COL1A1 (collagen type I alpha 1 chain) - Rat Genome Database

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Gene: COL1A1 (collagen type I alpha 1 chain) Sus scrofa
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Symbol: COL1A1
Name: collagen type I alpha 1 chain
RGD ID: 14297975
Description: ENCODES a protein that exhibits extracellular matrix structural constituent (inferred); identical protein binding (inferred); metal ion binding (inferred); 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); endoplasmic reticulum (ortholog); extracellular matrix (ortholog); INTERACTS WITH Bisphenol A diglycidyl ether; dexamethasone; dibromine
Type: protein-coding
RefSeq Status: MODEL
Also known as: alpha1 chain of type I collagen; collagen alpha-1(I) chain; collagen type I alpha 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1226,379,090 - 26,397,003 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11226,379,087 - 26,397,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
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)
autoimmune disease  (ISO)
beta thalassemia  (ISO)
Bisphosphonate-Associated Osteonecrosis of the Jaw  (ISO)
bladder neck obstruction  (ISO)
Bone Fractures  (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)
connective tissue disease  (ISO)
Contracture  (ISO)
cutaneous leishmaniasis  (ISO)
degenerative disc disease  (ISO)
dentinogenesis imperfecta  (ISO)
dermatofibrosarcoma protuberans  (ISO)
Diabetic Nephropathies  (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)
Ehlers-Danlos Syndrome Type 7  (ISO)
end stage renal disease  (ISO)
Experimental Liver Cirrhosis  (ISO)
extrahepatic cholestasis  (ISO)
Femoral Fractures  (ISO)
Fibrosis  (ISO)
Fractures, Multiple  (ISO)
genetic disease  (ISO)
heart valve disease  (ISO)
hemorrhagic disease  (ISO)
Hernia, Ventral  (ISO)
High Myopia  (ISO)
Human Viral Hepatitis  (ISO)
Hypertelorism  (ISO)
hypertension  (ISO)
Hypertensive Nephropathy  (ISO)
Intervertebral Disc Disease  (ISO)
Joint Instability  (ISO)
Keloid  (ISO)
Left Ventricular Hypertrophy  (ISO)
Lipodermatosclerosis  (ISO)
liver benign neoplasm  (ISO)
liver cirrhosis  (ISO)
lupus nephritis  (ISO)
Metabolic Bone Diseases  (ISO)
multiple sclerosis  (ISO)
myocardial infarction  (ISO)
myocarditis  (ISO)
myopia  (ISO)
Nephrogenic Fibrosing Dermopathy  (ISO)
nephrosclerosis  (ISO)
nephrotic syndrome  (ISO)
non-alcoholic fatty liver disease  (ISO)
non-alcoholic steatohepatitis  (ISO)
ocular hypertension  (ISO)
open-angle glaucoma  (ISO)
oral submucous fibrosis  (ISO)
osteoarthritis  (ISO)
Osteoarthritis, Experimental  (ISO)
Osteoarthritis, Hip  (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)
Postmenopausal Osteoporosis  (ISO)
primary biliary cholangitis  (ISO)
prostate cancer  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (ISO)
Spontaneous Abortions  (ISO)
systemic scleroderma  (ISO)
Tendon Injuries  (ISO)
thoracic aortic aneurysm  (ISO)
Trachomatous Trichiasis  (ISO)
ulcerative colitis  (ISO)
ureteral obstruction  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blood vessel development  (IBA,IEA,ISO)
bone trabecula formation  (IEA,ISO)
cartilage development involved in endochondral bone morphogenesis  (IEA,ISO)
cellular response to amino acid stimulus  (IEA,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 mechanical stimulus  (IEA,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  (IEA)
collagen fibril organization  (IEA)
collagen-activated tyrosine kinase receptor signaling pathway  (ISO)
embryonic skeletal system development  (IEA)
endochondral ossification  (IEA,ISO)
extracellular matrix organization  (IBA)
face morphogenesis  (IEA,ISO)
intramembranous ossification  (IEA,ISO)
negative regulation of cell-substrate adhesion  (IEA,ISO)
ossification  (IBA,ISO)
osteoblast differentiation  (IEA,ISO)
positive regulation of canonical Wnt signaling pathway  (IEA)
positive regulation of cell migration  (IEA)
positive regulation of epithelial to mesenchymal transition  (IEA)
positive regulation of transcription, DNA-templated  (IEA)
protein localization to nucleus  (IEA)
protein transport  (IEA,ISO)
response to cAMP  (ISO)
response to corticosteroid  (ISO)
response to estradiol  (ISO)
response to fluoride  (ISO)
response to hydrogen peroxide  (ISO)
response to hyperoxia  (ISO)
response to mechanical stimulus  (IBA,ISO)
response to nutrient  (ISO)
response to nutrient levels  (ISO)
response to peptide hormone  (ISO)
response to steroid hormone  (ISO)
response to xenobiotic stimulus  (ISO)
sensory perception of sound  (IEA)
skeletal system development  (IBA,ISO)
skeletal system morphogenesis  (ISO)
skin development  (IBA,ISO)
skin morphogenesis  (IEA)
tooth eruption  (ISO)
tooth mineralization  (IEA)
visual perception  (IEA)
wound healing  (ISO)

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:17145712  


Genomics

Comparative Map Data
COL1A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1226,379,090 - 26,397,003 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11226,379,087 - 26,397,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COL1A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1750,184,101 - 50,201,632 (-)EnsemblGRCh38hg38GRCh38
GRCh381750,184,096 - 50,201,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371748,261,462 - 48,278,992 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361745,616,456 - 45,633,999 (-)NCBINCBI36hg18NCBI36
Build 341745,616,455 - 45,633,992NCBI
Celera1744,722,303 - 44,739,829 (-)NCBI
Cytogenetic Map17q21.33NCBI
HuRef1743,630,129 - 43,647,463 (-)NCBIHuRef
CHM1_11748,325,754 - 48,343,284 (-)NCBICHM1_1
Col1a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391194,827,050 - 94,843,868 (+)NCBIGRCm39mm39
GRCm39 Ensembl1194,827,050 - 94,843,868 (+)Ensembl
GRCm381194,936,224 - 94,953,042 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1194,936,224 - 94,953,042 (+)EnsemblGRCm38mm10GRCm38
MGSCv371194,797,584 - 94,813,181 (+)NCBIGRCm37mm9NCBIm37
MGSCv361194,752,360 - 94,767,957 (+)NCBImm8
Celera11104,549,617 - 104,565,301 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1159.01NCBI
Col1a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21079,883,622 - 79,900,625 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1082,745,801 - 82,762,789 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01082,745,801 - 82,762,790 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01082,563,434 - 82,580,364 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41083,622,438 - 83,639,368 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11083,636,918 - 83,653,733 (+)NCBI
Celera1078,658,450 - 78,675,438 (+)NCBICelera
Cytogenetic Map10q26NCBI
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
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11749,149,277 - 49,166,833 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1749,150,677 - 49,166,677 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01744,274,349 - 44,291,764 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0926,978,359 - 26,994,434 (-)NCBI
UMICH_Zoey_3.1925,746,094 - 25,762,176 (-)NCBI
UNSW_CanFamBas_1.0926,004,757 - 26,020,835 (-)NCBI
UU_Cfam_GSD_1.0926,134,702 - 26,150,789 (-)NCBI
Col1a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560225,609,297 - 25,626,616 (-)NCBI
SpeTri2.0NW_00493649011,448,552 - 11,465,836 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL1A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11643,134,648 - 43,152,313 (+)NCBI
ChlSab1.1 Ensembl1643,134,779 - 43,150,930 (+)Ensembl
Vero_WHO_p1.0NW_02366607713,850,099 - 13,867,746 (+)NCBI
Col1a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247956,167,504 - 6,183,208 (-)NCBI


Expression


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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 1 3 2 4 1 3 1
Low 2 2 19 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000040712   ⟹   ENSSSCP00000057325
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1226,379,090 - 26,397,002 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000061988   ⟹   ENSSSCP00000037874
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1226,379,090 - 26,397,002 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000073214   ⟹   ENSSSCP00000066291
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1226,380,310 - 26,397,003 (-)Ensembl
RefSeq Acc Id: XM_021067153   ⟹   XP_020922812
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11226,379,087 - 26,397,180 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021067154   ⟹   XP_020922813
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11226,379,087 - 26,397,041 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021067155   ⟹   XP_020922814
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11226,379,087 - 26,397,041 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_020922812   ⟸   XM_021067153
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_020922814   ⟸   XM_021067155
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_020922813   ⟸   XM_021067154
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSSSCP00000057325   ⟸   ENSSSCT00000040712
RefSeq Acc Id: ENSSSCP00000037874   ⟸   ENSSSCT00000061988
RefSeq Acc Id: ENSSSCP00000066291   ⟸   ENSSSCT00000073214
Protein Domains
Fibrillar collagen NC1   VWFC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000036135 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000037874 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000057325 UniProtKB/TrEMBL
  ENSSSCP00000066291 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000040712 UniProtKB/TrEMBL
  ENSSSCT00000061988 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000073214 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
  VWF_dom UniProtKB/TrEMBL
NCBI Gene COL1A1 ENTREZGENE
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
UniProt A0A287A1S6_PIG UniProtKB/TrEMBL
  A0A287BLD2_PIG UniProtKB/TrEMBL
  A0A5G2QQE9_PIG UniProtKB/TrEMBL
  Q1HNM7_PIG UniProtKB/TrEMBL
  Q2A126_PIG UniProtKB/TrEMBL
  Q6H2X9_PIG UniProtKB/TrEMBL
  Q9MYT7_PIG UniProtKB/TrEMBL
VGNC ID VGNC:86870 ENTREZGENE