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

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Gene: Col4a1 (collagen type IV alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col4a1
Name: collagen type IV alpha 1 chain
RGD ID: 1307148
Description: Predicted to enable platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in epithelial cell differentiation. Predicted to be located in basement membrane. Predicted to be part of collagen type IV trimer. Predicted to be active in extracellular matrix. Biomarker of obesity and pulmonary hypertension. Human ortholog(s) of this gene implicated in brain small vessel disease 1; myocardial infarction; retinal arterial tortuosity; and uterine fibroid. Orthologous to human COL4A1 (collagen type IV alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile; 1-naphthyl isothiocyanate; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alpha 1 type IV collagen; collagen alpha-1(IV) chain; collagen, type IV, alpha 1; LOC290905; procollagen, type IV, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81684,885,597 - 84,996,482 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1684,885,597 - 84,996,482 (+)EnsemblGRCr8
mRatBN7.21678,183,533 - 78,294,412 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1678,183,533 - 78,294,412 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1683,463,953 - 83,574,826 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01686,916,625 - 87,027,510 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01682,157,396 - 82,268,610 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01683,522,162 - 83,632,153 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,522,162 - 83,632,153 (+)Ensemblrn6Rnor6.0
Rnor_5.01682,987,857 - 83,097,435 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41683,045,183 - 83,157,835 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1675,981,231 - 76,092,476 (+)NCBICelera
RGSC_v3.11683,031,106 - 83,143,679 (+)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




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

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Type I collagen gel modulates extracellular matrix synthesis and deposition by tracheal epithelial cells. Davenport EA and Nettesheim P, Exp Cell Res. 1996 Feb 25;223(1):155-62.
2. High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy. Dower K, etal., PLoS One. 2017 Jul 26;12(7):e0181861. doi: 10.1371/journal.pone.0181861. eCollection 2017.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Role of COL4A1 in small-vessel disease and hemorrhagic stroke. Gould DB, etal., N Engl J Med. 2006 Apr 6;354(14):1489-96.
6. 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.
7. 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.
8. Genome-wide DNA methylation analysis reveals a potential mechanism for the pathogenesis and development of uterine leiomyomas. Maekawa R, etal., PLoS One. 2013 Jun 20;8(6):e66632. doi: 10.1371/journal.pone.0066632. Print 2013.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
12. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Comprehensive gene review and curation RGD comprehensive gene curation
17. 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.
18. 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.
19. 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:8900172   PMID:8950183   PMID:10970885   PMID:11511678   PMID:11732842   PMID:12101409   PMID:12477932   PMID:15895400   PMID:16041630   PMID:16107487   PMID:17418794   PMID:18160688  
PMID:18757743   PMID:19794980   PMID:19949034   PMID:20548288   PMID:20818663   PMID:23065703   PMID:23658023   PMID:23979707   PMID:24006456   PMID:27068509   PMID:27530924   PMID:27559042  
PMID:31480394   PMID:36281728  


Genomics

Comparative Map Data
Col4a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81684,885,597 - 84,996,482 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1684,885,597 - 84,996,482 (+)EnsemblGRCr8
mRatBN7.21678,183,533 - 78,294,412 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1678,183,533 - 78,294,412 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1683,463,953 - 83,574,826 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01686,916,625 - 87,027,510 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01682,157,396 - 82,268,610 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01683,522,162 - 83,632,153 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,522,162 - 83,632,153 (+)Ensemblrn6Rnor6.0
Rnor_5.01682,987,857 - 83,097,435 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41683,045,183 - 83,157,835 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1675,981,231 - 76,092,476 (+)NCBICelera
RGSC_v3.11683,031,106 - 83,143,679 (+)NCBI
Cytogenetic Map16q12.5NCBI
COL4A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813110,148,963 - 110,307,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13110,148,963 - 110,307,202 (-)Ensemblhg38GRCh38
GRCh3713110,801,310 - 110,959,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613109,599,311 - 109,757,497 (-)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm38811,198,423 - 11,312,889 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,198,423 - 11,312,826 (-)Ensemblmm10GRCm38
MGSCv37811,198,423 - 11,312,826 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36811,198,403 - 11,312,702 (-)NCBIMGSCv36mm8
Celera811,372,057 - 11,487,438 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.53NCBI
Col4a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554042,260,029 - 2,326,074 (+)Ensembl
ChiLan1.0NW_0049554042,196,193 - 2,327,324 (+)NCBIChiLan1.0ChiLan1.0
COL4A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214111,642,358 - 111,800,305 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113110,324,917 - 110,482,747 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01391,282,617 - 91,440,187 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113110,407,009 - 110,562,529 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13110,407,009 - 110,562,529 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2258,264,155 - 58,360,735 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02259,132,853 - 59,274,724 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 Ensembl
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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247932,325,104 - 2,426,814 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Col4a1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11372,545,321 - 72,655,537 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:112
Interacting mature miRNAs:118
Transcripts:ENSRNOT00000057386
Prediction methods:Miranda
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat

Markers in Region
D13S1449  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81684,995,185 - 84,995,287 (+)Marker Load Pipeline
mRatBN7.21678,293,115 - 78,293,216 (+)MAPPERmRatBN7.2
Rnor_6.01683,630,857 - 83,630,957NCBIRnor6.0
Rnor_5.01683,096,139 - 83,096,239UniSTSRnor5.0
RGSC_v3.41683,156,539 - 83,156,639UniSTSRGSC3.4
Celera1676,091,180 - 76,091,280UniSTS
Cytogenetic Map16q12.5UniSTS
D16Nds29  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21678,293,623 - 78,293,735 (+)MAPPERmRatBN7.2
Rnor_6.01683,631,365 - 83,631,476NCBIRnor6.0
Rnor_5.01683,096,647 - 83,096,758UniSTSRnor5.0
RGSC_v3.41683,157,047 - 83,157,158UniSTSRGSC3.4
Celera1676,091,688 - 76,091,799UniSTS
Cytogenetic Map16q12.5UniSTS
RH128563  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21678,293,891 - 78,294,076 (+)MAPPERmRatBN7.2
Rnor_6.01683,631,633 - 83,631,817NCBIRnor6.0
Rnor_5.01683,096,915 - 83,097,099UniSTSRnor5.0
RGSC_v3.41683,157,315 - 83,157,499UniSTSRGSC3.4
Celera1676,091,956 - 76,092,140UniSTS
Cytogenetic Map16q12.5UniSTS
RH129454  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21678,293,113 - 78,293,293 (+)MAPPERmRatBN7.2
Rnor_6.01683,630,855 - 83,631,034NCBIRnor6.0
Rnor_5.01683,096,137 - 83,096,316UniSTSRnor5.0
RGSC_v3.41683,156,537 - 83,156,716UniSTSRGSC3.4
Celera1676,091,178 - 76,091,357UniSTS
RH 3.4 Map16760.3UniSTS
Cytogenetic Map16q12.5UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 74 59 6 338 174 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000057386   ⟹   ENSRNOP00000054197
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1684,885,597 - 84,996,482 (+)Ensembl
mRatBN7.2 Ensembl1678,183,533 - 78,294,412 (+)Ensembl
Rnor_6.0 Ensembl1683,522,162 - 83,632,153 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114480   ⟹   ENSRNOP00000091137
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1684,885,597 - 84,992,248 (+)Ensembl
mRatBN7.2 Ensembl1678,183,533 - 78,293,330 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000125691   ⟹   ENSRNOP00000110576
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1684,885,597 - 84,996,482 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000161095   ⟹   ENSRNOP00000102947
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1684,885,597 - 84,996,482 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000173991   ⟹   ENSRNOP00000101670
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1684,885,597 - 84,996,482 (+)Ensembl
RefSeq Acc Id: NM_001135009   ⟹   NP_001128481
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81684,885,597 - 84,996,482 (+)NCBI
mRatBN7.21678,183,533 - 78,294,412 (+)NCBI
Rnor_6.01683,522,162 - 83,632,153 (+)NCBI
Rnor_5.01682,987,857 - 83,097,435 (+)NCBI
RGSC_v3.41683,045,183 - 83,157,835 (+)RGD
Celera1675,981,231 - 76,092,476 (+)RGD
Sequence:
RefSeq Acc Id: NP_001128481   ⟸   NM_001135009
- Peptide Label: precursor
- UniProtKB: F1MA59 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000054197   ⟸   ENSRNOT00000057386
Ensembl Acc Id: ENSRNOP00000091137   ⟸   ENSRNOT00000114480
Ensembl Acc Id: ENSRNOP00000110576   ⟸   ENSRNOT00000125691
Ensembl Acc Id: ENSRNOP00000102947   ⟸   ENSRNOT00000161095
Ensembl Acc Id: ENSRNOP00000101670   ⟸   ENSRNOT00000173991
Protein Domains
Collagen IV NC1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MA59-F1-model_v2 AlphaFold F1MA59 1-1669 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700247
Promoter ID:EPDNEW_R10770
Type:multiple initiation site
Name:Col4a1_1
Description:collagen type IV alpha 1 chain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01683,522,214 - 83,522,274EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307148 AgrOrtholog
BioCyc Gene G2FUF-10651 BioCyc
Ensembl Genes ENSRNOG00000016281 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057386 ENTREZGENE
  ENSRNOT00000057386.4 UniProtKB/TrEMBL
  ENSRNOT00000114480.2 UniProtKB/TrEMBL
  ENSRNOT00000125691.1 UniProtKB/TrEMBL
  ENSRNOT00000161095.1 UniProtKB/TrEMBL
  ENSRNOT00000173991.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304280 IMAGE-MGC_LOAD
InterPro C-type_lectin_fold UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/TrEMBL
  Collagen_Structural_Proteins UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
  Collagen_VI_NC UniProtKB/TrEMBL
  NDNF UniProtKB/TrEMBL
KEGG Report rno:290905 UniProtKB/TrEMBL
MGC_CLONE MGC:106017 IMAGE-MGC_LOAD
NCBI Gene 290905 ENTREZGENE
PANTHER COLLAGEN UniProtKB/TrEMBL
  COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(X) CHAIN UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XXIII) CHAIN-LIKE ISOFORM X2 UniProtKB/TrEMBL
  COLLAGEN TYPE XIII ALPHA 1 CHAIN UniProtKB/TrEMBL
  NEURON-DERIVED NEUROTROPHIC FACTOR UniProtKB/TrEMBL
  PTHR14619:SF7 UniProtKB/TrEMBL
  SI:CH211-266K2.1 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PhenoGen Col4a1 PhenoGen
PROSITE NC1_IV UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016281 RatGTEx
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A8I6AFK7_RAT UniProtKB/TrEMBL
  A0ABK0LBV2_RAT UniProtKB/TrEMBL
  A0ABK0LIA4_RAT UniProtKB/TrEMBL
  A0ABK0LJC6_RAT UniProtKB/TrEMBL
  A6IWQ2_RAT UniProtKB/TrEMBL
  A6IWQ3_RAT UniProtKB/TrEMBL
  A6IWQ4_RAT UniProtKB/TrEMBL
  F1MA59 ENTREZGENE, UniProtKB/TrEMBL
  Q5FWY9_RAT UniProtKB/TrEMBL
  Q62677_RAT UniProtKB/TrEMBL
UniProt Secondary O09065 UniProtKB/TrEMBL
  O09145 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col4a1  collagen type IV alpha 1 chain  Col4a1  collagen, type IV, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Col4a1  collagen, type IV, alpha 1  Col4a1  procollagen, type IV, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Col4a1  procollagen, type IV, alpha 1  Col4a1_predicted  procollagen, type IV, alpha 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Col4a1_predicted  procollagen, type IV, alpha 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED