Col4a3 (collagen type IV alpha 3 chain) - Rat Genome Database

Send us a Message



Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Grant Resources Citing RGD About Us Contact Us
Search by Genomic Position Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quantitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Col4a3 (collagen type IV alpha 3 chain) Rattus norvegicus
Analyze
Symbol: Col4a3
Name: collagen type IV alpha 3 chain
RGD ID: 71085
Description: Predicted to enable integrin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in response to glucose. Predicted to be located in basement membrane. Predicted to be part of collagen type IV trimer. Predicted to be active in extracellular matrix. Used to study glomerulonephritis. Human ortholog(s) of this gene implicated in Alport syndrome; Alport syndrome 2; Alport syndrome 3A; benign familial hematuria; and end stage renal disease. Orthologous to human COL4A3 (collagen type IV alpha 3 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-3(IV) chain; collagen alpha-3(IV) chain-like; collagen type IV alpha 3 (Goodpasture antigen); collagen, type IV, alpha 3; collagen, type IV, alpha 3 (Goodpasture antigen); LOC100911572; LOC363265; procollagen, type IV, alpha 3; similar to procollagen, type IV, alpha 3
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
GRCr8991,323,990 - 91,453,088 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl991,323,990 - 91,453,077 (+)EnsemblGRCr8
mRatBN7.2983,875,849 - 84,004,955 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl983,875,561 - 84,001,895 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx992,306,254 - 92,432,137 (+)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,434,733 - 97,560,624 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0995,817,678 - 95,943,557 (+)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd994,930,531 - 95,059,628 (+)NCBI
Lyon_Normotensive990,750,777 - 90,879,860 (+)NCBI
Lyon_Hypertensive990,898,255 - 91,027,339 (+)NCBI
F344_StmMcwi992,897,450 - 93,026,537 (+)NCBI
Rnor_6.0988,357,528 - 88,484,735 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,357,556 - 88,485,830 (+)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.0988,104,667 - 88,233,491 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4981,910,656 - 82,036,998 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera981,318,911 - 81,443,381 (+)NCBICelera
RGSC_v3.1982,217,087 - 82,220,407 (+)NCBI
Cytogenetic Map9q34NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
andrographolide  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
diazinon  (ISO)
diiodine  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
fonofos  (ISO)
graphene oxide  (ISO)
lead diacetate  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
okadaic acid  (ISO)
orphenadrine  (EXP)
ozone  (EXP)
paracetamol  (EXP)
paraquat  (EXP,ISO)
parathion  (ISO)
PCB138  (EXP)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
potassium dichromate  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
streptozocin  (EXP)
sulfadimethoxine  (EXP)
terbufos  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vandetanib  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (EXP,ISO)
zinc atom  (EXP)
zinc(0)  (EXP)
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. Clinical biomarkers of pulmonary carcinoid tumors in never smokers via profiling miRNA and target mRNA. Deng B, etal., Cell Biosci. 2014 Jul 9;4:35. doi: 10.1186/2045-3701-4-35. eCollection 2014.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Mutations in the type IV collagen alpha 3 (COL4A3) gene in autosomal recessive Alport syndrome. Lemmink HH, etal., Hum Mol Genet. 1994 Aug;3(8):1269-73.
5. Gene Data Set MGD Curation, June 12, 2002
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. Clinico-pathological correlations in 127 patients in 11 large pedigrees, segregating one of three heterozygous mutations in the COL4A3/ COL4A4 genes associated with familial haematuria and significant late progression to proteinuria and chronic kidney disease from focal segmental glomerulosclerosis. Pierides A, etal., Nephrol Dial Transplant. 2009 Sep;24(9):2721-9. doi: 10.1093/ndt/gfp158. Epub 2009 Apr 8.
10. Segregation of experimental autoimmune glomerulonephritis as a complex genetic trait and exclusion of Col4a3 as a candidate gene. Reynolds J, etal., Exp Nephrol 2002;10(5-6):402-7.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. Sequence analysis of the 'Goodpasture antigen' of mammals. Ryan JJ, etal., Nephrol Dial Transplant 1998 Mar;13(3):602-7.
16. Expression and characterization of recombinant rat alpha 3(IV)NC1 and its use in induction of experimental autoimmune glomerulonephritis. Ryan JJ, etal., Nephrol Dial Transplant. 2001 Feb;16(2):253-61.
17. The interplay of collagen IV, tumor necrosis factor-alpha, gelatinase B (matrix metalloprotease-9), and tissue inhibitor of metalloproteases-1 in the basal lamina regulates Sertoli cell-tight junction dynamics in the rat testis. Siu MK, etal., Endocrinology 2003 Jan;144(1):371-87.
18. A self T cell epitope induces autoantibody response: mechanism for production of antibodies to diverse glomerular basement membrane antigens. Wu J, etal., J Immunol 2004 Apr 1;172(7):4567-74.
19. Differential expression of type IV collagen isoforms in rat glomerular endothelial and mesangial cells. Zeisberg M, etal., Biochem Biophys Res Commun. 2002 Jul 12;295(2):401-7.
Additional References at PubMed
PMID:10766752   PMID:10970885   PMID:11732842   PMID:12101409   PMID:12631063   PMID:12682293   PMID:12842087   PMID:16041630   PMID:16105036   PMID:16877525   PMID:17028444   PMID:18757743  
PMID:19794980   PMID:27323108   PMID:27363275   PMID:28632965  


Genomics

Comparative Map Data
Col4a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,323,990 - 91,453,088 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl991,323,990 - 91,453,077 (+)EnsemblGRCr8
mRatBN7.2983,875,849 - 84,004,955 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl983,875,561 - 84,001,895 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx992,306,254 - 92,432,137 (+)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,434,733 - 97,560,624 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0995,817,678 - 95,943,557 (+)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd994,930,531 - 95,059,628 (+)NCBI
Lyon_Normotensive990,750,777 - 90,879,860 (+)NCBI
Lyon_Hypertensive990,898,255 - 91,027,339 (+)NCBI
F344_StmMcwi992,897,450 - 93,026,537 (+)NCBI
Rnor_6.0988,357,528 - 88,484,735 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,357,556 - 88,485,830 (+)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.0988,104,667 - 88,233,491 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4981,910,656 - 82,036,998 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera981,318,911 - 81,443,381 (+)NCBICelera
RGSC_v3.1982,217,087 - 82,220,407 (+)NCBI
Cytogenetic Map9q34NCBI
COL4A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382227,164,624 - 227,314,792 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2227,164,509 - 227,314,792 (+)EnsemblGRCh38.p14 Ensemblhg38GRCh38
GRCh372228,029,340 - 228,179,508 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362227,737,525 - 227,887,751 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342227,854,785 - 228,005,012NCBI
Celera2221,798,804 - 221,948,638 (+)NCBICelera
Cytogenetic Map2q36.3NCBI
HuRef2219,872,788 - 220,022,916 (+)NCBIHuRef
CHM1_12228,035,474 - 228,185,321 (+)NCBICHM1_1
T2T-CHM13v2.02227,647,382 - 227,797,471 (+)NCBIT2T-CHM13v2.0
Col4a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39182,564,647 - 82,699,778 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl182,564,642 - 82,699,780 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38182,586,921 - 82,722,059 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl182,586,921 - 82,722,059 (+)EnsemblGRCm38.p6 Ensemblmm10GRCm38
MGSCv37182,583,496 - 82,718,634 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36182,466,000 - 82,600,292 (+)NCBIMGSCv36mm8
Celera182,656,003 - 82,788,458 (+)NCBICelera
Cytogenetic Map1C5NCBI
cM Map142.32NCBI
Col4a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554537,261,278 - 7,351,414 (-)NCBIChiLan1.0ChiLan1.0
COL4A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213129,784,746 - 129,933,404 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B129,799,716 - 129,948,374 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B114,410,703 - 114,559,336 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B233,222,978 - 233,371,021 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B233,294,783 - 233,371,021 (+)EnsemblPanPan1.1 EnsemblpanPan2panpan1.1
COL4A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12539,975,547 - 40,106,833 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2539,975,586 - 40,104,782 (+)EnsemblCanFam3.1 EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2540,594,141 - 40,724,413 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02540,223,476 - 40,354,004 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2540,223,428 - 40,354,004 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12540,160,971 - 40,291,219 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02540,001,099 - 40,131,636 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02540,174,823 - 40,305,251 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Col4a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mIctTri1.hap17187,781,983 - 187,914,522 (+)NCBImIctTri1.hap1
HiC_Itri_2NW_024405303182,165,021 - 182,295,213 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365258,642,744 - 8,774,975 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15128,611,866 - 128,763,122 (+)EnsemblSscrofa11.1 EnsemblsusScr11Sscrofa11.1
Sscrofa11.115128,611,640 - 128,763,331 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215142,421,820 - 142,537,606 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL4A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mChlSab1.0.hap110114,726,741 - 114,878,657 (+)NCBImChlSab1.0.hap1
Vero_WHO_p1.0NW_02366604086,112,929 - 86,269,658 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
ChlSab1.110113,183,843 - 113,338,230 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10113,257,483 - 113,335,312 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Col4a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248431,557,756 - 1,623,936 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Naked mole-rat maternal Ensembl2536,358,138 - 36,494,892 (+)Ensembl
Col4a3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14155,450,358 - 155,578,260 (+)NCBIRrattus_CSIRO_v1Rrattus_CSIRO_v1

Variants

.
Variants in Col4a3
1282 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:15
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000020669
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)986720043110356905Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)986720043121768150Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)98672213292642305Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)99062451792642305Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)985262459109044727Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)985262459118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat

Markers in Region
D9Wox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2983,940,738 - 83,940,871 (+)MAPPERmRatBN7.2
Rnor_6.0988,421,737 - 88,421,869NCBIRnor6.0
Rnor_5.0988,169,066 - 88,169,198UniSTSRnor5.0
RGSC_v3.4981,975,531 - 81,975,663UniSTSRGSC3.4
Celera981,382,300 - 81,382,432UniSTS
Cytogenetic Map9q34UniSTS
BE110813  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2983,933,537 - 83,933,709 (+)MAPPERmRatBN7.2
Rnor_6.0988,414,537 - 88,414,708NCBIRnor6.0
Rnor_5.0988,161,866 - 88,162,037UniSTSRnor5.0
RGSC_v3.4981,968,329 - 81,968,500UniSTSRGSC3.4
Celera981,375,100 - 81,375,271UniSTS
Cytogenetic Map9q34UniSTS
OMM1056  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2983,927,470 - 83,928,025 (+)MAPPERmRatBN7.2
Rnor_6.0988,408,470 - 88,409,024NCBIRnor6.0
Rnor_5.0988,155,799 - 88,156,353UniSTSRnor5.0
RGSC_v3.4981,962,262 - 81,962,816UniSTSRGSC3.4
Celera981,369,040 - 81,369,594UniSTS
Cytogenetic Map9q34UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
274 150 727 1591 4009 971 1688 109 834 459 816 155 5291 2532 438 3916 38 1390 713 909 160 158

Sequence


Ensembl Acc Id: ENSRNOT00000020669   ⟹   ENSRNOP00000020669
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl991,379,540 - 91,453,077 (+)Ensembl
mRatBN7.2 Ensembl983,875,561 - 84,001,895 (+)Ensembl
Rnor_6.0 Ensembl988,357,556 - 88,485,830 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000073993   ⟹   ENSRNOP00000065586
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl990,857,308 - 90,874,704 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111608   ⟹   ENSRNOP00000108770
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl991,323,990 - 91,453,077 (+)Ensembl
RefSeq Acc Id: NM_001413988   ⟹   NP_001400917
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,323,990 - 91,453,088 (+)NCBI
mRatBN7.2983,875,849 - 84,004,955 (+)NCBI
Dahl_SR_JrHsd994,930,531 - 95,059,628 (+)NCBI
Lyon_Normotensive990,750,777 - 90,879,860 (+)NCBI
Lyon_Hypertensive990,898,255 - 91,027,339 (+)NCBI
F344_StmMcwi992,897,450 - 93,026,537 (+)NCBI
RefSeq Acc Id: XM_039083897   ⟹   XP_038939825
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,407,230 - 91,453,087 (+)NCBI
mRatBN7.2983,959,093 - 84,004,955 (+)NCBI
RefSeq Acc Id: XR_005488938
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,324,095 - 91,432,825 (+)NCBI
mRatBN7.2983,875,958 - 83,984,694 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001400917 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939825 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB72238 (Get FASTA)   NCBI Sequence Viewer  
  EDL75510 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020669.6
  ENSRNOP00000108770
  ENSRNOP00000108770.1
Ensembl Acc Id: ENSRNOP00000020669   ⟸   ENSRNOT00000020669
RefSeq Acc Id: XP_038939825   ⟸   XM_039083897
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000065586   ⟸   ENSRNOT00000073993
RefSeq Acc Id: NP_001400917   ⟸   NM_001413988
- Peptide Label: precursor
- UniProtKB: A0ABK0LX72 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000108770   ⟸   ENSRNOT00000111608
Protein Domains
Collagen IV NC1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R7Z7-F1-model_v2 AlphaFold M0R7Z7 1-471 view protein structure
AF-F1LRJ1-F1-model_v2 AlphaFold F1LRJ1 1-1671 view protein structure

Transcriptome

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

Promoters
RGD ID:13696800
Promoter ID:EPDNEW_R7324
Type:multiple initiation site
Name:Col4a3_1
Description:collagen type IV alpha 3 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_6.0988,357,596 - 88,357,656EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71085 AgrOrtholog
BioCyc Gene G2FUF-26979 BioCyc
Ensembl Genes ENSRNOG00000015365 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000046521 Ensembl
Ensembl Transcript ENSRNOT00000020669.7 UniProtKB/TrEMBL
  ENSRNOT00000111608 ENTREZGENE
  ENSRNOT00000111608.2 UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/TrEMBL
InterPro C-type_lectin_fold UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
  Collagen_VI_NC UniProtKB/TrEMBL
  NDNF UniProtKB/TrEMBL
KEGG Report rno:363265 UniProtKB/TrEMBL
NCBI Gene Col4a3 ENTREZGENE
PANTHER ALPHA2(IV)-LIKE COLLAGEN UniProtKB/TrEMBL
  COLLAGEN ALPHA UniProtKB/TrEMBL
  NEURON-DERIVED NEUROTROPHIC FACTOR UniProtKB/TrEMBL
  PTHR14619:SF7 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PhenoGen Col4a3 PhenoGen
PROSITE NC1_IV UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015365 RatGTEx
  ENSRNOG00000046521 RatGTEx
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0ABK0LX72 ENTREZGENE, UniProtKB/TrEMBL
  F1LRJ1_RAT UniProtKB/TrEMBL
  Q63122_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Col4a3  collagen type IV alpha 3 chain  LOC100911572  collagen alpha-3(IV) chain-like  Data merged from RGD:6491864 737654 PROVISIONAL
2016-06-01 Col4a3  collagen type IV alpha 3 chain  Col4a3  collagen, type IV, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911572  collagen alpha-3(IV) chain-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-06-23 Col4a3  collagen, type IV, alpha 3  LOC363265  similar to procollagen, type IV, alpha 3  Data merged from RGD:1592052 737654 APPROVED
2008-02-18 Col4a3  collagen, type IV, alpha 3  Col4a3  procollagen, type IV, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC363265  similar to procollagen, type IV, alpha 3      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Col4a3  procollagen, type IV, alpha 3    collagen, type IV, alpha 3  Name updated 1299863 APPROVED
2002-07-09 Col4a3  collagen, type IV, alpha 3      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease The peptide pCol(28-40), representing the non-collagen domain 1 of Col4a3, constitutes a T cell epitope which induces severe glomerulonephritis and elicits diverse anti-GBM antibodies in 76% of immunized rats; production of antibodies is not dependent on a peptidic B cell epitope nested within pCol(28-40), suggesting that antibody production may be a consequence of T cell-mediated glomerulonephritis 1304311
gene_disease Induction of experimental autoimmune glomerulonephritis (EAG) by immunization with rat glomerular basement membrane in adjuvant results in focal necrotizing glomerulonephritis with crescent formation in Wistar-Kyoto (WKY) rats 1299240
gene_disease immunization of Lewis (LEW) rats with rat glomerular basement membrane in adjuvant results in production of antibodies but no evidence of nephritis 1299240
gene_disease predicted amino acid sequences of the NC1 region of Col4a3 in the WKY and LEW strains are identical, and linkage analysis does not show significant linkage between EAG and the region of chromosome 9 where the Col4a3 gene is located, implying that Col4a3 is not a recessive susceptibility gene for EAG 1299240
gene_homology 91% amino acid identity with human COL4A3 and 95% amino acid identity with mouse Col4a3 70692
gene_other the non-collagenous domain of the rat Col4a3 reacts poorly to the human Goodpasture autoantigen, unlike other species such as bovine, horse and sheep 70692
gene_other Application of anti-Col4a3 antibody disrupts the formation of Sertoli cell tight junctions in vitro 727488
gene_regulation Application of TNFalpha disrupts the formation of Sertoli cell tight junctions in vitro and also upregulates expression of Col4a3, possibly as a result of a negative feedback loop initiated by TNFalpha-stimulated Mmp9 cleavage of extracellular matrix components 727488