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

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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. Involved in response to glucose. Predicted to be located in endoplasmic reticulum. Predicted to be part of collagen type IV trimer. Predicted to be active in basement membrane and extracellular space. Used to study glomerulonephritis. Human ortholog(s) of this gene implicated in Alport syndrome; autosomal dominant Alport syndrome; autosomal recessive Alport syndrome; 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: PROVISIONAL
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2983,875,958 - 84,004,955 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl983,875,561 - 84,001,895 (+)Ensembl
Rnor_6.0988,357,528 - 88,484,735 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,357,556 - 88,485,830 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,104,667 - 88,233,491 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4981,910,656 - 82,036,998 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1982,217,087 - 82,220,407 (+)NCBI
Celera981,318,911 - 81,443,381 (+)NCBICelera
Cytogenetic Map9q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
mRatBN7.2983,875,958 - 84,004,955 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl983,875,561 - 84,001,895 (+)Ensembl
Rnor_6.0988,357,528 - 88,484,735 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,357,556 - 88,485,830 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,104,667 - 88,233,491 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4981,910,656 - 82,036,998 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1982,217,087 - 82,220,407 (+)NCBI
Celera981,318,911 - 81,443,381 (+)NCBICelera
Cytogenetic Map9q34NCBI
COL4A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382227,164,624 - 227,314,792 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2227,164,624 - 227,314,792 (+)EnsemblGRCh38hg38GRCh38
GRCh372228,029,340 - 228,179,508 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362227,737,525 - 227,887,751 (+)NCBINCBI36hg18NCBI36
Build 342227,854,785 - 228,005,012NCBI
Celera2221,798,804 - 221,948,638 (+)NCBI
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 (+)NCBI
Col4a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39182,564,642 - 82,699,780 (+)NCBIGRCm39mm39
GRCm39 Ensembl182,564,642 - 82,699,780 (+)Ensembl
GRCm38182,586,921 - 82,722,059 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl182,586,921 - 82,722,059 (+)EnsemblGRCm38mm10GRCm38
MGSCv37182,583,496 - 82,718,634 (+)NCBIGRCm37mm9NCBIm37
MGSCv36182,466,000 - 82,600,292 (+)NCBImm8
Celera182,656,003 - 82,788,458 (+)NCBICelera
Cytogenetic Map1C5NCBI
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
PanPan1.12B233,222,978 - 233,371,021 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B233,294,783 - 233,371,021 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B114,410,703 - 114,559,336 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2540,594,141 - 40,724,413 (+)NCBI
ROS_Cfam_1.02540,223,476 - 40,354,004 (+)NCBI
ROS_Cfam_1.0 Ensembl2540,223,428 - 40,354,004 (+)Ensembl
UMICH_Zoey_3.12540,160,971 - 40,291,219 (+)NCBI
UNSW_CanFamBas_1.02540,001,099 - 40,131,636 (+)NCBI
UU_Cfam_GSD_1.02540,174,823 - 40,305,251 (+)NCBI
Col4a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303182,165,021 - 182,295,213 (+)NCBI
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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
ChlSab1.110113,183,843 - 113,338,230 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl10113,257,483 - 113,335,312 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604086,112,929 - 86,269,658 (-)NCBIVero_WHO_p1.0
Col4a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248431,557,756 - 1,623,936 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat

miRNA Target Status

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 2 27 9 11
Low 3 36 23 9 19 9 8 10 39 4 22 8
Below cutoff 6 26 26 26 1 27 4 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020669   ⟹   ENSRNOP00000020669
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl983,875,561 - 84,001,895 (+)Ensembl
Rnor_6.0 Ensembl988,357,556 - 88,485,830 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000073993   ⟹   ENSRNOP00000065586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl990,857,308 - 90,874,704 (+)Ensembl
RefSeq Acc Id: NM_001135759   ⟹   NP_001129231
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2983,876,004 - 84,001,895 (+)NCBI
Rnor_6.0988,357,751 - 88,484,376 (+)NCBI
Rnor_5.0988,104,667 - 88,233,491 (+)NCBI
RGSC_v3.4981,910,656 - 82,036,998 (+)RGD
Celera981,318,911 - 81,443,381 (+)RGD
Sequence:
RefSeq Acc Id: XM_039083896   ⟹   XP_038939824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2983,875,958 - 84,004,955 (+)NCBI
RefSeq Acc Id: XM_039083897   ⟹   XP_038939825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2983,959,093 - 84,004,955 (+)NCBI
RefSeq Acc Id: XR_005488938
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2983,875,958 - 83,984,694 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001129231 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939824 (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  
Reference Sequences
RefSeq Acc Id: NP_001129231   ⟸   NM_001135759
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000020669   ⟸   ENSRNOT00000020669
RefSeq Acc Id: XP_038939824   ⟸   XM_039083896
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939825   ⟸   XM_039083897
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000065586   ⟸   ENSRNOT00000073993
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

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 81977724 81977725 C T snv BUF/N (KNAW), GH/OmrMcwi (MCW), MHS/Gib (ICL), MNS/Gib (ICL), GK/Ox (ICL)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 83942932 83942933 C T snv BUF/N (2020), MWF/Hsd (2019), GK/FarMcwi (2019)


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 Protein ENSRNOP00000020669 ENTREZGENE
  ENSRNOP00000020669.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020669 ENTREZGENE
  ENSRNOT00000020669.6 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_VI_NC UniProtKB/TrEMBL
NCBI Gene 363265 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PhenoGen Col4a3 PhenoGen
PROSITE NC1_IV UniProtKB/TrEMBL
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt 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 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 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