Col4a1 (collagen, type IV, alpha 1) - Rat Genome Database

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Gene: Col4a1 (collagen, type IV, alpha 1) Mus musculus
Analyze
Symbol: Col4a1
Name: collagen, type IV, alpha 1
RGD ID: 1316171
MGI Page MGI
Description: Predicted to enable platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within cellular response to amino acid stimulus; collagen-activated tyrosine kinase receptor signaling pathway; and neuromuscular junction development. Located in basement membrane. Part of collagen type IV trimer. Is expressed in several structures, including alimentary system; brain; egg cylinder; genitourinary system; and sensory organ. Used to study Walker-Warburg syndrome; brain small vessel disease 1; kidney disease; and porencephaly. Human ortholog(s) of this gene implicated in brain small vessel disease 1; myocardial infarction; and retinal arterial tortuosity. Orthologous to human COL4A1 (collagen type IV alpha 1 chain).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: alpha-1 type IV collagen; alpha1(IV) collagen; Br; Bru; Col4; Col4a-1; collagen alpha-1(IV) chain; Del(8)44; Del(8)44H; Del(8)Bru44H; procollagen, type IV, alpha 1; R; Raw; retinal anterior wiring; S; Svc
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39811,248,423 - 11,362,889 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl811,248,423 - 11,362,826 (-)EnsemblGRCm39 Ensembl
GRCm38811,198,423 - 11,312,889 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,198,423 - 11,312,826 (-)EnsemblGRCm38mm10GRCm38
MGSCv37811,198,423 - 11,312,826 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36811,198,403 - 11,312,702 (-)NCBIMGSCv36mm8
Celera811,372,057 - 11,487,438 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.53NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (EXP)
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2-butoxyethanol  (EXP)
2-methylcholine  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
6alpha-methylprednisolone  (ISO)
8'-apo-beta,psi-caroten-8'-al  (ISO)
acetaldehyde  (ISO)
acetamide  (ISO)
acrylamide  (ISO)
adefovir pivoxil  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
aldosterone  (ISO)
all-trans-retinoic acid  (EXP,ISO)
AM-251  (ISO)
ammonium chloride  (ISO)
amphetamine  (ISO)
antimycin A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benazepril  (ISO)
benidipine  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
beta-carotene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
busulfan  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calciol  (EXP)
cannabidiol  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP,ISO)
chlordecone  (EXP)
chloroacetaldehyde  (ISO)
chlorpromazine  (ISO)
choline  (EXP)
cidofovir anhydrous  (ISO)
ciglitazone  (ISO)
cisplatin  (EXP,ISO)
clofibric acid  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
CU-O LINKAGE  (ISO)
curcumin  (EXP,ISO)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
DDT  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (EXP)
dibenz[a,h]anthracene  (EXP)
dibutyl phthalate  (EXP,ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
enalapril  (ISO)
endosulfan  (ISO)
eplerenone  (ISO)
ethanol  (EXP)
etoposide  (EXP)
fenofibrate  (EXP)
fenthion  (EXP)
fipronil  (ISO)
folic acid  (EXP,ISO)
folpet  (EXP)
fulvestrant  (ISO)
furan  (ISO)
glafenine  (ISO)
glucose  (EXP,ISO)
griseofulvin  (EXP)
hydroquinone  (ISO)
ivermectin  (ISO)
L-methionine  (EXP)
lead diacetate  (ISO)
lipopolysaccharide  (EXP,ISO)
losartan  (ISO)
LY294002  (EXP)
mangiferin  (ISO)
metformin  (EXP)
methapyrilene  (ISO)
methidathion  (EXP)
methylmercury chloride  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (ISO)
ozone  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
PCB138  (ISO)
pentane-2,3-dione  (ISO)
perfluorobutyric acid  (EXP)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirfenidone  (EXP)
pirinixic acid  (EXP)
potassium chromate  (ISO)
progesterone  (ISO)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
serpentine asbestos  (EXP)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP)
sodium arsenite  (EXP,ISO)
Soman  (ISO)
sorafenib  (ISO)
streptozocin  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (EXP)
tebufenpyrad  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
thioacetamide  (ISO)
thymoquinone  (EXP)
titanium dioxide  (EXP)
toluene  (ISO)
topotecan  (ISO)
trichostatin A  (EXP)
trimellitic anhydride  (EXP)
triphenyl phosphate  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vancomycin  (EXP)
vinclozolin  (ISO)
vitamin E  (ISO)
Y-27632  (ISO)
zoledronic acid  (EXP)

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

Mammalian Phenotype
abnormal basement membrane morphology  (IAGP)
abnormal blood vessel morphology  (IAGP)
abnormal brain morphology  (IAGP)
abnormal brain pia mater morphology  (IAGP)
abnormal cerebral cortex morphology  (IAGP)
abnormal cornea morphology  (IAGP)
abnormal eye morphology  (IAGP)
abnormal glomerular capsule parietal layer morphology  (IAGP)
abnormal glomerular mesangium morphology  (IAGP)
abnormal hippocampus morphology  (IAGP)
abnormal iris morphology  (IEA)
abnormal kidney collecting duct epithelium morphology  (IAGP)
abnormal kidney collecting duct morphology  (IAGP)
abnormal kidney morphology  (IAGP)
abnormal kidney papilla morphology  (IAGP)
abnormal kidney physiology  (IAGP)
abnormal lens capsule morphology  (IAGP)
abnormal lens morphology  (IAGP)
abnormal parietal endoderm morphology  (IAGP)
abnormal podocyte foot process morphology  (IAGP)
abnormal podocyte morphology  (IAGP)
abnormal podocyte slit diaphragm morphology  (IAGP)
abnormal proximal convoluted tubule morphology  (IAGP)
abnormal Reichert's membrane morphology  (IAGP)
abnormal renal glomerular capsule morphology  (IAGP)
abnormal renal glomerulus basement membrane morphology  (IAGP)
abnormal renal glomerulus morphology  (IAGP)
abnormal retina blood vessel pattern  (IAGP)
abnormal retina ganglion cell morphology  (IAGP)
abnormal retina inner limiting membrane morphology  (IAGP)
abnormal retina morphology  (IAGP)
abnormal retina neuronal layer morphology  (IAGP)
abnormal retina vasculature morphology  (IAGP)
abnormal urine albumin level  (IAGP)
albuminuria  (IAGP)
anemia  (IEA)
anterior iris synechia  (IAGP)
anterior polar cataract  (IAGP)
anterior subcapsular cataract  (IAGP)
astrocytosis  (IAGP)
brain lesion  (IAGP)
bruising  (IAGP)
buphthalmos  (IAGP)
cataract  (IAGP)
corneal opacity  (IAGP)
corneal vascularization  (IAGP)
cyanosis  (IAGP)
decreased body size  (IAGP)
decreased body weight  (IAGP)
decreased collagen level  (IAGP)
decreased erythrocyte cell number  (IAGP)
decreased grip strength  (IAGP)
decreased hematocrit  (IAGP)
decreased hemoglobin content  (IAGP)
decreased urine osmolality  (IAGP)
delaminated cerebral cortex  (IAGP)
delayed kidney development  (IAGP)
dilated glomerular capillary  (IAGP)
dilated kidney collecting duct  (IAGP)
dilated proximal convoluted tubule  (IAGP)
dystrophic muscle  (IAGP)
embryonic lethality, complete penetrance  (IAGP)
enlarged brain ventricles  (IAGP)
erythrocyturia  (IAGP)
eye hemorrhage  (IAGP)
hematuria  (IAGP)
increased blood urea nitrogen level  (IAGP)
increased circulating creatine kinase level  (IAGP)
increased glomerular capsule space  (IAGP)
increased urine microalbumin level  (IAGP)
infertility  (IEA)
intracerebral hemorrhage  (IAGP)
intracranial hemorrhage  (IAGP)
irregularly shaped pupil  (IAGP)
kidney inflammation  (IAGP)
lethality throughout fetal growth and development, complete penetrance  (IAGP)
microphthalmia  (IAGP)
myopathy  (IAGP)
optic nerve hypoplasia  (IAGP)
parietal capsular epithelium metaplasia  (IAGP)
perinatal lethality, incomplete penetrance  (IAGP)
podocyte foot process effacement  (IAGP)
polyuria  (IAGP)
postnatal lethality, incomplete penetrance  (IEA)
premature death  (IAGP)
prenatal lethality, complete penetrance  (IEA)
prenatal lethality, incomplete penetrance  (IAGP)
reduced fertility  (IAGP)
renal cast  (IAGP)
renal glomerulus cyst  (IAGP)
respiratory distress  (IAGP)
seizures  (IAGP)
subarachnoid hemorrhage  (IAGP)
sutural cataract  (IAGP)
total cataract  (IAGP)
vacuolated lens  (IAGP)
vitreal fibroplasia  (IAGP)
weakness  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Role of COL4A1 in small-vessel disease and hemorrhagic stroke. Gould DB, etal., N Engl J Med. 2006 Apr 6;354(14):1489-96.
2. A possible role of thioredoxin interacting protein in the pathogenesis of streptozotocin-induced diabetic nephropathy. Hamada Y and Fukagawa M, Kobe J Med Sci. 2007;53(1-2):53-61.
3. Antibody blockade of c-fms suppresses the progression of inflammation and injury in early diabetic nephropathy in obese db/db mice. Lim AK, etal., Diabetologia. 2009 May 23.
4. MGDs mouse GO annotations MGD data from the GO Consortium
5. MGD IEA MGD IEA
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9. Mouse MP Annotation Import Pipeline RGD automated import pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Neonatal porencephaly and adult stroke related to mutations in collagen IV A1. van der Knaap MS, etal., Ann Neurol. 2006 Mar;59(3):504-11.
13. Effects of angiotensin II intervention on MMP-2, MMP-9, TIMP-1, and collagen expression in rats with pulmonary hypertension. Wang XM, etal., Genet Mol Res. 2015 Mar 6;14(1):1707-17. doi: 10.4238/2015.March.6.17.
14. Complex patterns of expression suggest extensive roles for the alpha 2 beta 1 integrin in murine development. Wu JE and Santoro SA, Dev Dyn 1994 Apr;199(4):292-314.
15. Genetic risk for myocardial infarction determined by polymorphisms of candidate genes in a Japanese population. Yamada Y, etal., J Med Genet. 2008 Apr;45(4):216-21. Epub 2007 Dec 12.
Additional References at PubMed
PMID:1383086   PMID:1630813   PMID:2436975   PMID:2578961   PMID:2703490   PMID:2842328   PMID:3009468   PMID:3198626   PMID:3200851   PMID:3338568   PMID:3352637   PMID:3379041  
PMID:3597383   PMID:3724777   PMID:3755692   PMID:3821762   PMID:6312413   PMID:7516699   PMID:7579895   PMID:7613031   PMID:7678834   PMID:8105479   PMID:8153091   PMID:8359228  
PMID:8562707   PMID:8725284   PMID:8760252   PMID:8812145   PMID:8900172   PMID:8918877   PMID:8922394   PMID:9013772   PMID:9096311   PMID:9160753   PMID:9175728   PMID:9264260  
PMID:9287114   PMID:9382709   PMID:9390635   PMID:9415455   PMID:9524110   PMID:9731539   PMID:9808783   PMID:9826522   PMID:9833687   PMID:9892176   PMID:10051567   PMID:10087208  
PMID:10349636   PMID:10534397   PMID:10625553   PMID:10639489   PMID:10700190   PMID:10706142   PMID:10716744   PMID:10716993   PMID:10880400   PMID:10886015   PMID:10922068   PMID:10970885  
PMID:11042159   PMID:11076861   PMID:11217851   PMID:11511678   PMID:11516395   PMID:11732842   PMID:11784073   PMID:11929848   PMID:11970952   PMID:12011424   PMID:12101409   PMID:12225806  
PMID:12466851   PMID:12477932   PMID:12571105   PMID:14595844   PMID:14610273   PMID:14681479   PMID:14998921   PMID:15102706   PMID:15377789   PMID:15489334   PMID:15689378   PMID:15837576  
PMID:15878328   PMID:15895400   PMID:15905400   PMID:16024816   PMID:16041630   PMID:16100707   PMID:16141072   PMID:16141073   PMID:16159887   PMID:16192629   PMID:16498405   PMID:16565260  
PMID:16875435   PMID:16880404   PMID:17179069   PMID:17317786   PMID:17418794   PMID:17506979   PMID:17881772   PMID:17986615   PMID:18083160   PMID:18356808   PMID:18606782   PMID:18694874  
PMID:18757743   PMID:19275937   PMID:19373938   PMID:19521566   PMID:19858219   PMID:19924818   PMID:20056676   PMID:20091789   PMID:20522651   PMID:20548288   PMID:20687112   PMID:20858856  
PMID:21203896   PMID:21267068   PMID:21298098   PMID:21423341   PMID:21606205   PMID:21625620   PMID:21873635   PMID:21880836   PMID:22159717   PMID:22171010   PMID:22209247   PMID:22274697  
PMID:22535408   PMID:22613833   PMID:22643896   PMID:22925884   PMID:23100420   PMID:23237810   PMID:23273220   PMID:23325811   PMID:23658023   PMID:24000064   PMID:24006456   PMID:24176640  
PMID:24203695   PMID:24335256   PMID:24457600   PMID:24952961   PMID:24983472   PMID:25354942   PMID:25572963   PMID:25686533   PMID:25753534   PMID:26027930   PMID:26120030   PMID:26260163  
PMID:26494538   PMID:26567795   PMID:26794322   PMID:26813606   PMID:26839400   PMID:26872874   PMID:26943318   PMID:27068110   PMID:27371534   PMID:27412481   PMID:27435625   PMID:27575556  
PMID:27619726   PMID:27648120   PMID:27687499   PMID:27856617   PMID:27899284   PMID:27915093   PMID:28056338   PMID:28057519   PMID:28071719   PMID:28164238   PMID:28237965   PMID:28535372  
PMID:28929539   PMID:29266233   PMID:29380551   PMID:29422532   PMID:29456135   PMID:29491144   PMID:29665133   PMID:29884675   PMID:29895609   PMID:30135482   PMID:30351356   PMID:31051113  
PMID:31171666   PMID:31331924   PMID:32020708   PMID:32049039   PMID:32109382   PMID:32183562   PMID:32290105   PMID:32325033   PMID:32433954   PMID:32496646   PMID:32580934   PMID:32882513  
PMID:33580754   PMID:33722606   PMID:34032267   PMID:34133940   PMID:34189436   PMID:34274976   PMID:34323105   PMID:34424299   PMID:34699385   PMID:34815802   PMID:34908109   PMID:34927678  
PMID:35089129   PMID:35358427   PMID:35525525   PMID:35927244   PMID:36350252  


Genomics

Comparative Map Data
Col4a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39811,248,423 - 11,362,889 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl811,248,423 - 11,362,826 (-)EnsemblGRCm39 Ensembl
GRCm38811,198,423 - 11,312,889 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,198,423 - 11,312,826 (-)EnsemblGRCm38mm10GRCm38
MGSCv37811,198,423 - 11,312,826 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36811,198,403 - 11,312,702 (-)NCBIMGSCv36mm8
Celera811,372,057 - 11,487,438 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.53NCBI
COL4A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813110,148,963 - 110,307,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl13110,148,963 - 110,307,157 (-)EnsemblGRCh38hg38GRCh38
GRCh3713110,801,310 - 110,959,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613109,599,311 - 109,757,497 (-)NCBINCBI36Build 36hg18NCBI36
Build 3413109,599,311 - 109,757,459NCBI
Celera1391,645,588 - 91,803,669 (-)NCBICelera
Cytogenetic Map13q34NCBI
HuRef1391,400,456 - 91,558,957 (-)NCBIHuRef
CHM1_113110,770,028 - 110,927,927 (-)NCBICHM1_1
T2T-CHM13v2.013109,377,773 - 109,536,621 (-)NCBIT2T-CHM13v2.0
Col4a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21678,183,533 - 78,294,412 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1678,183,533 - 78,294,412 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1683,463,953 - 83,574,826 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01686,916,625 - 87,027,510 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01682,157,396 - 82,268,610 (+)NCBIRnor_WKY
Rnor_6.01683,522,162 - 83,632,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,522,162 - 83,632,153 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01682,987,857 - 83,097,435 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41683,045,183 - 83,157,835 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11683,031,106 - 83,143,679 (+)NCBI
Celera1675,981,231 - 76,092,476 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
Col4a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554042,260,029 - 2,326,074 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554042,196,193 - 2,327,324 (+)NCBIChiLan1.0ChiLan1.0
COL4A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113110,407,009 - 110,562,529 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13110,407,009 - 110,562,529 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01391,282,617 - 91,440,187 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
COL4A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12258,511,210 - 58,651,949 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2258,512,212 - 58,588,666 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2258,264,155 - 58,360,735 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02259,132,853 - 59,274,724 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2259,133,398 - 59,274,709 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12258,634,288 - 58,774,752 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02258,625,802 - 58,767,327 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02258,660,825 - 58,801,735 (-)NCBIUU_Cfam_GSD_1.0
Col4a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945193,408,026 - 193,536,112 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364722,416,566 - 2,542,814 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049364722,416,043 - 2,543,561 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1176,858,356 - 76,997,322 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11176,858,332 - 76,997,409 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21184,372,388 - 84,460,293 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL4A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1388,410,800 - 88,564,191 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl388,412,168 - 88,564,057 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604645,126,545 - 45,280,009 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col4a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247932,325,128 - 2,426,817 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247932,325,104 - 2,426,814 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:770
Count of miRNA genes:481
Interacting mature miRNAs:580
Transcripts:ENSMUST00000033898, ENSMUST00000130488
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13432571Scvg1_msubcutaneous vessel growth QTL 1 (mouse)8124751082Mouse
11533914Mts5_mmammary tumor susceptibility 5 (mouse)8130447432Mouse
4140978Nilac5_mnicotine induced locomotor activity 5 (mouse)Not determined8131773288Mouse
27226756Femd2_mfemur midshaft diameter 2, 5 week (mouse)8495000035067154Mouse
1357525Pnhdlc3_mplasma non-HDL cholesterol 3 (mouse)Not determined8721249923753815Mouse
1301532Scc8_mcolon tumor susceptibility 8 (mouse)Not determined8721249935110107Mouse
1300906Ap8q_malcohol preference 8 QTL (mouse)Not determined8798418941984342Mouse
10412209Cypr7_mcytokine production 7 (mouse)Not determined8810320142103372Mouse
1301929Eae24_msusceptibility to experimental allergic encephalomyelitis 24 (mouse)Not determined8810320142103372Mouse
1301128Sluc20_msusceptibility to lung cancer 20 (mouse)Not determined8810320142103372Mouse
14700791Mencq6_mmeniscus calcification QTL 6 (mouse)81102200012200000Mouse
14697703Stsl1_mSalmonella typhimurium susceptibility locus 1 (mouse)81135000017050016Mouse

Markers in Region
Col4a1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8A1.1UniSTS
cM Map85.0UniSTS
RH128563  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38811,198,748 - 11,198,937UniSTSGRCm38
MGSCv37811,198,748 - 11,198,937UniSTSGRCm37
Celera811,372,382 - 11,372,571UniSTS
Cytogenetic Map8A1.1UniSTS
J04694  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38811,199,253 - 11,199,384UniSTSGRCm38
MGSCv37811,199,253 - 11,199,384UniSTSGRCm37
Celera811,372,887 - 11,373,018UniSTS
Cytogenetic Map8A1.1UniSTS
Whitehead/MRC_RH8137.91UniSTS
D0Nds29  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38811,199,100 - 11,199,218UniSTSGRCm38
MGSCv37811,199,100 - 11,199,218UniSTSGRCm37
Celera811,372,734 - 11,372,852UniSTS
Cytogenetic Map8A1.1UniSTS
cM MapUN UniSTS
cM Map8 UniSTS
Col4a1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8A1.1UniSTS
cM Map85.0UniSTS
Col4a1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8A1.1UniSTS
Col4a1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8A1.1UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_009931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_133670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004934755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC114598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC115800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH001864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK142097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK146487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK147284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK147355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK147661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK159130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC002269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC056620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC072650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BY303228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CJ108618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CJ248638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J03758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J03944 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M14042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M15832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X02201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X92439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000033898   ⟹   ENSMUSP00000033898
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,248,423 - 11,362,826 (-)Ensembl
GRCm38.p6 Ensembl811,198,423 - 11,312,826 (-)Ensembl
RefSeq Acc Id: ENSMUST00000130488
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,262,401 - 11,267,269 (-)Ensembl
GRCm38.p6 Ensembl811,212,401 - 11,217,269 (-)Ensembl
RefSeq Acc Id: ENSMUST00000208095   ⟹   ENSMUSP00000146554
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,294,363 - 11,329,656 (-)Ensembl
GRCm38.p6 Ensembl811,244,363 - 11,279,656 (-)Ensembl
RefSeq Acc Id: ENSMUST00000208386
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,276,953 - 11,282,439 (-)Ensembl
GRCm38.p6 Ensembl811,226,953 - 11,232,439 (-)Ensembl
RefSeq Acc Id: ENSMUST00000209000
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,295,002 - 11,295,605 (-)Ensembl
GRCm38.p6 Ensembl811,245,002 - 11,245,605 (-)Ensembl
RefSeq Acc Id: ENSMUST00000209598   ⟹   ENSMUSP00000147459
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,249,519 - 11,260,831 (-)Ensembl
GRCm38.p6 Ensembl811,199,519 - 11,210,831 (-)Ensembl
RefSeq Acc Id: ENSMUST00000209661   ⟹   ENSMUSP00000148226
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,268,035 - 11,291,148 (-)Ensembl
GRCm38.p6 Ensembl811,218,035 - 11,241,148 (-)Ensembl
RefSeq Acc Id: ENSMUST00000209735   ⟹   ENSMUSP00000147951
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl811,248,431 - 11,362,689 (-)Ensembl
GRCm38.p6 Ensembl811,198,431 - 11,312,689 (-)Ensembl
RefSeq Acc Id: NM_009931   ⟹   NP_034061
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39811,248,423 - 11,362,826 (-)NCBI
GRCm38811,198,423 - 11,312,826 (-)ENTREZGENE
MGSCv37811,198,423 - 11,312,826 (-)RGD
Celera811,372,057 - 11,487,438 (-)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_133670
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39811,248,423 - 11,362,826 (-)NCBI
GRCm38811,198,423 - 11,312,826 (-)NCBI
Sequence:
RefSeq Acc Id: XR_004934755
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39811,248,430 - 11,362,889 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_034061   ⟸   NM_009931
- Peptide Label: precursor
- UniProtKB: Q99LQ8 (UniProtKB/Swiss-Prot),   P02463 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000033898   ⟸   ENSMUST00000033898
RefSeq Acc Id: ENSMUSP00000146554   ⟸   ENSMUST00000208095
RefSeq Acc Id: ENSMUSP00000147951   ⟸   ENSMUST00000209735
RefSeq Acc Id: ENSMUSP00000148226   ⟸   ENSMUST00000209661
RefSeq Acc Id: ENSMUSP00000147459   ⟸   ENSMUST00000209598
Protein Domains
Collagen IV NC1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02463-F1-model_v2 AlphaFold P02463 1-1669 view protein structure

Promoters
RGD ID:6848879
Promoter ID:MM_TRO:9304
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day2,   3T3L1_Day3
Transcripts:MTR028813.8.147.10
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36811,199,439 - 11,199,939 (-)MPROMDB
RGD ID:6848880
Promoter ID:MM_TRO:9305
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   MEF_B6
Transcripts:MTR028813.8.147.9
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36811,201,474 - 11,201,974 (-)MPROMDB
RGD ID:6842957
Promoter ID:MM_KWN:53610
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   Lung,   MEF_B6,   Spleen
Transcripts:OTTMUST00000050537
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36811,216,391 - 11,217,632 (-)MPROMDB
RGD ID:8666419
Promoter ID:EPDNEW_M11241
Type:single initiation site
Name:Col4a1_2
Description:Mus musculus collagen, type IV, alpha 1 , transcript variant1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M11242  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38811,307,347 - 11,307,407EPDNEW
RGD ID:6842959
Promoter ID:MM_KWN:53611
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   Brain,   Lung,   MEF_B4,   MEF_B6
Transcripts:NM_009931
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36811,312,621 - 11,313,792 (-)MPROMDB
RGD ID:8666421
Promoter ID:EPDNEW_M11242
Type:initiation region
Name:Col4a1_1
Description:Mus musculus collagen, type IV, alpha 1 , transcript variant1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M11241  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38811,312,749 - 11,312,809EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:88454 AgrOrtholog
Ensembl Genes ENSMUSG00000031502 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000033898 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000146554.2 UniProtKB/TrEMBL
  ENSMUSP00000147459.2 UniProtKB/TrEMBL
  ENSMUSP00000147951.2 UniProtKB/TrEMBL
  ENSMUSP00000148226.2 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000033898 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000208095.2 UniProtKB/TrEMBL
  ENSMUST00000209598.2 UniProtKB/TrEMBL
  ENSMUST00000209661.2 UniProtKB/TrEMBL
  ENSMUST00000209735 ENTREZGENE
  ENSMUST00000209735.2 UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen_IV_NC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12826 UniProtKB/Swiss-Prot
MGD MGI:88454 ENTREZGENE
NCBI Gene 12826 ENTREZGENE
Pfam Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF01413 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Col4a1 PhenoGen
PROSITE NC1_IV UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00111 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140LHU8_MOUSE UniProtKB/TrEMBL
  A0A1B0GRC0_MOUSE UniProtKB/TrEMBL
  A0A1B0GSI7_MOUSE UniProtKB/TrEMBL
  A0A1B0GT69_MOUSE UniProtKB/TrEMBL
  CO4A1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q99LQ8 ENTREZGENE
UniProt Secondary Q3UHJ4 UniProtKB/Swiss-Prot
  Q3UJE7 UniProtKB/Swiss-Prot
  Q3UQV2 UniProtKB/Swiss-Prot
  Q53X35 UniProtKB/Swiss-Prot
  Q6GQS7 UniProtKB/Swiss-Prot
  Q6PHB5 UniProtKB/Swiss-Prot
  Q99LQ8 UniProtKB/Swiss-Prot