicol Lett. 2012 Nov 15;214(3):279-87. doi: 10.1016/j.toxlet.2012.09.007. Epub 2012 Sep 17.
59. Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma. Tarpey PS, etal., Nat Genet. 2013 Aug;45(8):923-6. doi: 10.1038/ng.2668. Epub 2013 Jun 16.
60. Fibroblast growth factor 10 regulates Meckel's cartilage formation during early mandibular morphogenesis in rats. Terao F, etal., Dev Biol. 2011 Feb 15;350(2):337-47. doi: 10.1016/j.ydbio.2010.11.029. Epub 2010 Dec 11.
61. Mutation in collagen II alpha 1 isoforms delineates Stickler and Wagner syndrome phenotypes. Tran-Viet KN, etal., Mol Vis. 2013 Apr 5;19:759-66. Print 2013.
62. Czech dysplasia: report of a large family and further delineation of the phenotype. Tzschach A, etal., Am J Med Genet A. 2008 Jul 15;146A(14):1859-64. doi: 10.1002/ajmg.a.32389.
63. Occurrence of deletion of a COL2A1 allele as the mutation in Stickler syndrome shows that a collagen type II dosage effect underlies this syndrome. Van Der Hout AH, etal., Hum Mutat. 2002 Sep;20(3):236.
64. Posterior chorioretinal atrophy and vitreous phenotype in a family with Stickler syndrome from a mutation in the COL2A1 gene. Vu CD, etal., Ophthalmology. 2003 Jan;110(1):70-7.
65. All-trans-retinoid acid (ATRA) may have inhibited chondrogenesis of primary hind limb bud mesenchymal cells by downregulating Pitx1 expression. Wang YG, etal., Toxicol Lett. 2014 Jan 13;224(2):282-9. doi: 10.1016/j.toxlet.2013.06.220. Epub 2013 Jun 27.
66. A-2-->G transition at the 3' acceptor splice site of IVS17 characterizes the COL2A1 gene mutation in the original Stickler syndrome kindred. Williams CJ, etal., Am J Med Genet. 1996 Jun 14;63(3):461-7.
67. Autosomal dominant spondylarthropathy due to a type II procollagen gene (COL2A1) point mutation. Winterpacht A, etal., Hum Mutat. 1994;4(4):257-62.
68. Collagen mRNA expression during tissue development: the temporospacial order coordinates bone morphogenesis with collagen fiber formation. Wurtz T, etal., Matrix Biol 1998 Oct;17(5):349-60.
69. Analysis of the association of COL2A1 and IGF-1 with mandibular prognathism in a Chinese population. Xue F, etal., Orthod Craniofac Res. 2014 Aug;17(3):144-9. doi: 10.1111/ocr.12038. Epub 2014 Jan 5.
70. Clinical evaluation and COL2A1 gene analysis in 21 Brazilian families with Stickler syndrome: identification of novel mutations, further genotype/phenotype correlation, and its implications for the diagnosis. Zechi-Ceide RM, etal., Eur J Med Genet. 2008 May-Jun;51(3):183-96. doi: 10.1016/j.ejmg.2007.12.008. Epub 2008 Jan 9.
71. Growth plate zonal microarray analysis shows upregulation of extracellular matrix genes and downregulation of metalloproteinases and cathepsins following irradiation. Zhang M, etal., Calcif Tissue Int. 2007 Jul;81(1):26-38. Epub 2007 Jun 5.
72. IGF-1 regulation of type II collagen and MMP-13 expression in rat endplate chondrocytes via distinct signaling pathways. Zhang M, etal., Osteoarthritis Cartilage. 2009 Jan;17(1):100-6. doi: 10.1016/j.joca.2008.05.007. Epub 2008 Jul 1.
Additional References at PubMed
PMID:1429602   PMID:1879364   PMID:3070812   PMID:6094525   PMID:7276808   PMID:7590256   PMID:8046350   PMID:8192242   PMID:8626777   PMID:8660302   PMID:8900172   PMID:8989518  
PMID:9022054   PMID:9061443   PMID:9119111   PMID:9165353   PMID:9299161   PMID:9354468   PMID:9449075   PMID:9832566   PMID:9880238   PMID:9915573   PMID:10100048   PMID:10486316  
PMID:11171689   PMID:11237662   PMID:11254354   PMID:11273670   PMID:11680679   PMID:12799063   PMID:14614991   PMID:15324928   PMID:16079159   PMID:16752401   PMID:16947421   PMID:17530714  
PMID:17683922   PMID:18304733   PMID:18849019   PMID:19000792   PMID:19441084   PMID:19537875   PMID:20404928   PMID:20501701   PMID:20603131   PMID:20812917   PMID:20875682   PMID:20940257  
PMID:21055467   PMID:21624478   PMID:22206015   PMID:22206666   PMID:22248926   PMID:23019346   PMID:23658023   PMID:23900597   PMID:24191021   PMID:24823363   PMID:26165845   PMID:26234751  
PMID:27068509   PMID:27559042   PMID:27881681   PMID:29030641   PMID:30938133   PMID:30981839   PMID:33383116  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr87130,977,561 - 131,006,627 (-)NCBIGRCr8
mRatBN7.27129,098,489 - 129,127,560 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7129,098,786 - 129,127,546 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,895,443 - 130,924,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07133,120,981 - 133,149,729 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07133,033,447 - 133,062,197 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07139,454,945 - 139,484,403 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7139,455,242 - 139,483,997 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,646,698 - 139,675,832 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,679,219 - 136,707,976 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17136,755,655 - 136,784,413 (-)NCBI
Celera7125,589,749 - 125,618,504 (-)NCBICelera
RH 3.4 Map71096.2RGD
Cytogenetic Map7q36NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh381247,972,967 - 48,006,212 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1247,972,967 - 48,004,554 (-)EnsemblGRCh38hg38GRCh38
GRCh371248,366,750 - 48,398,259 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361246,653,015 - 46,684,552 (-)NCBINCBI36Build 36hg18NCBI36
Build 341246,653,017 - 46,684,528NCBI
Celera1247,164,396 - 47,195,933 (-)NCBICelera
Cytogenetic Map12q13.11NCBI
HuRef1245,398,588 - 45,430,128 (-)NCBIHuRef
CHM1_11248,332,620 - 48,364,163 (-)NCBICHM1_1
T2T-CHM13v2.01247,934,691 - 47,967,944 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391597,873,483 - 97,902,525 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1597,873,483 - 97,902,576 (-)EnsemblGRCm39 Ensembl
GRCm381597,975,602 - 98,004,724 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,975,602 - 98,004,695 (-)EnsemblGRCm38mm10GRCm38
MGSCv371597,806,033 - 97,835,155 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361597,803,005 - 97,832,679 (-)NCBIMGSCv36mm8
Celera15100,100,464 - 100,129,552 (-)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1553.97NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_0049555006,860,771 - 6,885,473 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,860,771 - 6,885,466 (-)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan1-v21046,160,541 - 46,192,087 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11246,157,299 - 46,188,845 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01240,726,137 - 40,757,690 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11241,600,206 - 41,631,789 (+)NCBIpanpan1.1PanPan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.1276,756,994 - 6,787,733 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl276,756,994 - 6,787,733 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2739,518,936 - 39,549,645 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0276,824,733 - 6,855,569 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl276,824,865 - 6,855,569 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1276,762,038 - 6,792,716 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0276,796,986 - 6,827,666 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02739,807,429 - 39,838,181 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_02440494567,272,043 - 67,302,897 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365125,861,933 - 5,892,853 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365125,861,933 - 5,894,898 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl578,350,137 - 78,380,718 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1578,350,131 - 78,380,893 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2581,530,406 - 81,554,481 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.11144,196,213 - 44,227,718 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1144,196,094 - 44,227,468 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037202,151,602 - 202,183,142 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_0046248164,274,219 - 4,304,513 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248164,273,969 - 4,304,519 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Col2a1
188 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:66
Interacting mature miRNAs:68
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,128,041 - 129,128,235 (+)MAPPERmRatBN7.2
Rnor_6.07139,484,493 - 139,484,686NCBIRnor6.0
Rnor_5.07139,676,246 - 139,676,439UniSTSRnor5.0
RGSC_v3.47136,708,472 - 136,708,665UniSTSRGSC3.4
Celera7125,619,000 - 125,619,193UniSTS
RH 3.4 Map71097.4UniSTS
RH 3.4 Map71097.4RGD
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,099,604 - 129,100,122 (+)MAPPERmRatBN7.2
Rnor_6.07139,456,061 - 139,456,578NCBIRnor6.0
Rnor_5.07139,647,814 - 139,648,331UniSTSRnor5.0
RGSC_v3.47136,680,038 - 136,680,555UniSTSRGSC3.4
Celera7125,590,568 - 125,591,085UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,098,650 - 129,098,836 (+)MAPPERmRatBN7.2
Rnor_6.07139,455,107 - 139,455,292NCBIRnor6.0
Rnor_5.07139,646,860 - 139,647,045UniSTSRnor5.0
RGSC_v3.47136,679,084 - 136,679,269UniSTSRGSC3.4
Celera7125,589,614 - 125,589,799UniSTS
RH 3.4 Map71098.9UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,123,501 - 129,123,577 (+)MAPPERmRatBN7.2
Rnor_6.07139,479,953 - 139,480,028NCBIRnor6.0
Rnor_5.07139,671,706 - 139,671,781UniSTSRnor5.0
RGSC_v3.47136,703,930 - 136,704,005UniSTSRGSC3.4
Celera7125,614,460 - 125,614,535UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,098,818 - 129,098,920 (+)MAPPERmRatBN7.2
Rnor_6.07139,455,275 - 139,455,376NCBIRnor6.0
Rnor_5.07139,647,028 - 139,647,129UniSTSRnor5.0
RGSC_v3.47136,679,252 - 136,679,353UniSTSRGSC3.4
Celera7125,589,782 - 125,589,883UniSTS
RH 3.4 Map71096.2UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,116,789 - 129,116,977 (+)MAPPERmRatBN7.2
Rnor_6.07139,473,242 - 139,473,429NCBIRnor6.0
Rnor_5.07139,664,995 - 139,665,182UniSTSRnor5.0
RGSC_v3.47136,697,219 - 136,697,406UniSTSRGSC3.4
Celera7125,607,749 - 125,607,936UniSTS
RH 3.4 Map71096.2UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.07139,647,866 - 139,648,445NCBIRnor5.0
Rnor_5.0429,475,523 - 29,476,477NCBIRnor5.0
Rnor_5.0431,437,598 - 31,438,552NCBIRnor5.0
RGSC_v3.4429,425,991 - 29,426,944UniSTSRGSC3.4
RGSC_v3.47136,680,091 - 136,680,669UniSTSRGSC3.4
Celera427,980,077 - 27,981,030UniSTS
Celera7125,590,621 - 125,591,199UniSTS
Cytogenetic Map4q13UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,099,574 - 129,099,704 (+)MAPPERmRatBN7.2
Rnor_6.07139,456,031 - 139,456,160NCBIRnor6.0
Rnor_5.07139,647,784 - 139,647,913UniSTSRnor5.0
RGSC_v3.47136,680,008 - 136,680,137UniSTSRGSC3.4
Celera7125,590,538 - 125,590,667UniSTS
Cytogenetic Map7q36UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,099,045 - 129,100,120 (+)MAPPERmRatBN7.2
Rnor_6.07139,455,502 - 139,456,576NCBIRnor6.0
Rnor_5.07139,647,255 - 139,648,329UniSTSRnor5.0
RGSC_v3.47136,679,479 - 136,680,553UniSTSRGSC3.4
Celera7125,590,009 - 125,591,083UniSTS
Cytogenetic Map7q36UniSTS


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
Medium 14 2 2 2 1 1 49 18 12 2 1
Low 7 14 6 8 6 3 6 23 6 13 5 3
Below cutoff 1 18 9 6 6 3 3 2 6 11 1 3


RefSeq Acc Id: ENSRNOT00000086062   ⟹   ENSRNOP00000071077
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7129,098,786 - 129,127,546 (-)Ensembl
Rnor_6.0 Ensembl7139,455,242 - 139,483,997 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107179   ⟹   ENSRNOP00000094699
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7129,098,786 - 129,127,405 (-)Ensembl
RefSeq Acc Id: NM_001414896   ⟹   NP_001401825
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
GRCr87130,977,561 - 131,006,627 (-)NCBI
mRatBN7.27129,098,489 - 129,127,560 (-)NCBI
RefSeq Acc Id: NM_012929   ⟹   NP_037061
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
GRCr87130,977,561 - 131,006,627 (-)NCBI
mRatBN7.27129,098,489 - 129,127,560 (-)NCBI
Rnor_6.07139,455,242 - 139,483,997 (-)NCBI
Rnor_5.07139,646,698 - 139,675,832 (-)NCBI
RGSC_v3.47136,679,219 - 136,707,976 (-)RGD
Celera7125,589,749 - 125,618,504 (-)RGD
RefSeq Acc Id: NP_037061   ⟸   NM_012929
- Peptide Label: isoform 2 precursor
- UniProtKB: F1LRM7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071077   ⟸   ENSRNOT00000086062
RefSeq Acc Id: ENSRNOP00000094699   ⟸   ENSRNOT00000107179
RefSeq Acc Id: NP_001401825   ⟸   NM_001414896
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A8I6AM44 (UniProtKB/TrEMBL)
Protein Domains
Fibrillar collagen NC1   VWFC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P05539-F1-model_v2 AlphaFold P05539 1-1419 view protein structure


eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

RGD ID:13695620
Promoter ID:EPDNEW_R6145
Type:single initiation site
Description:collagen type II alpha 1 chain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.07139,484,011 - 139,484,071EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2375 AgrOrtholog
BioCyc Gene G2FUF-32164 BioCyc
Ensembl Genes ENSRNOG00000058560 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000086062 ENTREZGENE
  ENSRNOT00000086062.2 UniProtKB/TrEMBL
  ENSRNOT00000107179.1 UniProtKB/TrEMBL
Gene3D-CATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
  Complement Module, domain 1 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWF_dom UniProtKB/TrEMBL
KEGG Report rno:25412 UniProtKB/Swiss-Prot
Pfam COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Col2a1 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058560 RatGTEx
SMART COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP FnI-like domain UniProtKB/TrEMBL
  CO2A1_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q63123 UniProtKB/Swiss-Prot
  Q63565 UniProtKB/Swiss-Prot
  Q78DY3 UniProtKB/Swiss-Prot

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col2a1  collagen type II alpha 1 chain  Col2a1  collagen, type II, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Col2a1  collagen, type II, alpha 1  Col2a1  procollagen, type II, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Col2a1  procollagen, type II, alpha 1    Procollagen II alpha 1  Name updated 625702 APPROVED
2002-06-10 Col2a1  Procollagen II alpha 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog is mutated in spondyloepiphyseal dysplasia (SED) congenita 729929
gene_expression expressed in nasal chondroblasts 70694