Col6a3 (collagen type VI alpha 3 chain) - Rat Genome Database
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Gene: Col6a3 (collagen type VI alpha 3 chain) Rattus norvegicus
Analyze
Symbol: Col6a3
Name: collagen type VI alpha 3 chain
RGD ID: 1308704
Description: Involved in response to glucose. Predicted to localize to several cellular components, including collagen trimer; extracellular space; and sarcolemma. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy; dystonia 27; and muscular dystrophy. Orthologous to human COL6A3 (collagen type VI alpha 3 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,2,2-tetramine; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: MODEL
Also known as: collagen alpha-3(VI) chain; collagen, type VI, alpha 3; LOC367313; procollagen, type VI, alpha 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2991,361,578 - 91,439,434 (-)NCBI
Rnor_6.0 Ensembl997,926,787 - 98,004,546 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0997,926,784 - 98,004,643 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0997,607,496 - 97,685,349 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4989,990,129 - 90,043,697 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1990,169,794 - 90,232,286 (-)NCBI
Celera988,906,089 - 88,983,949 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
8-Br-cAMP  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
folic acid  (ISO)
folpet  (ISO)
fonofos  (ISO)
genistein  (ISO)
isoflavones  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
methyl methanesulfonate  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nickel sulfate  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
parathion  (ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (EXP)
rotenone  (EXP,ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
streptozocin  (EXP)
sulindac  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
tributylstannane  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)

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

Additional References at PubMed
PMID:8806434   PMID:10444069   PMID:16810681   PMID:18400749   PMID:19056867   PMID:20551380   PMID:23376485   PMID:23533145   PMID:23658023   PMID:24563484   PMID:24769233   PMID:27068509  
PMID:27559042  


Genomics

Comparative Map Data
Col6a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2991,361,578 - 91,439,434 (-)NCBI
Rnor_6.0 Ensembl997,926,787 - 98,004,546 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0997,926,784 - 98,004,643 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0997,607,496 - 97,685,349 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4989,990,129 - 90,043,697 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1990,169,794 - 90,232,286 (-)NCBI
Celera988,906,089 - 88,983,949 (-)NCBICelera
Cytogenetic Map9q36NCBI
COL6A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2237,324,003 - 237,414,375 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2237,324,003 - 237,414,207 (-)EnsemblGRCh38hg38GRCh38
GRCh382237,324,018 - 237,434,822 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372238,232,655 - 238,322,850 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372238,232,661 - 238,322,807 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362237,897,401 - 237,987,559 (-)NCBINCBI36hg18NCBI36
Build 342238,014,661 - 238,104,820NCBI
Celera2231,946,425 - 232,036,576 (-)NCBI
Cytogenetic Map2q37.3NCBI
HuRef2230,024,688 - 230,114,910 (-)NCBIHuRef
CHM1_12238,238,749 - 238,328,955 (-)NCBICHM1_1
Col6a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39190,694,582 - 90,771,710 (-)NCBIGRCm39mm39
GRCm38190,766,860 - 90,844,001 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl190,765,923 - 90,843,971 (-)EnsemblGRCm38mm10GRCm38
MGSCv37192,663,435 - 92,740,514 (-)NCBIGRCm37mm9NCBIm37
MGSCv36192,597,264 - 92,674,343 (-)NCBImm8
MGSCv36191,192,168 - 91,253,776 (-)NCBImm8
Celera193,712,460 - 93,789,439 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map145.53NCBI
Col6a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555422,887,723 - 2,949,062 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555422,869,183 - 2,950,569 (+)NCBIChiLan1.0ChiLan1.0
COL6A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B243,407,786 - 243,497,700 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02B124,554,478 - 124,644,482 (-)NCBIMhudiblu_PPA_v0panPan3
COL6A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2547,971,315 - 48,052,402 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12547,971,439 - 48,052,673 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Col6a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936525905,419 - 983,486 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL6A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15137,011,433 - 137,103,709 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115137,011,549 - 137,103,687 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215151,450,581 - 151,542,424 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL6A3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110123,326,337 - 123,418,836 (-)NCBI
ChlSab1.1 Ensembl10123,327,102 - 123,400,114 (-)Ensembl
Col6a3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248472,786,560 - 2,863,800 (-)NCBI

Position Markers
D9Got112  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0997,989,706 - 97,989,827NCBIRnor6.0
Rnor_5.0997,670,418 - 97,670,539UniSTSRnor5.0
RGSC_v3.4990,027,925 - 90,028,047RGDRGSC3.4
RGSC_v3.4990,027,926 - 90,028,047UniSTSRGSC3.4
RGSC_v3.1990,232,695 - 90,232,816RGD
Celera988,969,000 - 88,969,121UniSTS
RH 3.4 Map9784.69RGD
RH 3.4 Map9784.69UniSTS
RH 2.0 Map9936.5RGD
Cytogenetic Map9q35-q36UniSTS
D9Mco92  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0997,960,626 - 97,960,905NCBIRnor6.0
Rnor_5.0997,641,338 - 97,641,617UniSTSRnor5.0
RGSC_v3.4989,998,846 - 89,999,125UniSTSRGSC3.4
Celera988,939,924 - 88,940,201UniSTS
Cytogenetic Map9q35-q36UniSTS
RH129385  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0997,926,842 - 97,927,061NCBIRnor6.0
Rnor_5.0997,607,554 - 97,607,773UniSTSRnor5.0
RGSC_v3.4989,965,060 - 89,965,279UniSTSRGSC3.4
Celera988,906,147 - 88,906,366UniSTS
RH 3.4 Map9783.99UniSTS
Cytogenetic Map9q35-q36UniSTS
01.MMHAP90FLA1.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0997,996,619 - 97,996,773NCBIRnor6.0
Rnor_5.0997,677,337 - 97,677,491UniSTSRnor5.0
RGSC_v3.4990,035,767 - 90,035,921UniSTSRGSC3.4
Celera988,975,924 - 88,976,078UniSTS
Cytogenetic Map9q35-q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)98368615398164303Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)98368615398164303Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)98368615398164303Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)99274129798606834Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:155
Count of miRNA genes:107
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000026707, ENSRNOT00000026719
Prediction methods:Microtar, 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 3 33 10 2 9 2 7 10 19 31 27 11 7
Low 4 47 39 10 39 1 1 53 4 11 1
Below cutoff 6 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026707
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl997,927,981 - 97,989,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000026719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl997,927,981 - 97,989,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl997,926,787 - 98,004,546 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl997,927,981 - 97,989,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl997,927,814 - 97,989,297 (-)Ensembl
RefSeq Acc Id: XM_003754548   ⟹   XP_003754596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,949 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006226938   ⟹   XP_006227000
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,949 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006226939   ⟹   XP_006227001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,949 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006226940   ⟹   XP_006227002
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,949 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006226941   ⟹   XP_006227003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,947 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006226942   ⟹   XP_006227004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,947 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758075   ⟹   XP_008756297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera988,906,089 - 88,983,949 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767340   ⟹   XP_008765562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767341   ⟹   XP_008765563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767342   ⟹   XP_008765564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767343   ⟹   XP_008765565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,642 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767344   ⟹   XP_008765566
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,641 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767345   ⟹   XP_008765567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,641 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596855   ⟹   XP_017452344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0997,926,784 - 98,004,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039084727   ⟹   XP_038940655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2991,361,578 - 91,439,433 (-)NCBI
RefSeq Acc Id: XM_039084728   ⟹   XP_038940656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2991,361,578 - 91,439,434 (-)NCBI
RefSeq Acc Id: XM_039084729   ⟹   XP_038940657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2991,361,578 - 91,439,431 (-)NCBI
RefSeq Acc Id: XM_039084730   ⟹   XP_038940658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2991,361,578 - 91,439,431 (-)NCBI
RefSeq Acc Id: XM_039084732   ⟹   XP_038940660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2991,361,578 - 91,439,428 (-)NCBI
RefSeq Acc Id: XM_039084733   ⟹   XP_038940661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2991,361,578 - 91,439,425 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_003754596   ⟸   XM_003754548
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006227000   ⟸   XM_006226938
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006227002   ⟸   XM_006226940
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006227001   ⟸   XM_006226939
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006227003   ⟸   XM_006226941
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006227004   ⟸   XM_006226942
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_008756297   ⟸   XM_008758075
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765563   ⟸   XM_008767341
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008765562   ⟸   XM_008767340
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765565   ⟸   XM_008767343
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008765564   ⟸   XM_008767342
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008765566   ⟸   XM_008767344
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008765567   ⟸   XM_008767345
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017452344   ⟸   XM_017596855
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_038940656   ⟸   XM_039084728
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038940655   ⟸   XM_039084727
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940658   ⟸   XM_039084730
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038940657   ⟸   XM_039084729
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038940660   ⟸   XM_039084732
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038940661   ⟸   XM_039084733
- Peptide Label: isoform X6

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)
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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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
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: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 97936304 97936305 C A snv CDS, LE/Stm (RGD), FHL/EurMcwi (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
9 97940047 97940048 C T snv SBN/Ygl (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), SBH/Ygl (MCW)
9 97946333 97946334 C T snv CDS
9 97958429 97958430 G T snv CDS, MR/N (MCW)
9 97963287 97963288 C T snv WKY/Gcrc (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD)
9 97963288 97963289 G A snv SBH/Ygl (RGD), SBH/Ygl (MCW), SBN/Ygl (MCW), SBN/Ygl (RGD)
9 97967478 97967479 C A snv Buf/N (MCW), WN/N (MCW)
9 97969814 97969815 G A snv FHH/EurMcwi (MCW), LE/Stm (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW)
9 97972819 97972820 C T snv CDS


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308704 AgrOrtholog
Ensembl Genes ENSRNOG00000019648 Ensembl, ENTREZGENE
NCBI Gene 367313 ENTREZGENE
PhenoGen Col6a3 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col6a3  collagen type VI alpha 3 chain  Col6a3  collagen, type VI, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Col6a3  collagen, type VI, alpha 3  Col6a3  procollagen, type VI, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Col6a3  procollagen, type VI, alpha 3   Col6a3_predicted  procollagen, type VI, alpha 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Col6a3_predicted  procollagen, type VI, alpha 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED