Col6a1 (collagen type VI alpha 1 chain) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
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 1A. 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: GRCr8 - GRCr8 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



  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1RatBethlem Myopathy 1A susceptibilityISORGD:13528801600934Bethlem myopathy, OMIM:158810;DNA:mutation:cds:962G>T,p.G286V(human)RGD 
Col6a1RatMycoplasma pneumoniae pneumonia severityISORGD:13528809068941 RGDPMID:28302172|REF_RGD_ID:32716376
1 to 15 of 15 rows
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Ratautistic disorder  ISORGD:13528808554872ClinVar Annotator: match by term: AutismClinVarPMID:21681106|PMID:30208311
Col6a1RatAxenfeld-Rieger syndrome type 3  ISORGD:13528808554872ClinVar Annotator: match by term: Axenfeld-Rieger syndrome type 3ClinVarPMID:11170889|PMID:21681106
Col6a1RatBethlem myopathy  ISORGD:13528808554872ClinVar Annotator: match by term: MYOPATHY, BENIGN CONGENITAL, WITH CONTRACTURES | ClinVar Annotator: match by more ...ClinVarPMID:10419498|PMID:11707460|PMID:12840783|PMID:15689448|PMID:15955946|PMID:16088929|PMID:16130093|PMID:16199547|PMID:17015493|PMID:17576681|PMID:17785673|PMID:17785674|PMID:17886299|PMID:18366090|PMID:18414213|PMID:18642359|PMID:18825676|PMID:19204719|PMID:19344236|PMID:19564581|PMID:20301676|PMID:20302629|PMID:20882040|PMID:20976770|PMID:20981092|PMID:21280092|PMID:22075033|PMID:22789865|PMID:22975586|PMID:23040494|PMID:23572247|PMID:23757202|PMID:24033266|PMID:24038877|PMID:24223098|PMID:24271325|PMID:24801232|PMID:24959844|PMID:25741868|PMID:25749816|PMID:26467025|PMID:26566670|PMID:26867126|PMID:27363342|PMID:27418678|PMID:27708273|PMID:27854213|PMID:27884173|PMID:28182637|PMID:28492532|PMID:29419890|PMID:30564623|PMID:32154989|PMID:34008892|PMID:34167565|PMID:39825153|PMID:7551830|PMID:7695699|PMID:8218237|PMID:8730294|PMID:9536098|PMID:9724608
Col6a1RatBethlem Myopathy 1A  ISORGD:13528808554872ClinVar Annotator: match by term: Bethlem myopathy 1 | ClinVar Annotator: match by term: Bethlem more ...ClinVarPMID:10329467|PMID:10419498|PMID:11707460|PMID:11865138|PMID:11932968|PMID:12840783|PMID:15563506|PMID:15689448|PMID:15955946|PMID:16088929|PMID:16130093|PMID:16199547|PMID:16278855|PMID:16935502|PMID:17015493|PMID:17576681|PMID:17785673|PMID:17785674|PMID:1788629|PMID:17886299|PMID:18160674|PMID:18366090|PMID:18378883|PMID:18414213|PMID:18642359|PMID:18825676|PMID:19204719|PMID:19344236|PMID:19564581|PMID:19884007|PMID:20301468|PMID:20301676|PMID:20302629|PMID:20576434|PMID:20882040|PMID:20976770|PMID:20981092|PMID:21280092|PMID:21520333|PMID:22075033|PMID:22789865|PMID:22975586|PMID:23040494|PMID:23326386|PMID:23572247|PMID:23738969|PMID:23757202|PMID:24033266|PMID:24038877|PMID:24223098|PMID:24271325|PMID:24801232|PMID:24959844|PMID:25204870|PMID:25535305|PMID:25635128|PMID:25640679|PMID:25741868|PMID:25749816|PMID:25978941|PMID:26436962|PMID:26467025|PMID:26566670|PMID:26867126|PMID:27363342|PMID:27418678|PMID:27447704|PMID:27708273|PMID:27854213|PMID:27854218|PMID:27884173|PMID:28182637|PMID:28424332|PMID:28492532|PMID:28688748|PMID:28771251|PMID:28831785|PMID:28877744|PMID:28984114|PMID:29382405|PMID:29406609|PMID:29417091|PMID:29419890|PMID:29465610|PMID:30564623|PMID:30706156|PMID:30895940|PMID:31130284|PMID:31273343|PMID:31589614|PMID:32065942|PMID:32154989|PMID:32389683|PMID:32403337|PMID:32528171|PMID:33250842|PMID:34008892|PMID:34167565|PMID:35533453|PMID:37010288|PMID:38155714|PMID:39825153|PMID:7551830|PMID:7695699|PMID:7881296|PMID:8218237|PMID:8268929|PMID:8730294|PMID:8782832|PMID:9536098|PMID:9580662|PMID:963533|PMID:9724608
Col6a1Ratcataract 9 multiple types  ISORGD:13528808554872ClinVar Annotator: match by term: Cataract 9 multiple typesClinVarPMID:28492532
Col6a1RatCollagen VI-related Myopathy  ISORGD:13528808554872ClinVar Annotator: match by term: Collagen VI-related myopathyClinVarPMID:11707460|PMID:15689448|PMID:15955946|PMID:16088929|PMID:16130093|PMID:17015493|PMID:17576681|PMID:17785673|PMID:17785674|PMID:18378883|PMID:18414213|PMID:18642359|PMID:18825676|PMID:19344236|PMID:19564581|PMID:20301676|PMID:20302629|PMID:20882040|PMID:20976770|PMID:20981092|PMID:22075033|PMID:22789865|PMID:22975586|PMID:23040494|PMID:23572247|PMID:23757202|PMID:24033266|PMID:24038877|PMID:24223098|PMID:24801232|PMID:24959844|PMID:25741868|PMID:26467025|PMID:26566670|PMID:26867126|PMID:27363342|PMID:27418678|PMID:27854213|PMID:27884173|PMID:28492532|PMID:28831785|PMID:30564623|PMID:32154989|PMID:32389683|PMID:34008892|PMID:34167565|PMID:7551830|PMID:7695699|PMID:8218237|PMID:8730294|PMID:9536098
Col6a1Ratdevelopmental and epileptic encephalopathy 30  ISORGD:13528808554872ClinVar Annotator: match by term: Developmental and epileptic encephalopathy, 30ClinVarPMID:28492532|PMID:8596935
Col6a1Ratgenetic disease  ISORGD:13528808554872ClinVar Annotator: match by term: Inborn genetic diseasesClinVarPMID:15689448|PMID:15955946|PMID:18825676|PMID:19204719|PMID:19344236|PMID:20576434|PMID:24038877|PMID:25741868|PMID:26467025|PMID:26566670|PMID:27363342|PMID:27708273|PMID:28182637|PMID:28492532|PMID:34167565|PMID:39825153|PMID:7695699|PMID:8218237|PMID:9724608
Col6a1Rathomocystinuria  ISORGD:13528808554872ClinVar Annotator: match by term: HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATEDClinVarPMID:10338090|PMID:12124992|PMID:28492532
Col6a1Ratmyopathy  ISORGD:13528808554872ClinVar Annotator: match by term: MyopathyClinVarPMID:16199547|PMID:18366090|PMID:20976770|PMID:21280092|PMID:25635128|PMID:25741868|PMID:27854213|PMID:28492532|PMID:28771251
Col6a1Ratprimary cerebellar degeneration  ISORGD:13528808554872ClinVar Annotator: match by term: Sensorimotor neuropathyClinVarPMID:10419498|PMID:12840783|PMID:15955946|PMID:16199547|PMID:17886299|PMID:18366090|PMID:20301676|PMID:20976770|PMID:21280092|PMID:24271325|PMID:25741868|PMID:25749816|PMID:28492532|PMID:29419890
Col6a1Ratprimary ciliary dyskinesia  ISORGD:13528808554872ClinVar Annotator: match by term: Primary ciliary dyskinesiaClinVarPMID:28492532
Col6a1Ratprogressive myoclonus epilepsy  ISORGD:13528808554872ClinVar Annotator: match by term: Progressive myoclonic epilepsyClinVarPMID:28492532|PMID:8596935
Col6a1RatUllrich congenital muscular dystrophy  ISORGD:13528808554872ClinVar Annotator: match by term: COL6A1-related DisorderClinVarPMID:11865138|PMID:15689448|PMID:15955946|PMID:16199547|PMID:17576681|PMID:18366090|PMID:19344236|PMID:19884007|PMID:20302629|PMID:20576434|PMID:20976770|PMID:21280092|PMID:22075033|PMID:24038877|PMID:25204870|PMID:25535305|PMID:25635128|PMID:25741868|PMID:26436962|PMID:26467025|PMID:27854213|PMID:27854218|PMID:28492532|PMID:28771251|PMID:30564623|PMID:32065942|PMID:32403337|PMID:32528171|PMID:38155714|PMID:7695699|PMID:8218237|PMID:9536098
Col6a1RatUllrich congenital muscular dystrophy 1A  ISORGD:13528808554872ClinVar Annotator: match by term: COL6A1-related condition | ClinVar Annotator: match by term: Ullrich congenital more ...ClinVarPMID:15689448|PMID:16088929|PMID:16130093|PMID:16935502|PMID:17015493|PMID:17785673|PMID:17785674|PMID:17886299|PMID:18160674|PMID:18414213|PMID:18642359|PMID:18825676|PMID:19204719|PMID:19344236|PMID:19564581|PMID:20301676|PMID:20302629|PMID:20576434|PMID:20882040|PMID:20976770|PMID:22075033|PMID:22789865|PMID:22975586|PMID:23572247|PMID:24038877|PMID:24223098|PMID:24801232|PMID:24959844|PMID:25741868|PMID:26467025|PMID:26867126|PMID:27363342|PMID:27447704|PMID:27708273|PMID:27854213|PMID:28182637|PMID:28424332|PMID:28492532|PMID:30895940|PMID:32154989|PMID:34008892|PMID:34167565|PMID:39825153|PMID:7551830|PMID:7695699|PMID:8218237|PMID:8730294|PMID:9724608
1 to 15 of 15 rows
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1RatBethlem myopathy  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTD 
Col6a1Ratdiastolic heart failure  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTDPMID:29556499
Col6a1RatExperimental Liver Cirrhosis  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTDPMID:25380136
Col6a1RatLung Neoplasms  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTDPMID:23692979
Col6a1Ratmuscular dystrophy  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTDPMID:20716577
Col6a1RatSpontaneous Abortions  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTDPMID:18539642
Col6a1RatUllrich congenital muscular dystrophy  ISORGD:135288011554173CTD Direct Evidence: marker/mechanismCTD 
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1RatBethlem myopathy  ISSRGD:155823113592920OMIM:158810MouseDO 
Col6a1RatUllrich congenital muscular dystrophy  ISSRGD:155823113592920OMIM:254090MouseDO 
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1RatBethlem Myopathy 1A  ISORGD:13528807240710 OMIM 
Col6a1RatUllrich congenital muscular dystrophy 1A  ISORGD:13528807240710 OMIM 

1 to 20 of 191 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Rat(-)-epigallocatechin 3-gallate multiple interactionsISORGD:13528806480464[potassium chromate(VI) co-treated with epigallocatechin gallate] results in increased expression of COL6A1 mRNACTDPMID:22079256
Col6a1Rat(1->4)-beta-D-glucan multiple interactionsISORGD:15582316480464[perfluorooctane sulfonic acid co-treated with Cellulose] results in increased expression of COL6A1 mRNACTDPMID:36331819
Col6a1Rat(S)-nicotine multiple interactionsISORGD:15582316480464[Nicotine co-treated with 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine] results in increased expression of COL6A1 mRNA; Nicotine inhibits the reaction more ...CTDPMID:20230807
Col6a1Rat1,2-dimethylhydrazine multiple interactionsISORGD:15582316480464[1,2-Dimethylhydrazine co-treated with Folic Acid] results in increased expression of COL6A1 mRNACTDPMID:22206623
Col6a1Rat1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine increases expressionISORGD:155823164804641-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine results in increased expression of COL6A1 mRNACTDPMID:20230807
Col6a1Rat1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine multiple interactionsISORGD:15582316480464[Nicotine co-treated with 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine] results in increased expression of COL6A1 mRNA; Nicotine inhibits the reaction more ...CTDPMID:20230807
Col6a1Rat1-naphthyl isothiocyanate increases expressionEXP 64804641-Naphthylisothiocyanate results in increased expression of COL6A1 mRNACTDPMID:25380136
Col6a1Rat17alpha-ethynylestradiol increases expressionISORGD:15582316480464Ethinyl Estradiol results in increased expression of COL6A1 mRNACTDPMID:17942748
Col6a1Rat17alpha-ethynylestradiol multiple interactionsISORGD:15582316480464[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of COL6A1 mRNACTDPMID:17942748
Col6a1Rat17beta-estradiol multiple interactionsISORGD:15582316480464Estradiol inhibits the reaction [Lipopolysaccharides results in increased expression of COL6A1 mRNA]CTDPMID:16977382
Col6a1Rat17beta-estradiol multiple interactionsISORGD:13528806480464[Estradiol co-treated with TGFB1 protein] results in increased expression of COL6A1 mRNACTDPMID:30165855
Col6a1Rat17beta-estradiol increases expressionISORGD:15582316480464Estradiol results in increased expression of COL6A1 mRNACTDPMID:19484750
Col6a1Rat17beta-estradiol increases expressionISORGD:13528806480464Estradiol results in increased expression of COL6A1 mRNACTDPMID:23019147
Col6a1Rat17beta-hydroxy-5alpha-androstan-3-one decreases expressionISORGD:15582316480464Dihydrotestosterone results in decreased expression of COL6A1 mRNACTDPMID:17023530
Col6a1Rat2,2',4,4'-Tetrabromodiphenyl ether multiple interactionsISORGD:15582316480464[Flame Retardants results in increased abundance of 2,2',4,4'-tetrabromodiphenyl ether] which results in decreased expression of more ...CTDPMID:38995820
Col6a1Rat2,2,2-tetramine multiple interactionsEXP 6480464Trientine inhibits the reaction [Streptozocin results in increased expression of COL6A1 protein]CTDPMID:19634143
Col6a1Rat2,3,7,8-tetrachlorodibenzodioxine multiple interactionsISORGD:15582316480464[Tetrachlorodibenzodioxin co-treated with Ethinyl Estradiol] results in increased expression of COL6A1 mRNACTDPMID:17942748
Col6a1Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionEXP 6480464Tetrachlorodibenzodioxin affects the expression of COL6A1 mRNACTDPMID:34747641
Col6a1Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionISORGD:15582316480464Tetrachlorodibenzodioxin affects the expression of COL6A1 mRNACTDPMID:21570461
Col6a1Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionISORGD:13528806480464Tetrachlorodibenzodioxin results in increased expression of COL6A1 mRNACTDPMID:12377990

1 to 20 of 191 rows

Biological Process
1 to 20 of 170 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Rat2-oxoglutarate metabolic process acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:23437220RGDPMID:23437220
Col6a1Rat2-oxoglutarate metabolic process acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratadipose tissue development acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratadipose tissue development acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:19114551RGDPMID:19114551
Col6a1Ratapoptotic nuclear changes acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratapoptotic nuclear changes acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:14625552RGDPMID:14625552
Col6a1Ratapoptotic process acts_upstream_of_or_withinISORGD:15582311624291MGI:2145814|MGI:2153356 PMID:14625552, PMID:19293339, PMID:20716577, PMID:21037586, PMID:22024752, PMID:22343710, PMID:24852368, PMID:26565691RGDPMID:14625552|PMID:19293339|PMID:20716577|PMID:21037586|PMID:22024752|PMID:22343710|PMID:24852368|PMID:26565691
Col6a1Ratapoptotic process acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratautophagy acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:21037586, PMID:22024752, PMID:26565691RGDPMID:21037586|PMID:22024752|PMID:26565691
Col6a1Ratautophagy acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratbasement membrane organization acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:25158062RGDPMID:25158062
Col6a1Ratbasement membrane organization acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratbiological_process  ND 159840703/2007: no relevant rat dataRGD 
Col6a1Ratbone development acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:22448243RGDPMID:22448243
Col6a1Ratbone development acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratbone mineralization acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:19248115RGDPMID:19248115
Col6a1Ratbone mineralization acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratcanonical Wnt signaling pathway acts_upstream_of_or_withinIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratcanonical Wnt signaling pathway acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:25989472RGDPMID:25989472
Col6a1Ratcartilage development acts_upstream_of_or_withinISORGD:15582311624291MGI:2153356 PMID:19248115, PMID:22448243RGDPMID:19248115|PMID:22448243
1 to 20 of 170 rows

Cellular Component
1 to 20 of 23 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Ratbasement membrane is_active_inIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratbasement membrane is_active_inISORGD:15582311624291 PMID:31837950RGDPMID:31837950
Col6a1Ratbasement membrane is_active_inIBAMGI:88449|MGI:88462|PANTHER:PTN0027708181600115GO_REF:0000033GO_CentralGO_REF:0000033
Col6a1Ratextracellular matrix located_inISORGD:15582311624291 PMID:16810681, PMID:8806434RGDPMID:16810681|PMID:8806434
Col6a1Ratextracellular matrix located_inIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratextracellular matrix is_active_inISORGD:15582311624291MGI:2153356 PMID:19248115, PMID:20951202, PMID:23300779RGDPMID:19248115|PMID:20951202|PMID:23300779
Col6a1Ratextracellular region located_inISORGD:13528801624291 PMID:18400749RGDPMID:18400749
Col6a1Ratextracellular region located_inIEAUniProtKB:P12109|ensembl:ENSP000003551801600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratextracellular region located_inTAS 1600115Reactome:R-NUL-2465871ReactomeReactome:R-NUL-2465871
Col6a1Ratextracellular space is_active_inIBAMGI:88452|MGI:88467|MGI:88468|PANTHER:PTN008390299|RGD:61817|RGD:70936|RGD:727898|UniProtKB:P02458|UniProtKB:P02461|UniProtKB:P08123|WB:WBGene000006741600115GO_REF:0000033GO_CentralGO_REF:0000033
Col6a1Ratintracellular vesicle is_active_inISORGD:15582311624291 PMID:24357721RGDPMID:24357721
Col6a1Ratintracellular vesicle is_active_inIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratlysosome is_active_inIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratlysosome is_active_inISORGD:15582311624291 PMID:28604699RGDPMID:28604699
Col6a1Ratmitochondrion located_inIEAGO:00518821600115GO_REF:0000108GOCGO_REF:0000108
Col6a1Ratmyofibril is_active_inISORGD:15582311624291MGI:2153356 PMID:20716577RGDPMID:20716577
Col6a1Ratmyofibril is_active_inIEAUniProtKB:Q04857|ensembl:ENSMUSP000000011471600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratprotein-containing complex part_ofISORGD:13528801624291UniProtKB:P12110 PMID:18400749RGDPMID:18400749
Col6a1Ratprotein-containing complex part_ofIEAUniProtKB:P12109|ensembl:ENSP000003551801600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratsarcolemma located_inISORGD:15582311624291 PMID:16810681RGDPMID:16810681
1 to 20 of 23 rows

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Ratcollagen binding enablesISORGD:13528801624291UniProtKB:P12110 PMID:18400749RGDPMID:18400749
Col6a1Ratcollagen binding enablesIEAUniProtKB:P12109|ensembl:ENSP000003551801600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratextracellular matrix structural constituent conferring tensile strength enablesIBAPANTHER:PTN001166351|UniProtKB:P02462|WB:WBGene000022801600115GO_REF:0000033GO_CentralGO_REF:0000033
Col6a1Ratplatelet-derived growth factor binding enablesISORGD:13528801624291 PMID:8900172RGDPMID:8900172
Col6a1Ratplatelet-derived growth factor binding enablesIEAUniProtKB:P12109|ensembl:ENSP000003551801600115GO_REF:0000107EnsemblGO_REF:0000107
Col6a1Ratprotein binding enablesISORGD:13528801624291UniProtKB:P20849 PMID:33961781RGDPMID:33961781
Col6a1Ratprotein binding enablesISORGD:15582311624291UniProtKB:Q04857|UniProtKB:Q8R2Z5 PMID:23300779, PMID:24357721RGDPMID:23300779|PMID:24357721

Imported Annotations - KEGG (archival)

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Ratcell-extracellular matrix signaling pathway  IEA 6907045 KEGGrno:04512

Imported Annotations - PID (archival)

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col6a1Ratsyndecan signaling pathway  ISORGD:13528806484113 PIDPID:200156

#
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
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  



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 in Col6a1
172 total Variants

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.


1 to 10 of 26 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
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
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat

1 to 10 of 26 rows
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




alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31



Ensembl 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
Ensembl 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 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
  ENSRNOP00000001679.5
  ENSRNOP00000067777.2
Ensembl Acc Id: ENSRNOP00000067777   ⟸   ENSRNOT00000072951
Ensembl Acc Id: ENSRNOP00000001679   ⟸   ENSRNOT00000001679
RefSeq Acc Id: NP_001414192   ⟸   NM_001427263
- Peptide Label: precursor
- UniProtKB: A6JKB7 (UniProtKB/TrEMBL),   D3ZUL3 (UniProtKB/TrEMBL)
VWFA

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


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



1 to 28 of 28 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-4197 BioCyc
Ensembl Genes ENSRNOG00000001249 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001679 ENTREZGENE
  ENSRNOT00000001679.8 UniProtKB/TrEMBL
  ENSRNOT00000072951.3 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen-VI/PIF UniProtKB/TrEMBL
  ECM_Assembly_Org UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 294337 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(VI) CHAIN UniProtKB/TrEMBL
  VWFA DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  VWFA DOMAIN-CONTAINING PROTEIN 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
1 to 28 of 28 rows


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