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 enable collagen binding activity and platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in endodermal cell differentiation and extracellular matrix organization. Predicted to act upstream of or within several processes, including extracellular matrix organization; lung development; and skeletal muscle tissue development. Predicted to be located in extracellular region and sarcolemma. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including lysosome; myofibril; and sarcoplasmic reticulum. Human ortholog(s) of this gene implicated in Bethlem myopathy and 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; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82011,905,690 - 11,924,111 (+)NCBIGRCr8
mRatBN7.22011,906,105 - 11,924,599 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2011,905,957 - 11,924,597 (+)EnsemblmRatBN7.2 Ensembl
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)
(1->4)-beta-D-glucan  (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  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Nitrobenzanthrone  (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)
aristolochic acid A  (ISO)
atrazine  (ISO)
azelastine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cantharidin  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corosolic acid  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
DDT  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
diethyl malate  (ISO)
dimethylarsinic acid  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
glucose  (ISO)
indometacin  (ISO)
inulin  (ISO)
ionomycin  (ISO)
irinotecan  (ISO)
isotretinoin  (ISO)
ivermectin  (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)
perfluorooctane-1-sulfonic acid  (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)
thioacetamide  (EXP)
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

Biological Process
2-oxoglutarate metabolic process  (ISO)
adipose tissue development  (ISO)
apoptotic nuclear changes  (ISO)
apoptotic process  (ISO)
autophagy  (ISO)
basement membrane organization  (ISO)
biological_process  (ND)
bone development  (ISO)
bone mineralization  (ISO)
canonical Wnt signaling pathway  (ISO)
cartilage development  (ISO)
caveola assembly  (ISO)
cell morphogenesis  (ISO)
cellular response to amino acid stimulus  (ISO)
circadian rhythm  (ISO)
collagen fibril organization  (ISO)
collagen metabolic process  (ISO)
endodermal cell differentiation  (ISO)
energy homeostasis  (ISO)
energy reserve metabolic process  (ISO)
extracellular matrix assembly  (ISO)
extracellular matrix organization  (IBA)
fat cell proliferation  (ISO)
gene expression  (ISO)
glycolytic process  (ISO)
hair follicle development  (ISO)
heart development  (ISO)
homeostasis of number of cells  (ISO)
inflammatory response  (ISO)
insulin receptor signaling pathway  (ISO)
insulin-like growth factor receptor signaling pathway  (ISO)
limb joint morphogenesis  (ISO)
lung alveolus development  (ISO)
lung development  (ISO)
lung epithelial cell differentiation  (ISO)
lung morphogenesis  (ISO)
mitochondrial depolarization  (ISO)
mitochondrial transmembrane transport  (ISO)
mitochondrion organization  (ISO)
multicellular organismal locomotion  (ISO)
muscle cell apoptotic process  (ISO)
muscle cell development  (ISO)
muscle organ development  (ISO)
muscle structure development  (ISO)
muscle system process  (ISO)
myelination in peripheral nervous system  (ISO)
nervous system process  (ISO)
neuron apoptotic process  (ISO)
ossification  (ISO)
peripheral nervous system development  (ISO)
phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
protein tetramerization  (ISO)
reactive oxygen species metabolic process  (ISO)
reduction of food intake in response to dietary excess  (ISO)
regulation of cell size  (ISO)
regulation of collagen fibril organization  (ISO)
respiratory system process  (ISO)
response to activity  (ISO)
response to bleomycin  (ISO)
response to decreased oxygen levels  (ISO)
response to lipid  (ISO)
response to lipopolysaccharide  (ISO)
response to mechanical stimulus  (ISO)
response to muscle activity  (ISO)
response to pain  (ISO)
response to peptide  (ISO)
response to polyamine macromolecule  (ISO)
response to reactive oxygen species  (ISO)
response to toxic substance  (ISO)
response to UV  (ISO)
response to wounding  (ISO)
response to xenobiotic stimulus  (ISO)
sensory perception of mechanical stimulus  (ISO)
single fertilization  (ISO)
skeletal muscle fiber development  (ISO)
skeletal muscle fiber differentiation  (ISO)
skeletal muscle organ development  (ISO)
skeletal muscle tissue development  (ISO)
skeletal muscle tissue growth  (ISO)
skeletal muscle tissue regeneration  (ISO)
skin development  (ISO)
tissue remodeling  (ISO)
transmission of nerve impulse  (ISO)
tricarboxylic acid cycle  (ISO)
uterus development  (ISO)

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. Type VI collagen mutations in Bethlem myopathy, an autosomal dominant myopathy with contractures. Jobsis GJ, etal., Nat Genet. 1996 Sep;14(1):113-5.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
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
GRCr82011,905,690 - 11,924,111 (+)NCBIGRCr8
mRatBN7.22011,906,105 - 11,924,599 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2011,905,957 - 11,924,597 (+)EnsemblmRatBN7.2 Ensembl
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2013,404,454 - 13,422,911 (+)NCBICelera
Cytogenetic Map20p12NCBI
COL6A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382145,981,770 - 46,005,048 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2145,981,770 - 46,005,050 (+)EnsemblGRCh38hg38GRCh38
GRCh372147,401,684 - 47,424,962 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,226,091 - 46,249,391 (+)NCBINCBI36Build 36hg18NCBI36
Build 342146,226,095 - 46,249,390NCBI
Celera2132,514,265 - 32,537,566 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2132,782,505 - 32,806,491 (+)NCBIHuRef
CHM1_12146,962,501 - 46,985,646 (+)NCBICHM1_1
T2T-CHM13v2.02144,356,236 - 44,380,470 (+)NCBIT2T-CHM13v2.0
Col6a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,544,626 - 76,561,869 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1076,544,626 - 76,562,002 (-)EnsemblGRCm39 Ensembl
GRCm381076,708,792 - 76,726,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,708,792 - 76,726,168 (-)EnsemblGRCm38mm10GRCm38
MGSCv371076,171,537 - 76,188,789 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361076,152,508 - 76,169,760 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v22242,077,933 - 42,102,997 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12136,947,012 - 36,972,513 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02132,322,185 - 32,346,850 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12145,583,978 - 45,608,233 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,584,096 - 45,607,240 (+)Ensemblpanpan1.1panPan2
COL6A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13139,301,718 - 39,319,895 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3139,301,748 - 39,448,062 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3138,528,763 - 38,546,613 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03138,938,729 - 38,956,907 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3138,938,716 - 38,957,205 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13138,802,006 - 38,820,369 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03138,762,850 - 38,780,772 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03139,282,131 - 39,299,654 (+)NCBIUU_Cfam_GSD_1.0
Col6a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497138,599,408 - 38,614,610 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936778515,600 - 530,828 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100623720
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13208,295,451 - 208,313,127 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113208,295,245 - 208,321,789 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COL6A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,608,525 - 89,649,823 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605417,903,578 - 17,927,870 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col6a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474531,125,265 - 31,139,318 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474531,125,136 - 31,140,126 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Col6a1
172 total Variants
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.


QTLs in Region (mRatBN7.2)
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)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
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)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat

Markers in Region
RH129493  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22011,924,377 - 11,924,568 (+)MAPPERmRatBN7.2
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
RH 3.4 Map20154.5UniSTS
Cytogenetic Map20p12UniSTS
RH129051  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22011,924,311 - 11,924,512 (+)MAPPERmRatBN7.2
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
RH 3.4 Map20151.3UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:531308  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22011,906,322 - 11,907,228 (+)MAPPERmRatBN7.2
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


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


RefSeq Acc Id: ENSRNOT00000001679   ⟹   ENSRNOP00000001679
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2011,905,957 - 11,924,597 (+)Ensembl
Rnor_6.0 Ensembl2012,658,065 - 12,675,561 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000072951   ⟹   ENSRNOP00000067777
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2011,905,957 - 11,924,597 (+)Ensembl
Rnor_6.0 Ensembl2012,658,065 - 12,663,173 (+)Ensembl
RefSeq Acc Id: NM_001427263   ⟹   NP_001414192
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82011,905,690 - 11,924,111 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414192 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97133 (Get FASTA)   NCBI Sequence Viewer  
  EDL97134 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000001679.5
  ENSRNOP00000067777.2
RefSeq Acc Id: ENSRNOP00000067777   ⟸   ENSRNOT00000072951
RefSeq Acc Id: ENSRNOP00000001679   ⟸   ENSRNOT00000001679
RefSeq Acc Id: NP_001414192   ⟸   NM_001427263
- Peptide Label: precursor
- UniProtKB: A6JKB7 (UniProtKB/TrEMBL),   D3ZUL3 (UniProtKB/TrEMBL)
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUL3-F1-model_v2 AlphaFold D3ZUL3 1-1025 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565398 AgrOrtholog
BioCyc Gene G2FUF-4197 BioCyc
Ensembl Genes ENSRNOG00000001249 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001679.8 UniProtKB/TrEMBL
  ENSRNOT00000072951.3 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:294337 UniProtKB/TrEMBL
NCBI Gene 294337 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XXI) CHAIN-LIKE ISOFORM X1 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Col6a1 PhenoGen
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001249 RatGTEx
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A6JKB7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZUL3 ENTREZGENE, 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