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

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Gene: Col2a1 (collagen type II alpha 1 chain) Chinchilla lanigera
Analyze
Symbol: Col2a1
Name: collagen type II alpha 1 chain
RGD ID: 8882241
Description: ENCODES a protein that exhibits identical protein binding (ortholog); MHC class II protein binding (ortholog); platelet-derived growth factor binding (ortholog); INVOLVED IN anterior head development (ortholog); bone development (ortholog); cartilage condensation (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH achondrogenesis type II (ortholog); Animal Disease Models (ortholog); arthritis (ortholog); FOUND IN basement membrane (ortholog); collagen trimer (ortholog); collagen type II trimer (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(II) chain; collagen, type II, alpha 1
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555006,860,771 - 6,885,473 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,860,771 - 6,885,466 (-)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
achondrogenesis type II  (ISO)
Animal Disease Models  (ISO)
arthritis  (ISO)
asphyxiating thoracic dystrophy  (ISO)
Bethlem myopathy  (ISO)
Bethlem Myopathy 1  (ISO)
bone development disease  (ISO)
bone resorption disease  (ISO)
Bronchial Fistula  (ISO)
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  (ISO)
Dwarfism  (ISO)
Edema  (ISO)
Erythema  (ISO)
Experimental Arthritis  (ISO)
eye disease  (ISO)
Femur Head Necrosis  (ISO)
Fetal Growth Retardation  (ISO)
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  (ISO)
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)
osteoarthritis  (ISO)
Osteoarthritis with Mild Chondrodysplasia  (ISO)
osteochondrodysplasia  (ISO)
otospondylomegaepiphyseal dysplasia, autosomal dominant  (ISO)
otospondylomegaepiphyseal dysplasia, autosomal recessive  (ISO)
Prognathism  (ISO)
retinal detachment  (ISO)
Rhegmatogenous Retinal Detachment, Autosomal Dominant  (ISO)
rheumatoid arthritis  (ISO)
sensorineural hearing loss  (ISO)
SHORT STATURE AND ADVANCED BONE AGE, WITH OR WITHOUT EARLY-ONSET OSTEOARTHRITIS AND/OR OSTEOCHONDRITIS DISSECANS  (ISO)
spondyloarthropathy  (ISO)
spondyloepimetaphyseal dysplasia  (ISO)
spondyloepimetaphyseal dysplasia, Strudwick type  (ISO)
spondyloepiphyseal dysplasia congenita  (ISO)
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 Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. Ultrastructure and immunohistochemical identification of the extracellular matrix of the chinchilla cochlea. Tsuprun V and Santi P, Hear Res. 1999 Mar;129(1-2):35-49.

Genomics

Comparative Map Data
Col2a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555006,860,771 - 6,885,473 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,860,771 - 6,885,466 (-)NCBIChiLan1.0ChiLan1.0
COL2A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381247,972,967 - 48,006,212 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
Col2a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Col2a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27129,098,489 - 129,127,620 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7129,098,786 - 129,127,546 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,895,443 - 130,924,189 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07133,120,981 - 133,149,729 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07133,033,447 - 133,062,197 (-)NCBIRnor_WKY
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
COL2A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
COL2A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Col2a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494567,272,043 - 67,302,897 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365125,861,933 - 5,892,853 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365125,861,933 - 5,894,898 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL2A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
COL2A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Col2a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000017332   ⟹   ENSCLAP00000017163
RefSeq Status:
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049555006,860,771 - 6,885,473 (-)Ensembl
RefSeq Acc Id: XM_013505702   ⟹   XP_013361156
RefSeq Status:
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049555006,860,771 - 6,885,466 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013361156 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_013361156   ⟸   XM_013505702
- Sequence:
RefSeq Acc Id: ENSCLAP00000017163   ⟸   ENSCLAT00000017332
Protein Domains
Fibrillar collagen NC1   VWFC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000011781 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCLAP00000017163 ENTREZGENE
  ENSCLAP00000017163.1 UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000017332 ENTREZGENE
  ENSCLAT00000017332.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/TrEMBL
  Complement Module, domain 1 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
  VWF_dom UniProtKB/TrEMBL
NCBI Gene Col2a1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA CHAIN CG42342-RELATED UniProtKB/TrEMBL
Pfam COLFI UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  VWC UniProtKB/TrEMBL
PROSITE NC1_FIB UniProtKB/TrEMBL
  VWFC_1 UniProtKB/TrEMBL
  VWFC_2 UniProtKB/TrEMBL
SMART COLFI UniProtKB/TrEMBL
  VWC UniProtKB/TrEMBL
Superfamily-SCOP FnI-like domain UniProtKB/TrEMBL
UniProt A0A8C2VKT0_CHILA UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Col2a1  collagen type II alpha 1 chain    collagen, type II, alpha 1  Symbol and/or name change 5135510 APPROVED