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   new 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
Gene: COL6A1 (collagen type VI alpha 1 chain) Canis lupus familiaris
Analyze
Symbol: COL6A1
Name: collagen type VI alpha 1 chain
RGD ID: 12149221
Description: ENCODES a protein that exhibits collagen binding (inferred); extracellular matrix structural constituent conferring tensile strength (inferred); platelet-derived growth factor binding (inferred); INVOLVED IN 2-oxoglutarate metabolic process (ortholog); adipose tissue development (ortholog); apoptotic nuclear changes (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Ullrich congenital muscular dystrophy; autistic disorder (ortholog); Axenfeld-Rieger syndrome type 3 (ortholog); FOUND IN basement membrane (ortholog); extracellular matrix (ortholog); intracellular vesicle (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(VI) chain; collagen VI-alpha1 protein
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:10964405   PMID:33382107  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
582 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 5 18 4 6 4 6 3 4 10 6
Low 4 2 2 3 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000018918   ⟹   ENSCAFP00000017530
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3139,301,748 - 39,319,906 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000049047   ⟹   ENSCAFP00000041957
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3139,301,748 - 39,448,062 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845042470   ⟹   ENSCAFP00845033294
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl3138,938,716 - 38,957,205 (+)Ensembl
RefSeq Acc Id: XM_003434001   ⟹   XP_003434049
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13139,301,718 - 39,319,895 (+)NCBI
Dog10K_Boxer_Tasha3138,528,763 - 38,546,613 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038443726   ⟹   XP_038299654
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03138,938,729 - 38,956,907 (+)NCBI
RefSeq Acc Id: XM_038518137   ⟹   XP_038374065
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.13138,802,006 - 38,820,369 (+)NCBI
RefSeq Acc Id: XM_038581692   ⟹   XP_038437620
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.03139,282,131 - 39,299,654 (+)NCBI
RefSeq Acc Id: XM_038646096   ⟹   XP_038502024
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.03138,762,850 - 38,780,772 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_003434049   ⟸   XM_003434001
- UniProtKB: A0A8C0Z1U8 (UniProtKB/TrEMBL),   A0A8I3S7Z3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000041957   ⟸   ENSCAFT00000049047
RefSeq Acc Id: ENSCAFP00000017530   ⟸   ENSCAFT00000018918
RefSeq Acc Id: XP_038374065   ⟸   XM_038518137
RefSeq Acc Id: XP_038502024   ⟸   XM_038646096
RefSeq Acc Id: XP_038299654   ⟸   XM_038443726
- UniProtKB: A0A8C0Z1U8 (UniProtKB/TrEMBL),   A0A8I3S7Z3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038437620   ⟸   XM_038581692
- UniProtKB: A0A8C0Z1U8 (UniProtKB/TrEMBL),   A0A8I3S7Z3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845033294   ⟸   ENSCAFT00845042470
Protein Domains
VWFA

Promoters
RGD ID:13688669
Promoter ID:EPDNEW_C6737
Type:initiation region
Name:COL6A1_1
Description:collagen type VI alpha 1 chain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13139,301,743 - 39,301,803EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000011911 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030023737 UniProtKB/TrEMBL
  ENSCAFG00040018980 UniProtKB/TrEMBL
  ENSCAFG00845024031 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000018918.5 UniProtKB/TrEMBL
  ENSCAFT00000107848.1 UniProtKB/TrEMBL
  ENSCAFT00000109381.1 UniProtKB/TrEMBL
  ENSCAFT00030043693.1 UniProtKB/TrEMBL
  ENSCAFT00030043744.1 UniProtKB/TrEMBL
  ENSCAFT00040035210.1 UniProtKB/TrEMBL
  ENSCAFT00845042470 ENTREZGENE
  ENSCAFT00845042470.1 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 cfa:403668 UniProtKB/TrEMBL
NCBI Gene COL6A1 ENTREZGENE
PANTHER COLLAGEN UniProtKB/TrEMBL
  COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(X) CHAIN UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XXI) CHAIN-LIKE ISOFORM X1 UniProtKB/TrEMBL
  COLLAGEN TYPE VI ALPHA 1 CHAIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A8C0PC83_CANLF UniProtKB/TrEMBL
  A0A8C0Z1U8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3S7Z3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0PII6_CANLF UniProtKB/TrEMBL
  A0A8P0TU51_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:39480 ENTREZGENE