Col1a1 (collagen type I alpha 1 chain) - Rat Genome Database

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Gene: Col1a1 (collagen type I alpha 1 chain) Chinchilla lanigera
Analyze
Symbol: Col1a1
Name: collagen type I alpha 1 chain
RGD ID: 9015700
Description: ENCODES a protein that exhibits extracellular matrix structural constituent (ortholog); identical protein binding (ortholog); platelet-derived growth factor binding (ortholog); INVOLVED IN blood vessel development (ortholog); bone trabecula formation (ortholog); cartilage development involved in endochondral bone morphogenesis (ortholog); PARTICIPATES IN acenocoumarol pharmacodynamics pathway; alteplase pharmacodynamics pathway; aminocaproic acid pharmacodynamics pathway; ASSOCIATED WITH aggressive periodontitis (ortholog); alcoholic hepatitis (ortholog); aortic valve insufficiency (ortholog); FOUND IN collagen trimer (ortholog); collagen type I trimer (ortholog); collagen-containing extracellular matrix (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(I) chain; collagen, type I, 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
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545111,468,290 - 11,483,073 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545111,468,156 - 11,484,410 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
aggressive periodontitis  (ISO)
alcoholic hepatitis  (ISO)
aortic valve insufficiency  (ISO)
Arteriovenous Fistula  (ISO)
asphyxia neonatorum  (ISO)
autoimmune disease  (ISO)
autosomal recessive limb-girdle muscular dystrophy type 2D  (ISO)
beta thalassemia  (ISO)
Bisphosphonate-Associated Osteonecrosis of the Jaw  (ISO)
bladder neck obstruction  (ISO)
Bone Fractures  (ISO)
bone structure disease  (ISO)
Caffey disease  (ISO)
calcinosis  (ISO)
Cardiac Fibrosis  (ISO)
cholangitis  (ISO)
cholestasis  (ISO)
chronic obstructive pulmonary disease  (ISO)
Chronic Pancreatitis  (ISO)
Combined Osteogenesis Imperfecta and Ehlers-Danlos Syndrome 1  (ISO)
congenital heart disease  (ISO)
connective tissue disease  (ISO)
Contracture  (ISO)
cutaneous leishmaniasis  (ISO)
degenerative disc disease  (ISO)
dentinogenesis imperfecta  (ISO)
dermatofibrosarcoma protuberans  (ISO)
Diabetic Nephropathies  (ISO)
dilated cardiomyopathy  (ISO)
Dissecting Aneurysm  (ISO)
Ehlers-Danlos syndrome  (ISO)
Ehlers-Danlos syndrome arthrochalasia type 1  (ISO)
Ehlers-Danlos syndrome arthrochalasia type 2  (ISO)
Ehlers-Danlos syndrome cardiac valvular type  (ISO)
Ehlers-Danlos syndrome classic type 1  (ISO)
end stage renal disease  (ISO)
Experimental Liver Cirrhosis  (ISO)
extrahepatic cholestasis  (ISO)
Femoral Fractures  (ISO)
Fetal Nutrition Disorders  (ISO)
Fibrosis  (ISO)
genetic disease  (ISO)
heart valve disease  (ISO)
hemorrhagic disease  (ISO)
High Myopia  (ISO)
Human Viral Hepatitis  (ISO)
Hypertelorism  (ISO)
hypertension  (ISO)
Hypertensive Nephropathy  (ISO)
hypertrophic cardiomyopathy  (ISO)
Intervertebral Disc Disease  (ISO)
Joint Instability  (ISO)
Keloid  (ISO)
keratoconus  (ISO)
Kidney Reperfusion Injury  (ISO)
Left Ventricular Hypertrophy  (ISO)
Lipodermatosclerosis  (ISO)
liver benign neoplasm  (ISO)
liver cirrhosis  (ISO)
Lung Reperfusion Injury  (ISO)
lupus nephritis  (ISO)
Metabolic Bone Diseases  (ISO)
metabolic dysfunction-associated steatohepatitis  (ISO)
metabolic dysfunction-associated steatotic liver disease  (ISO)
multiple epiphyseal dysplasia 1  (ISO)
multiple sclerosis  (ISO)
Muscle Hypotonia  (ISO)
myocardial infarction  (ISO)
myocarditis  (ISO)
myopia  (ISO)
Nephrogenic Fibrosing Dermopathy  (ISO)
nephrosclerosis  (ISO)
nephrotic syndrome  (ISO)
obesity  (ISO)
ocular hypertension  (ISO)
open-angle glaucoma  (ISO)
oral submucous fibrosis  (ISO)
osteoarthritis  (ISO)
Osteoarthritis, Experimental  (ISO)
Osteoarthritis, Hip  (ISO)
osteochondrodysplasia  (ISO)
osteogenesis imperfecta  (ISO)
osteogenesis imperfecta type 1  (ISO)
osteogenesis imperfecta type 2  (ISO)
osteogenesis imperfecta type 2C  (ISO)
osteogenesis imperfecta type 3  (ISO)
osteogenesis imperfecta type 4  (ISO)
osteoporosis  (ISO)
otosclerosis  (ISO)
phenylketonuria  (ISO)
Postmenopausal Osteoporosis  (ISO)
Premature Birth  (ISO)
primary biliary cholangitis  (ISO)
prostate cancer  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (ISO)
rheumatic heart disease  (ISO)
Spontaneous Abortions  (ISO)
Spontaneous Fractures  (ISO)
systemic scleroderma  (ISO)
Tendon Injuries  (ISO)
thoracic aortic aneurysm  (ISO)
Trachomatous Trichiasis  (ISO)
trichodontoosseous syndrome  (ISO)
Tubulointerstitial Fibrosis  (ISO)
ulcerative colitis  (ISO)
ureteral obstruction  (ISO)
Ventral Hernia  (ISO)
Wiedemann-Rautenstrauch syndrome  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blood vessel development  (ISO)
bone trabecula formation  (ISO)
cartilage development involved in endochondral bone morphogenesis  (ISO)
cellular response to amino acid stimulus  (ISO)
cellular response to epidermal growth factor stimulus  (ISO)
cellular response to fibroblast growth factor stimulus  (ISO)
cellular response to fluoride  (ISO)
cellular response to glucose stimulus  (ISO)
cellular response to mechanical stimulus  (ISO)
cellular response to retinoic acid  (ISO)
cellular response to transforming growth factor beta stimulus  (ISO)
cellular response to tumor necrosis factor  (ISO)
cellular response to vitamin E  (ISO)
collagen biosynthetic process  (ISO)
collagen fibril organization  (ISO)
collagen-activated tyrosine kinase receptor signaling pathway  (ISO)
embryonic skeletal system development  (ISO)
endochondral ossification  (ISO)
face morphogenesis  (ISO)
intramembranous ossification  (ISO)
negative regulation of cell-substrate adhesion  (ISO)
ossification  (ISO)
osteoblast differentiation  (ISO)
positive regulation of canonical Wnt signaling pathway  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of epithelial to mesenchymal transition  (ISO)
protein localization to nucleus  (ISO)
protein transport  (ISO)
response to cAMP  (ISO)
response to estradiol  (ISO)
response to fluoride  (ISO)
response to hydrogen peroxide  (ISO)
response to hyperoxia  (ISO)
response to insulin  (ISO)
response to mechanical stimulus  (ISO)
response to nutrient  (ISO)
response to nutrient levels  (ISO)
response to organic cyclic compound  (ISO)
response to peptide hormone  (ISO)
response to steroid hormone  (ISO)
response to xenobiotic stimulus  (ISO)
sensory perception of sound  (ISO)
skeletal system development  (ISO)
skeletal system morphogenesis  (ISO)
skin development  (ISO)
skin morphogenesis  (ISO)
tooth mineralization  (ISO)
visual perception  (ISO)

Cellular Component

Molecular Function

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
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Col1a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545111,468,290 - 11,483,073 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545111,468,156 - 11,484,410 (+)NCBIChiLan1.0ChiLan1.0
COL1A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381750,184,101 - 50,201,631 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1750,184,101 - 50,201,632 (-)EnsemblGRCh38hg38GRCh38
GRCh371748,261,462 - 48,278,992 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361745,616,456 - 45,633,999 (-)NCBINCBI36Build 36hg18NCBI36
Build 341745,616,455 - 45,633,992NCBI
Celera1744,722,303 - 44,739,829 (-)NCBICelera
Cytogenetic Map17q21.33NCBI
HuRef1743,630,129 - 43,647,463 (-)NCBIHuRef
CHM1_11748,325,754 - 48,343,284 (-)NCBICHM1_1
T2T-CHM13v2.01751,051,162 - 51,068,680 (-)NCBIT2T-CHM13v2.0
Col1a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391194,827,050 - 94,843,868 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1194,827,050 - 94,843,868 (+)EnsemblGRCm39 Ensembl
GRCm381194,936,224 - 94,953,042 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1194,936,224 - 94,953,042 (+)EnsemblGRCm38mm10GRCm38
MGSCv371194,797,584 - 94,813,181 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361194,752,360 - 94,767,957 (+)NCBIMGSCv36mm8
Celera11104,549,617 - 104,565,301 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1159.01NCBI
Col1a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81080,380,458 - 80,397,461 (+)NCBIGRCr8
mRatBN7.21079,883,622 - 79,900,625 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1079,883,622 - 79,900,624 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1084,832,832 - 84,849,838 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01084,330,903 - 84,347,909 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01079,723,993 - 79,740,998 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01082,745,801 - 82,762,790 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1082,745,801 - 82,762,789 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01082,563,434 - 82,580,364 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41083,622,438 - 83,639,368 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11083,636,918 - 83,653,733 (+)NCBI
Celera1078,658,450 - 78,675,438 (+)NCBICelera
Cytogenetic Map10q26NCBI
COL1A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21966,373,893 - 66,390,381 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11771,180,391 - 71,196,792 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01744,274,349 - 44,291,764 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11749,149,277 - 49,166,833 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1749,150,677 - 49,166,677 (-)Ensemblpanpan1.1panPan2
COL1A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1926,183,852 - 26,199,927 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl926,183,852 - 26,199,927 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha925,576,913 - 25,592,983 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0926,978,359 - 26,994,434 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl926,978,317 - 26,994,453 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1925,746,094 - 25,762,176 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0926,004,757 - 26,020,835 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0926,134,702 - 26,150,789 (-)NCBIUU_Cfam_GSD_1.0
Col1a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560225,609,297 - 25,626,616 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649011,448,654 - 11,464,444 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649011,448,552 - 11,465,836 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL1A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1226,379,090 - 26,397,004 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11226,379,087 - 26,397,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COL1A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11643,134,648 - 43,152,313 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1643,134,779 - 43,150,930 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607713,850,099 - 13,867,746 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col1a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247956,168,797 - 6,183,071 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247956,167,504 - 6,183,208 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000023923   ⟹   ENSCLAP00000023697
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495545111,468,290 - 11,483,073 (+)Ensembl
RefSeq Acc Id: XM_005394176   ⟹   XP_005394233
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495545111,468,156 - 11,484,410 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013519103   ⟹   XP_013374557
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495545111,468,157 - 11,484,410 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005394233 (Get FASTA)   NCBI Sequence Viewer  
  XP_013374557 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000023697
  ENSCLAP00000023697.1
Reference Protein Sequences
RefSeq Acc Id: XP_005394233   ⟸   XM_005394176
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_013374557   ⟸   XM_013519103
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSCLAP00000023697   ⟸   ENSCLAT00000023923
Protein Domains
Fibrillar collagen NC1   VWFC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000016259 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000023923 ENTREZGENE
  ENSCLAT00000023923.1 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 LOC102014851 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  ENDOSTATIN DOMAIN-CONTAINING PROTEIN 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 A0A8C2W197_CHILA UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Col1a1  collagen type I alpha 1 chain    collagen, type I, alpha 1  Symbol and/or name change 5135510 APPROVED
2015-08-25 Col1a1  collagen, type I, alpha 1  LOC102014851  collagen alpha-1(I) chain-like  Symbol and/or name change 5135510 APPROVED