Col4a4 (collagen type IV alpha 4 chain) - Rat Genome Database

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Gene: Col4a4 (collagen type IV alpha 4 chain) Rattus norvegicus
Analyze
Symbol: Col4a4
Name: collagen type IV alpha 4 chain
RGD ID: 1305355
Description: Predicted to be an extracellular matrix structural constituent. Predicted to be involved in glomerular basement membrane development. Predicted to be located in membrane. Predicted to be part of collagen type IV trimer. Predicted to be active in basement membrane and extracellular space. Human ortholog(s) of this gene implicated in autosomal recessive Alport syndrome; benign familial hematuria; and end stage renal disease. Orthologous to human COL4A4 (collagen type IV alpha 4 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: collagen, type IV, alpha 4; LOC301562; MGC105542; procollagen, type IV, alpha 4
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
mRatBN7.2983,833,173 - 83,875,436 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl983,755,515 - 83,875,876 (-)Ensembl
Rnor_6.0988,314,763 - 88,357,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,232,455 - 88,357,182 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,062,426 - 88,104,120 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4981,866,835 - 81,910,088 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1982,050,254 - 82,093,507 (-)NCBI
Celera981,276,510 - 81,318,343 (-)NCBICelera
Cytogenetic Map9q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Autosomal dominant Alport syndrome: molecular analysis of the COL4A4 gene and clinical outcome. Marcocci E, etal., Nephrol Dial Transplant. 2009 May;24(5):1464-71. doi: 10.1093/ndt/gfn681. Epub 2009 Jan 7.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. 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.
7. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:2211832   PMID:7523402   PMID:7962065   PMID:9264260   PMID:10534397   PMID:11732842   PMID:12477932   PMID:17942953   PMID:19275937   PMID:19675380  


Genomics

Comparative Map Data
Col4a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2983,833,173 - 83,875,436 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl983,755,515 - 83,875,876 (-)Ensembl
Rnor_6.0988,314,763 - 88,357,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,232,455 - 88,357,182 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,062,426 - 88,104,120 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4981,866,835 - 81,910,088 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1982,050,254 - 82,093,507 (-)NCBI
Celera981,276,510 - 81,318,343 (-)NCBICelera
Cytogenetic Map9q34NCBI
COL4A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382226,967,360 - 227,164,488 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2227,002,714 - 227,164,453 (-)EnsemblGRCh38hg38GRCh38
GRCh372227,867,430 - 228,028,921 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362227,575,671 - 227,737,519 (-)NCBINCBI36hg18NCBI36
Build 342227,695,432 - 227,854,780NCBI
Celera2221,636,952 - 221,798,798 (-)NCBI
Cytogenetic Map2q36.3NCBI
HuRef2219,710,854 - 219,872,782 (-)NCBIHuRef
CHM1_12227,873,296 - 228,035,468 (-)NCBICHM1_1
T2T-CHM13v2.02227,485,408 - 227,646,963 (-)NCBI
Col4a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39182,426,140 - 82,564,570 (-)NCBIGRCm39mm39
GRCm39 Ensembl182,426,144 - 82,564,570 (-)Ensembl
GRCm38182,448,419 - 82,587,034 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl182,448,423 - 82,586,849 (-)EnsemblGRCm38mm10GRCm38
MGSCv37182,447,298 - 82,583,424 (-)NCBIGRCm37mm9NCBIm37
MGSCv36182,331,582 - 82,465,816 (-)NCBImm8
Celera182,519,390 - 82,655,931 (-)NCBICelera
Cytogenetic Map1C5NCBI
Col4a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554537,420,203 - 7,520,200 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554537,405,167 - 7,524,038 (+)NCBIChiLan1.0ChiLan1.0
COL4A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B233,061,067 - 233,222,541 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B233,065,678 - 233,205,892 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B114,227,135 - 114,410,564 (-)NCBIMhudiblu_PPA_v0panPan3
COL4A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12539,849,680 - 39,976,035 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2539,854,388 - 39,976,189 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2540,472,320 - 40,576,418 (-)NCBI
ROS_Cfam_1.02540,097,773 - 40,223,035 (-)NCBI
ROS_Cfam_1.0 Ensembl2540,102,484 - 40,205,769 (-)Ensembl
UMICH_Zoey_3.12540,038,958 - 40,143,270 (-)NCBI
UNSW_CanFamBas_1.02539,873,785 - 39,983,389 (-)NCBI
UU_Cfam_GSD_1.02540,052,828 - 40,157,117 (-)NCBI
Col4a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303182,032,869 - 182,171,485 (-)NCBI
SpeTri2.0NW_0049365258,788,753 - 8,899,671 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15128,476,257 - 128,595,477 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115128,472,228 - 128,612,302 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215142,283,500 - 142,421,620 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL4A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110113,028,552 - 113,183,240 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl10113,028,552 - 113,165,958 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604086,269,741 - 86,423,511 (+)NCBIVero_WHO_p1.0
Col4a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248431,364,674 - 1,486,250 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248431,364,674 - 1,486,813 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D9Rat144  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2983,851,531 - 83,851,658 (+)MAPPERmRatBN7.2
Rnor_6.0988,333,183 - 88,333,309NCBIRnor6.0
Rnor_5.0988,080,598 - 88,080,724UniSTSRnor5.0
RGSC_v3.4981,885,455 - 81,885,804RGDRGSC3.4
RGSC_v3.4981,885,484 - 81,885,610UniSTSRGSC3.4
RGSC_v3.1982,068,874 - 82,069,223RGD
Celera981,294,966 - 81,295,092UniSTS
FHH x ACI Map956.65RGD
FHH x ACI Map956.65UniSTS
Cytogenetic Map9q34UniSTS
RH134744  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2983,833,284 - 83,833,467 (+)MAPPERmRatBN7.2
Rnor_6.0988,314,875 - 88,315,057NCBIRnor6.0
Rnor_5.0988,062,538 - 88,062,720UniSTSRnor5.0
RGSC_v3.4981,866,947 - 81,867,129UniSTSRGSC3.4
Celera981,276,622 - 81,276,804UniSTS
Cytogenetic Map9q34UniSTS
AU048826  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2983,844,296 - 83,844,488 (+)MAPPERmRatBN7.2
Rnor_6.0988,325,843 - 88,326,034NCBIRnor6.0
Rnor_5.0988,073,258 - 88,073,449UniSTSRnor5.0
RGSC_v3.4981,878,249 - 81,878,440UniSTSRGSC3.4
Celera981,287,731 - 81,287,922UniSTS
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
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
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:88
Count of miRNA genes:68
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000041176
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 20 6 2 2 29 19 11 2
Low 3 23 39 29 19 29 6 9 74 6 22 6
Below cutoff 12 12 12

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041176   ⟹   ENSRNOP00000039933
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl988,314,784 - 88,357,182 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl983,755,779 - 83,875,876 (-)Ensembl
Rnor_6.0 Ensembl988,236,749 - 88,343,609 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076472   ⟹   ENSRNOP00000067935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl988,232,455 - 88,256,115 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl988,280,149 - 88,284,764 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077503   ⟹   ENSRNOP00000074055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl983,755,515 - 83,875,436 (-)Ensembl
Rnor_6.0 Ensembl988,237,089 - 88,356,716 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111693   ⟹   ENSRNOP00000084905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl983,755,515 - 83,773,068 (-)Ensembl
RefSeq Acc Id: NM_001008332   ⟹   NP_001008333
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2983,833,173 - 83,875,436 (-)NCBI
Rnor_6.0988,314,763 - 88,357,183 (-)NCBI
Rnor_5.0988,062,426 - 88,104,120 (-)NCBI
RGSC_v3.4981,866,835 - 81,910,088 (-)RGD
Celera981,276,510 - 81,318,343 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008333 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH86403 (Get FASTA)   NCBI Sequence Viewer  
  EDL75508 (Get FASTA)   NCBI Sequence Viewer  
  EDL75509 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001008333   ⟸   NM_001008332
- UniProtKB: Q5U1X9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039933   ⟸   ENSRNOT00000041176
RefSeq Acc Id: ENSRNOP00000074055   ⟸   ENSRNOT00000077503
RefSeq Acc Id: ENSRNOP00000067935   ⟸   ENSRNOT00000076472
RefSeq Acc Id: ENSRNOP00000084905   ⟸   ENSRNOT00000111693
Protein Domains
Collagen IV NC1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K742-F1-model_v2 AlphaFold A0A0G2K742 1-1682 view protein structure

Transcriptome

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

Promoters
RGD ID:13696798
Promoter ID:EPDNEW_R7323
Type:initiation region
Name:Col4a4_1
Description:collagen type IV alpha 4 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_6.0988,357,241 - 88,357,301EPDNEW

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)
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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/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)
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/Stm (2019)
Visual CSV TAB Printer
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)
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
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: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 88336261 88336262 G C snv LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305355 AgrOrtholog
BioCyc Gene G2FUF-26980 BioCyc
Ensembl Genes ENSRNOG00000014851 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000074055.1 UniProtKB/TrEMBL
  ENSRNOP00000084905.1 UniProtKB/TrEMBL
  ENSRNOP00000090067.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075968.2 UniProtKB/TrEMBL
  ENSRNOT00000077503.2 UniProtKB/TrEMBL
  ENSRNOT00000111693.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304199 IMAGE-MGC_LOAD
InterPro C-type_lectin_fold UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/TrEMBL
  Collagen_VI_NC UniProtKB/TrEMBL
KEGG Report rno:301562 UniProtKB/TrEMBL
MGC_CLONE MGC:105542 IMAGE-MGC_LOAD
NCBI Gene 301562 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PhenoGen Col4a4 PhenoGen
PROSITE NC1_IV UniProtKB/TrEMBL
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/TrEMBL
UniProt A0A0G2K742_RAT UniProtKB/TrEMBL
  A0A8I6A9Z5_RAT UniProtKB/TrEMBL
  A0A8I6GC95_RAT UniProtKB/TrEMBL
  Q5U1X9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col4a4  collagen type IV alpha 4 chain  Col4a4  collagen, type IV, alpha 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-01-29 Col4a4  collagen, type IV, alpha 4  Col4a4  procollagen, type IV, alpha 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Col4a4  procollagen, type IV, alpha 4  Col4a4_predicted  procollagen, type IV, alpha 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Col4a4_predicted  procollagen, type IV, alpha 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED