Col3a1 (collagen, type III, alpha 1) - Rat Genome Database

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Gene: Col3a1 (collagen, type III, alpha 1) Mus musculus
Analyze
Symbol: Col3a1
Name: collagen, type III, alpha 1
RGD ID: 732584
MGI Page MGI
Description: Exhibits SMAD binding activity. Involved in several processes, including aorta smooth muscle tissue morphogenesis; collagen fibril organization; and positive regulation of Rho protein signal transduction. Localizes to collagen type III trimer. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and heart and pericardium. Used to study systemic scleroderma and vascular type Ehlers-Danlos syndrome. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome; Ehlers-Danlos syndrome hypermobility type; end stage renal disease; and vascular type Ehlers-Danlos syndrome. Orthologous to human COL3A1 (collagen type III alpha 1 chain).
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: AW550625; Col3; Col3a-1; collagen alpha-1(III) chain; KIAA4231; minisatellite 10w detected by probe MMS10; mKIAA4231; MMS10-W; Ms10w; procollagen, type III, alpha 1; Tsk; Tsk-; Tsk-2; Tsk2
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm18395  
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39145,350,698 - 45,388,866 (+)NCBIGRCm39mm39
GRCm39 Ensembl145,350,698 - 45,388,866 (+)Ensembl
GRCm38145,311,538 - 45,349,706 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl145,311,538 - 45,349,706 (+)EnsemblGRCm38mm10GRCm38
MGSCv37145,368,383 - 45,406,551 (+)NCBIGRCm37mm9NCBIm37
MGSCv36145,256,192 - 45,293,566 (+)NCBImm8
Celera145,612,466 - 45,650,861 (+)NCBICelera
Cytogenetic Map1C1.1NCBI
cM Map123.67NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Otitis Media  (ISO)
alcoholic liver cirrhosis  (ISO)
Aneurysm  (ISO)
aortic aneurysm  (ISO)
aortic disease  (ISO)
aortic valve insufficiency  (ISO)
ARTERIAL DISSECTION  (ISO)
bladder neck obstruction  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
connective tissue disease  (ISO)
Contracture  (ISO)
Ehlers-Danlos syndrome  (IAGP,ISO)
Ehlers-Danlos syndrome hypermobility type  (ISO)
Ehlers-Danlos Syndrome Type 4  (ISO)
end stage renal disease  (ISO)
endomyocardial fibrosis  (ISO)
epilepsy  (ISO)
Experimental Liver Cirrhosis  (ISO)
extrahepatic cholestasis  (ISO)
facioscapulohumeral muscular dystrophy  (ISO)
Familial Thoracic Aortic Aneurysm 1  (ISO)
Familial Thoracic Aortic Aneurysm 2  (ISO)
fatty liver disease  (ISO)
Fibrosis  (ISO)
genetic disease  (ISO)
glomerulosclerosis  (ISO)
Hernia, Ventral  (ISO)
Hirschsprung's disease  (ISO)
Hypercholesterolemia  (ISO)
hyperglycemia  (ISO)
hyperinsulinism  (ISO)
hypertension  (ISO)
Keloid  (ISO)
Left Ventricular Hypertrophy  (ISO)
liver cirrhosis  (ISO)
liver disease  (ISO)
Loeys-Dietz syndrome  (ISO)
Malformations of Cortical Development, Group II  (ISO)
Marfan syndrome  (ISO)
Marfanoid Hypermobility Syndrome  (ISO)
Maxillofacial Abnormalities  (ISO)
Mycoplasma pneumoniae pneumonia  (ISO)
myocardial infarction  (ISO)
nephrosclerosis  (ISO)
Neurodevelopmental Disorders  (ISO)
Polymicrogyria with or without Vascular-Type Ehlers-Danlos Syndrome  (ISO)
pulmonary fibrosis  (IEP,ISO)
renal fibrosis  (IEP)
schizophrenia  (ISO)
systemic scleroderma  (IEA)
thoracic aortic aneurysm  (ISO)
Transplant Rejection  (ISO)
type 2 diabetes mellitus  (ISO)
ureteral obstruction  (ISO)
vascular type Ehlers-Danlos syndrome  (IEA,ISO)
visual epilepsy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(R)-noradrenaline  (ISO)
(S)-nicotine  (EXP)
1,1-dichloroethene  (EXP)
1,2-dichloroethane  (EXP)
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-galactopyranose  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-butoxyethanol  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-methylcholanthrene  (EXP)
3H-1,2-dithiole-3-thione  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (EXP)
4-hydroxyphenyl retinamide  (EXP)
5-(1,4-diazepane-1-sulfonyl)isoquinoline  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (ISO)
Ac-Ser-Asp-Lys-Pro-OH  (EXP)
acetamide  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (ISO)
adenine  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
aldosterone  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ambroxol  (ISO)
ammonium chloride  (ISO)
amphibole asbestos  (EXP,ISO)
andrographolide  (EXP,ISO)
anthocyanin  (EXP)
apocynin  (ISO)
arsenic acid  (EXP)
arsenite(3-)  (EXP)
azelastine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (EXP)
Benzo[k]fluoranthene  (EXP)
beta-D-glucosamine  (ISO)
bilirubin IXalpha  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bleomycin A2  (EXP,ISO)
boron nitride  (ISO)
bucladesine  (ISO)
buspirone  (ISO)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
camostat  (ISO)
Candesartan cilexetil  (ISO)
capsaicin  (ISO)
captopril  (EXP)
carbon atom  (ISO)
carbon nanotube  (EXP)
carvedilol  (ISO)
CGS-21680  (ISO)
chloroprene  (EXP)
choline  (EXP)
chrysene  (EXP)
cisplatin  (ISO)
clobetasol  (EXP)
clofibric acid  (ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (EXP,ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
DDT  (ISO)
dexamethasone  (ISO)
diclofenac  (EXP,ISO)
diethyl malate  (EXP)
diethyl maleate  (EXP)
dioxygen  (EXP,ISO)
diprotium oxide  (ISO)
dipyridamole  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
diuron  (ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor  (ISO)
elemental carbon  (ISO)
emodin  (ISO)
enalapril  (EXP,ISO)
endosulfan  (ISO)
eplerenone  (ISO)
eprosartan  (ISO)
ergosta-4,6,8(14),22-tetraen-3-one  (ISO)
ethanol  (ISO)
excitatory amino acid agonist  (ISO)
fasudil hydrochloride  (EXP)
fenofibrate  (EXP)
fingolimod hydrochloride  (EXP)
folic acid  (EXP)
fulvestrant  (ISO)
fumonisin B1  (EXP)
furan  (ISO)
genistein  (ISO)
glucose  (ISO)
gold atom  (EXP)
gold(0)  (EXP)
griseofulvin  (EXP)
Honokiol  (EXP)
indometacin  (ISO)
isoprenaline  (EXP,ISO)
isotretinoin  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (EXP)
lamivudine  (ISO)
limonene  (ISO)
linoleic acid  (EXP)
lipopolysaccharide  (EXP,ISO)
losartan  (EXP,ISO)
manidipine  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methylglyoxal  (EXP)
methylmercury(1+)  (ISO)
methylparaben  (ISO)
methyltestosterone  (ISO)
metoprolol  (ISO)
mifepristone  (ISO)
Monobutylphthalate  (EXP)
monosodium L-glutamate  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (ISO)
Nandrolone decanoate  (ISO)
nefazodone  (ISO)
nickel atom  (EXP)
nickel dichloride  (ISO)
nickel sulfate  (EXP)
nicotine  (EXP)
nimesulide  (ISO)
ochratoxin A  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
Pachymic acid  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
paricalcitol  (EXP)
Pentoxifylline  (ISO)
perfluorooctanoic acid  (ISO)
perindopril  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP)
Plantamajoside  (EXP)
poly(guanylic acid)  (ISO)
potassium dichromate  (EXP,ISO)
progesterone  (EXP)
puerarin  (ISO)
quercetin  (EXP,ISO)
quercitrin  (ISO)
Rebamipide  (ISO)
resveratrol  (EXP,ISO)
rosmarinic acid  (ISO)
rotenone  (ISO)
saralasin  (ISO)
sarin  (ISO)
SB 431542  (ISO)
SCH 23390  (ISO)
serpentine asbestos  (EXP)
Shikonin  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (EXP,ISO)
sorafenib  (ISO)
spironolactone  (ISO)
succimer  (EXP,ISO)
sunitinib  (ISO)
tacrolimus hydrate  (EXP)
tamoxifen  (EXP,ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetramethylpyrazine  (EXP)
tetraphene  (EXP)
thioacetamide  (ISO)
topotecan  (ISO)
toxaphene  (ISO)
trichloroethene  (ISO)
trichostatin A  (EXP)
triclosan  (ISO)
triptonide  (EXP)
ursodeoxycholic acid  (ISO)
valproic acid  (EXP,ISO)
valsartan  (EXP)
vancomycin  (EXP)
vinclozolin  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
water  (ISO)
Y-27632  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abrahamsen CT, etal., J Pharmacol Exp Ther. 2002 Apr;301(1):21-8. doi: 10.1124/jpet.301.1.21.
2. Abrass CK, etal., Am J Physiol Renal Physiol. 2011 Feb;300(2):F531-9. doi: 10.1152/ajprenal.00237.2010. Epub 2010 Jul 7.
3. Gaikwad AB, etal., Biochem J. 2010 Dec 1;432(2):333-41. doi: 10.1042/BJ20100414.
4. Kanazawa K, etal., Int J Clin Exp Pathol. 2015 Apr 1;8(4):3426-40. eCollection 2015.
5. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
6. Kim J, etal., J Microbiol Biotechnol. 2020 Mar 28;30(3):427-438. doi: 10.4014/jmb.1910.10055.
7. Kontusaari S, etal., Am J Hum Genet 1990 Jul;47(1):112-20.
8. Ling XB, etal., J Am Soc Nephrol. 2010 Apr;21(4):646-53. doi: 10.1681/ASN.2009080876. Epub 2010 Feb 11.
9. MGD and Homologene mouse data transfer
10. MGD data from the GO Consortium
11. MGD IEA
12. Narcisi P, etal., Hum Mol Genet. 1994 Sep;3(9):1617-20.
13. Oderich GS, etal., J Vasc Surg. 2005 Jul;42(1):98-106.
14. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
15. OMIM Disease Annotation Pipeline
16. Pepin M, etal., N Engl J Med 2000 Mar 9;342(10):673-80.
17. Phua YL, etal., J Pathol. 2013 Apr;229(5):685-96. doi: 10.1002/path.4155. Epub 2013 Feb 22.
18. Pipeline to import KEGG annotations from KEGG into RGD
19. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
20. RGD automated import pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Richards AJ, etal., Hum Genet. 1992 Jan;88(3):325-30.
24. Schroder A, etal., J Urol. 2013 Jun;189(6):2377-84. doi: 10.1016/j.juro.2012.12.110. Epub 2013 Jan 9.
25. Smith LB, etal., Cardiovasc Res. 2011 Apr 1;90(1):182-90. doi: 10.1093/cvr/cvq356. Epub 2010 Nov 10.
26. Van Eps J, etal., Surg Endosc. 2015 Nov 17.
27. Wertz K and Herrmann BG, Mech Dev 2000 Nov;98(1-2):51-70.
28. Wong VY, etal., Br J Pharmacol. 2001 Nov;134(5):977-84. doi: 10.1038/sj.bjp.0704329.
29. Yang F, etal., J Cardiovasc Pharmacol. 2015 May;65(5):456-64. doi: 10.1097/FJC.0000000000000214.
30. Yoshida T, etal., Int J Mol Med. 2009 Jun;23(6):785-92.
Additional References at PubMed
PMID:1347472   PMID:1358796   PMID:1879336   PMID:1981051   PMID:2054384   PMID:2209468   PMID:2981217   PMID:3443309   PMID:3972847   PMID:7752808   PMID:7777502   PMID:7825727  
PMID:7919967   PMID:7926795   PMID:8069308   PMID:8088797   PMID:8188220   PMID:8244386   PMID:8661741   PMID:8678985   PMID:8686743   PMID:8785585   PMID:8849351   PMID:8900172  
PMID:8948440   PMID:8984825   PMID:9021163   PMID:9037598   PMID:9050868   PMID:9164858   PMID:9382709   PMID:9614124   PMID:9832566   PMID:9870870   PMID:10022501   PMID:10088787  
PMID:10349636   PMID:10458099   PMID:10922068   PMID:10995453   PMID:11042159   PMID:11076861   PMID:11210178   PMID:11283268   PMID:12477932   PMID:12571105   PMID:12592609   PMID:12659831  
PMID:12874293   PMID:14559231   PMID:14758483   PMID:15371327   PMID:15489334   PMID:15582152   PMID:15733672   PMID:16081813   PMID:16107646   PMID:16141072   PMID:16141073   PMID:16236725  
PMID:16314533   PMID:16452166   PMID:16556917   PMID:16602821   PMID:16818445   PMID:17029294   PMID:17135260   PMID:17453912   PMID:17662583   PMID:17881772   PMID:17950069   PMID:17960558  
PMID:18287559   PMID:18554416   PMID:18816857   PMID:19217425   PMID:19334288   PMID:19411759   PMID:19560165   PMID:20498044   PMID:20548288   PMID:20587693   PMID:20858856   PMID:20864640  
PMID:20944625   PMID:21041952   PMID:21252470   PMID:21266775   PMID:21267068   PMID:21268075   PMID:21308778   PMID:21352494   PMID:21386911   PMID:21511879   PMID:21512159   PMID:21606205  
PMID:21677750   PMID:21768377   PMID:21873635   PMID:21979435   PMID:22151329   PMID:22158707   PMID:22159717   PMID:22171010   PMID:22206015   PMID:22235340   PMID:22351047   PMID:22560297  
PMID:22573622   PMID:22682244   PMID:23273220   PMID:23377784   PMID:23630948   PMID:23658023   PMID:23907538   PMID:23921644   PMID:24006456   PMID:24192074   PMID:24626604   PMID:24820199  
PMID:24952961   PMID:24994653   PMID:25330296   PMID:25344368   PMID:25516967   PMID:25572963   PMID:25715398   PMID:25715693   PMID:25795282   PMID:26362633   PMID:26446156   PMID:26494538  
PMID:26821812   PMID:27249171   PMID:27249321   PMID:27265328   PMID:27527664   PMID:27648120   PMID:27665369   PMID:27746183   PMID:27770432   PMID:27856617   PMID:27870967   PMID:27939132  
PMID:28049691   PMID:28052872   PMID:28071719   PMID:28218627   PMID:28237967   PMID:28527294   PMID:28535371   PMID:28684544   PMID:28809397   PMID:29091295   PMID:29191093   PMID:29530978  
PMID:29551664   PMID:29618652   PMID:30550785   PMID:30566624   PMID:30635555   PMID:30670377   PMID:30738849   PMID:30936179   PMID:31056650   PMID:31319059   PMID:31624071   PMID:31634485  
PMID:31655293   PMID:31844321   PMID:32325033   PMID:32546759   PMID:32580935   PMID:32979396  


Genomics

Comparative Map Data
Col3a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39145,350,698 - 45,388,866 (+)NCBIGRCm39mm39
GRCm39 Ensembl145,350,698 - 45,388,866 (+)Ensembl
GRCm38145,311,538 - 45,349,706 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl145,311,538 - 45,349,706 (+)EnsemblGRCm38mm10GRCm38
MGSCv37145,368,383 - 45,406,551 (+)NCBIGRCm37mm9NCBIm37
MGSCv36145,256,192 - 45,293,566 (+)NCBImm8
Celera145,612,466 - 45,650,861 (+)NCBICelera
Cytogenetic Map1C1.1NCBI
cM Map123.67NCBI
COL3A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2188,974,373 - 189,012,746 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2188,974,320 - 189,012,746 (+)EnsemblGRCh38hg38GRCh38
GRCh382188,974,373 - 189,012,746 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372189,839,099 - 189,877,472 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362189,547,344 - 189,585,717 (+)NCBINCBI36hg18NCBI36
Build 342189,664,604 - 189,702,978NCBI
Celera2183,433,958 - 183,472,272 (+)NCBI
Cytogenetic Map2q32.2NCBI
HuRef2181,698,732 - 181,737,119 (+)NCBIHuRef
CHM1_12189,845,032 - 189,883,377 (+)NCBICHM1_1
Col3a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2947,374,611 - 47,410,547 (+)NCBI
Rnor_6.0 Ensembl952,023,295 - 52,059,217 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0952,023,295 - 52,059,221 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0951,689,492 - 51,725,418 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,281,582 - 44,317,831 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1944,310,161 - 44,319,243 (+)NCBI
Celera945,061,755 - 45,097,754 (+)NCBICelera
RH 3.4 Map9388.09RGD
Cytogenetic Map9q22NCBI
Col3a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554039,721,114 - 9,757,887 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554039,720,831 - 9,758,019 (-)NCBIChiLan1.0ChiLan1.0
COL3A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B194,204,613 - 194,242,956 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B194,204,613 - 194,242,956 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B76,285,115 - 76,322,703 (+)NCBIMhudiblu_PPA_v0panPan3
COL3A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13630,488,250 - 30,526,367 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3630,488,488 - 30,536,765 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3630,394,214 - 30,431,773 (+)NCBI
ROS_Cfam_1.03630,718,700 - 30,756,283 (+)NCBI
UMICH_Zoey_3.13630,779,325 - 30,816,837 (+)NCBI
UNSW_CanFamBas_1.03630,715,289 - 30,752,838 (+)NCBI
UU_Cfam_GSD_1.03630,884,313 - 30,921,873 (+)NCBI
Col3a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303147,914,117 - 147,951,851 (+)NCBI
SpeTri2.0NW_0049365068,886,494 - 8,923,921 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL3A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1593,556,912 - 93,615,815 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11593,556,914 - 93,595,678 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215104,067,018 - 104,105,776 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL3A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11074,455,133 - 74,493,392 (+)NCBI
Col3a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248991,192,078 - 1,230,528 (-)NCBI

Position Markers
AW550625  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38145,349,234 - 45,349,382UniSTSGRCm38
MGSCv37145,406,079 - 45,406,227UniSTSGRCm37
Celera145,650,389 - 45,650,537UniSTS
Cytogenetic Map1C1.1UniSTS
Whitehead/MRC_RH1735.59UniSTS
Ms10w  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38145,329,593 - 45,330,111UniSTSGRCm38
MGSCv37145,386,438 - 45,386,956UniSTSGRCm37
Celera145,630,520 - 45,631,038UniSTS
Cytogenetic Map1C1.1UniSTS
cM Map120.0UniSTS
Col3a1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38145,321,677 - 45,322,443UniSTSGRCm38
MGSCv37145,378,522 - 45,379,288UniSTSGRCm37
Celera145,622,604 - 45,623,370UniSTS
Cytogenetic Map1C1.1UniSTS
cM Map125.0UniSTS
GDB:181238  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38145,347,661 - 45,348,706UniSTSGRCm38
MGSCv37145,404,506 - 45,405,551UniSTSGRCm37
Celera145,648,816 - 45,649,861UniSTS
Cytogenetic Map1C1.1UniSTS
X57983  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38145,348,815 - 45,348,987UniSTSGRCm38
MGSCv37145,405,660 - 45,405,832UniSTSGRCm37
Celera145,649,970 - 45,650,142UniSTS
Cytogenetic Map1C1.1UniSTS
Whitehead_YAC12 UniSTS
Col3a1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38145,347,854 - 45,349,400UniSTSGRCm38
MGSCv37145,404,699 - 45,406,245UniSTSGRCm37
Celera145,649,009 - 45,650,555UniSTS
Cytogenetic Map1C1.1UniSTS
cM Map125.0UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13824984Twq5_mtestis weight QTL 5 (mouse)13000000185000000Mouse
1301240Sluc15_msusceptibility to lung cancer 15 (mouse)Not determined11902627053026373Mouse
1301073Orch5_mautoimmune orchitis resistance 5 (mouse)Not determined11902627053026373Mouse
1301756Pgia1_mproteoglycan induced arthritis 1 (mouse)Not determined11902627053026373Mouse
12880407V125Dq2_mvitamin D active form serum level QTL 2 (mouse)11930000053300000Mouse
1357475w3q13_mweight 3 weeks QTL 13 (mouse)Not determined12307051073937756Mouse
4142433Hbnr1_mHeligmosomoides bakeri nematode resistance 1 (mouse)Not determined2551111058234112Mouse
11100001Col4a1m1_mcollagen, type IV, alpha 1 modifier 1 (mouse)12551111062907723Mouse
12880409V125Dq1_mvitamin D active form serum level QTL 1 (mouse)12600000060000000Mouse
1357822Lvrq3_mliver weight QTL 3 (mouse)Not determined13472105773937756Mouse
1357759W3q12_mweight 3 weeks QTL 12 (mouse)Not determined13472105773937756Mouse
1357651Lgq5_mlate growth QTL 5 (mouse)Not determined13472105773937756Mouse
1357506W10q6_mweight 10 weeks QTL 6 (mouse)Not determined13472105773937756Mouse
1357524W6q14_mweight 6 weeks QTL 14 (mouse)Not determined13472105773937756Mouse
1357824Estoq4_membryo survival total QTL 4 (mouse)Not determined13472105773937756Mouse
39128207Lwq16_mliver weight QTL 16 (mouse)13472105773937756Mouse
1357753Kidq2_mkidney weight QTL 2 (mouse)Not determined134721057150318120Mouse
1357488Splq3_mspleen weight QTL 3 (mouse)Not determined134721057150318120Mouse
1558860W10q7_mweight 10 weeks QTL 7 (mouse)Not determined134721057150318120Mouse
1301954Lrnx11_mlearning-contextual 11 (mouse)Not determined13909372774477206Mouse
1357721Sle17_msystematic lupus erythematosus susceptibility 17 (mouse)Not determined139093727126517573Mouse
12910780Pwgrq11_mpost-weaning growth rate QTL 11 (mouse)14082884867231097Mouse
12910786Pwgrq10_mpost-weaning growth rate QTL 10 (mouse)14082884867231097Mouse
12910788Pwgrq9_mpost-weaning growth rate QTL 9 (mouse)14082884867231097Mouse
1301166Thypr2_mthymocyte proliferative response 2 (mouse)Not determined14123396575234112Mouse
18182931Metl1_mmetabolite locus 1, pyridoxate (mouse)14123624075236240Mouse
4141032Wbcc1_mwhite blood cell count 1 (mouse)Not determined4222050876220508Mouse
1301714Vertcling_mvertical clinging (mouse)Not determined14289887276899008Mouse
12050090Shm1_msperm head morphology 1 (mouse)14414774450777776Mouse
12879917Shm3_msperm head morphology 3 (mouse)14414774462907723Mouse

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir29ammu-miR-29a-3pMirtarbaseexternal_infoLuciferase reporter assay//Microarray//Northern blFunctional MTI18723672

Predicted Target Of
Summary Value
Count of predictions:404
Count of miRNA genes:306
Interacting mature miRNAs:343
Transcripts:ENSMUST00000087883, ENSMUST00000123204, ENSMUST00000129611
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_009930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC125167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH001863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ243638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ243639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ243640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ243641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ243642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ248239 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ248240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ248241 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ248242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ248243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK013329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK019448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK029212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK029451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK031544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK041115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK048546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK079113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK147542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK157762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK159763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK159868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK159920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK159985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK160048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK160107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK160818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK220558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC013626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC028248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC043089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC052398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BY139268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M18933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X52046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X57983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000087883   ⟹   ENSMUSP00000085192
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,311,538 - 45,349,706 (+)Ensembl
RefSeq Acc Id: ENSMUST00000123204
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,327,589 - 45,328,894 (+)Ensembl
RefSeq Acc Id: ENSMUST00000129611
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,311,538 - 45,325,018 (+)Ensembl
RefSeq Acc Id: ENSMUST00000185687   ⟹   ENSMUSP00000139894
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,335,766 - 45,340,674 (+)Ensembl
RefSeq Acc Id: ENSMUST00000186021   ⟹   ENSMUSP00000139802
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,339,958 - 45,347,766 (+)Ensembl
RefSeq Acc Id: ENSMUST00000189818
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,311,647 - 45,317,003 (+)Ensembl
RefSeq Acc Id: ENSMUST00000190943
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl145,334,200 - 45,337,297 (+)Ensembl
RefSeq Acc Id: NM_009930   ⟹   NP_034060
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39145,350,698 - 45,388,866 (+)NCBI
GRCm38145,311,538 - 45,349,706 (+)ENTREZGENE
MGSCv37145,368,383 - 45,406,551 (+)RGD
Celera145,612,466 - 45,650,861 (+)RGD
cM Map1 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_034060   ⟸   NM_009930
- Peptide Label: preproprotein
- UniProtKB: P08121 (UniProtKB/Swiss-Prot),   Q3TVI5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000139802   ⟸   ENSMUST00000186021
RefSeq Acc Id: ENSMUSP00000085192   ⟸   ENSMUST00000087883
RefSeq Acc Id: ENSMUSP00000139894   ⟸   ENSMUST00000185687
Protein Domains
Fibrillar collagen NC1   VWFC

Promoters
RGD ID:6873634
Promoter ID:EPDNEW_M268
Type:initiation region
Name:Col3a1_1
Description:Mus musculus collagen, type III, alpha 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38145,311,631 - 45,311,691EPDNEW
RGD ID:6817527
Promoter ID:MM_KWN:625
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   Kidney,   Lung,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000050577,   OTTMUST00000050578
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36145,367,726 - 45,368,872 (+)MPROMDB
RGD ID:6849506
Promoter ID:EP25040
Type:single initiation site
Name:MM_CA13
Description:alpha 1 type III collagen, COL3A1 gene.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Notes:homology_group=Homology group 142; Mammalian alpha 1 type III collagen
Tissues & Cell Lines:fibroblasts
Experiment Methods:Primer extension with homologous sequence ladder; Nuclease protection with homologous sequence ladder; experiments; performed with closely related gene
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv37145,368,476 - 45,368,536EPD
MGSCv36145,368,476 - 45,368,536EPD
RGD ID:6817530
Promoter ID:MM_KWN:626
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000050579
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36145,383,466 - 45,384,867 (+)MPROMDB
RGD ID:6848551
Promoter ID:MM_TRO:146
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   MEF_B4,   MEF_B6
Transcripts:MTR011714.1.626.7
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36145,402,531 - 45,403,031 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:88453 AgrOrtholog
Ensembl Genes ENSMUSG00000026043 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000085192 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000139802 UniProtKB/TrEMBL
  ENSMUSP00000139894 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000087883 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000185687 UniProtKB/TrEMBL
  ENSMUST00000186021 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12825 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:88453 ENTREZGENE
NCBI Gene 12825 ENTREZGENE
Pfam COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Col3a1 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWFC_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWFC_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WPJ5_MOUSE UniProtKB/TrEMBL
  A0A087WPS3_MOUSE UniProtKB/TrEMBL
  CO3A1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q3TVI5 ENTREZGENE, UniProtKB/TrEMBL
  Q3TW25_MOUSE UniProtKB/TrEMBL
  Q3UH72_MOUSE UniProtKB/TrEMBL
  Q5DTG2_MOUSE UniProtKB/TrEMBL
  Q7TT32_MOUSE UniProtKB/TrEMBL
  Q8BJU6_MOUSE UniProtKB/TrEMBL
  Q8BKY2_MOUSE UniProtKB/TrEMBL
  Q8BLW4_MOUSE UniProtKB/TrEMBL
  Q8BMR6_MOUSE UniProtKB/TrEMBL
  Q8K173_MOUSE UniProtKB/TrEMBL
  Q9CSB7_MOUSE UniProtKB/TrEMBL
UniProt Secondary Q61429 UniProtKB/Swiss-Prot
  Q9CRN7 UniProtKB/Swiss-Prot