Col6a1 (collagen type VI alpha 1 chain) - Rat Genome Database
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Gene: Col6a1 (collagen type VI alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col6a1
Name: collagen type VI alpha 1 chain
RGD ID: 1565398
Description: Predicted to have collagen binding activity; extracellular matrix structural constituent; and platelet-derived growth factor binding activity. Predicted to be involved in several processes, including cellular response to amino acid stimulus; endodermal cell differentiation; and gonad development. Predicted to localize to several cellular components, including basement membrane; collagen type IX trimer; and sarcolemma. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL6A1 (collagen type VI alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,2,2-tetramine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: MODEL
Also known as: collagen alpha-1(VI) chain; collagen, type VI, alpha 1; LOC294337; procollagen, type VI, alpha 1; RGD1565398; similar to collagen alpha1 type VI-precursor
Orthologs:
Homo sapiens (human) : COL6A1 (collagen type VI alpha 1 chain)  HGNC  Alliance
Mus musculus (house mouse) : Col6a1 (collagen, type VI, alpha 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Col6a1 (collagen type VI alpha 1 chain)
Pan paniscus (bonobo/pygmy chimpanzee) : COL6A1 (collagen type VI alpha 1 chain)
Canis lupus familiaris (dog) : COL6A1 (collagen type VI alpha 1 chain)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Col6a1 (collagen type VI alpha 1 chain)
Sus scrofa (pig) : LOC100623720 (collagen alpha-1(VI) chain)
Chlorocebus sabaeus (African green monkey) : COL6A1 (collagen type VI alpha 1 chain)
Heterocephalus glaber (naked mole-rat) : Col6a1 (collagen type VI alpha 1 chain)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02012,657,913 - 12,676,370 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,658,065 - 12,675,561 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02014,817,411 - 14,835,868 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,320,102 - 12,338,500 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2013,404,454 - 13,422,911 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acrylamide  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
atrazine  (ISO)
azelastine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
DDT  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diethyl malate  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
glucose  (ISO)
indometacin  (ISO)
ionomycin  (ISO)
irinotecan  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
manganese(II) chloride  (EXP)
methotrexate  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (ISO)
nefazodone  (EXP)
nicotine  (ISO)
nimesulide  (EXP)
ochratoxin A  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
paclitaxel  (ISO)
panobinostat  (ISO)
paraquat  (ISO)
Pargyline  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
selenomethionine  (ISO)
silicon dioxide  (EXP)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
streptozocin  (EXP)
sunitinib  (ISO)
Tanshinone I  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
tributylstannane  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
Y-27632  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8806434   PMID:8900172   PMID:16210410   PMID:16810681   PMID:17897319   PMID:18400749   PMID:19056867   PMID:19199708   PMID:20548288   PMID:20551380   PMID:23154389   PMID:23376485  
PMID:23533145   PMID:23658023   PMID:24006456   PMID:27068509   PMID:27498042   PMID:27559042  


Genomics

Comparative Map Data
Col6a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02012,657,913 - 12,676,370 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,658,065 - 12,675,561 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02014,817,411 - 14,835,868 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,320,102 - 12,338,500 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2013,404,454 - 13,422,911 (+)NCBICelera
Cytogenetic Map20p12NCBI
COL6A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2145,981,769 - 46,005,050 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2145,981,737 - 46,005,050 (+)EnsemblGRCh38hg38GRCh38
GRCh382145,981,770 - 46,005,048 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372147,401,663 - 47,424,963 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,226,091 - 46,249,391 (+)NCBINCBI36hg18NCBI36
Build 342146,226,095 - 46,249,390NCBI
Celera2132,514,265 - 32,537,566 (+)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2132,782,505 - 32,806,491 (+)NCBIHuRef
CHM1_12146,962,501 - 46,985,646 (+)NCBICHM1_1
Col6a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,544,626 - 76,561,878 (-)NCBI
GRCm381076,708,792 - 76,726,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,708,792 - 76,726,168 (-)EnsemblGRCm38mm10GRCm38
MGSCv371076,171,537 - 76,188,789 (-)NCBIGRCm37mm9NCBIm37
MGSCv361076,152,508 - 76,169,760 (-)NCBImm8
Celera1077,753,031 - 77,770,283 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.71NCBI
Col6a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,461,952 - 42,478,261 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,461,837 - 42,479,048 (+)NCBIChiLan1.0ChiLan1.0
COL6A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12145,583,978 - 45,608,233 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,584,096 - 45,607,240 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02132,322,185 - 32,346,850 (+)NCBIMhudiblu_PPA_v0panPan3
COL6A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3139,301,748 - 39,448,062 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13139,301,718 - 39,319,895 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Col6a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936778515,600 - 530,828 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100623720
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13208,295,240 - 208,313,127 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113208,295,245 - 208,321,789 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COL6A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,608,525 - 89,649,823 (+)NCBI
Col6a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474531,125,136 - 31,140,126 (+)NCBI

Position Markers
RH129493  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,676,149 - 12,676,339NCBIRnor6.0
Rnor_5.02014,835,647 - 14,835,837UniSTSRnor5.0
RGSC_v3.42012,338,279 - 12,338,469UniSTSRGSC3.4
Celera2013,422,690 - 13,422,880UniSTS
Cytogenetic Map20p12UniSTS
RH 3.4 Map20154.5UniSTS
RH129051  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,676,083 - 12,676,283NCBIRnor6.0
Rnor_5.02014,835,581 - 14,835,781UniSTSRnor5.0
RGSC_v3.42012,338,213 - 12,338,413UniSTSRGSC3.4
Celera2013,422,624 - 13,422,824UniSTS
Cytogenetic Map20p12UniSTS
RH 3.4 Map20151.3UniSTS
UniSTS:531308  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02012,658,094 - 12,658,999NCBIRnor6.0
Rnor_5.02014,817,592 - 14,818,497UniSTSRnor5.0
Celera2013,404,635 - 13,405,540UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:411
Count of miRNA genes:202
Interacting mature miRNAs:229
Transcripts:ENSRNOT00000001679, ENSRNOT00000072951
Prediction methods:Microtar, Miranda, Rnahybrid
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 7
Medium 3 41 56 40 19 40 8 11 65 35 32 11 8
Low 2 1 1 1 9 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001679   ⟹   ENSRNOP00000001679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,658,065 - 12,675,561 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000072951   ⟹   ENSRNOP00000067777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2012,658,065 - 12,663,173 (+)Ensembl
RefSeq Acc Id: XM_001079629   ⟹   XP_001079629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2013,404,454 - 13,422,911 (+)NCBI
Sequence:
RefSeq Acc Id: XM_215375   ⟹   XP_215375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02012,657,913 - 12,676,370 (+)NCBI
Rnor_5.02014,817,411 - 14,835,868 (+)NCBI
RGSC_v3.42012,320,102 - 12,338,500 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_001079629 (Get FASTA)   NCBI Sequence Viewer  
  XP_215375 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97133 (Get FASTA)   NCBI Sequence Viewer  
  EDL97134 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001079629   ⟸   XM_001079629
- Sequence:
RefSeq Acc Id: XP_215375   ⟸   XM_215375
- Sequence:
RefSeq Acc Id: ENSRNOP00000067777   ⟸   ENSRNOT00000072951
RefSeq Acc Id: ENSRNOP00000001679   ⟸   ENSRNOT00000001679
Protein Domains
VWFA

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 12337306 12337307 C G snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565398 AgrOrtholog
Ensembl Genes ENSRNOG00000001249 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001679 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000067777 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001679 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000072951 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 294337 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Col6a1 PhenoGen
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniGene Rn.232118 ENTREZGENE
UniProt D3ZUL3_RAT UniProtKB/TrEMBL
  M0RDR9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col6a1  collagen type VI alpha 1 chain  Col6a1  collagen, type VI, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Col6a1  collagen, type VI, alpha 1  Col6a1_predicted  procollagen, type VI, alpha 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Col6a1_predicted  procollagen, type VI, alpha 1 (predicted)  RGD1565398_predicted  similar to collagen alpha1 type VI-precursor (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1565398_predicted  similar to collagen alpha1 type VI-precursor (predicted)  LOC294337  similar to collagen alpha1 type VI-precursor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC294337  similar to collagen alpha1 type VI-precursor      Symbol and Name status set to provisional 70820 PROVISIONAL