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

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Gene: Col6a1 (collagen type VI alpha 1 chain) Chinchilla lanigera
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Symbol: Col6a1
Name: collagen type VI alpha 1 chain
RGD ID: 9043169
Description: ENCODES a protein that exhibits collagen binding (ortholog); platelet-derived growth factor binding (ortholog); INVOLVED IN 2-oxoglutarate metabolic process (ortholog); adipose tissue development (ortholog); apoptotic nuclear changes (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH autistic disorder (ortholog); Axenfeld-Rieger syndrome type 3 (ortholog); Bethlem myopathy (ortholog); FOUND IN basement membrane (ortholog); extracellular matrix (ortholog); extracellular region (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(VI) chain; collagen, type VI, alpha 1
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
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)
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)
organelle organization  (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. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline

Genomics

Comparative Map Data
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
(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
(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


Expression


Sequence


RefSeq Acc Id: ENSCLAT00000006754   ⟹   ENSCLAP00000006644
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495540742,461,952 - 42,478,261 (+)Ensembl
RefSeq Acc Id: XM_005375923   ⟹   XP_005375980
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495540742,461,837 - 42,479,048 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005375980 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000006644
  ENSCLAP00000006644.1
RefSeq Acc Id: XP_005375980   ⟸   XM_005375923
- UniProtKB: A0A8C2UW28 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000006644   ⟸   ENSCLAT00000006754
Protein Domains
VWFA


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000004686 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000006754 ENTREZGENE
  ENSCLAT00000006754.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene Col6a1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XXI) CHAIN-LIKE ISOFORM X1 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A8C2UW28 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Col6a1  collagen type VI alpha 1 chain    collagen, type VI, alpha 1  Symbol and/or name change 5135510 APPROVED