Col6a1 collagen type VI alpha 1 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 294337, updated on 10-Jul-2024

Summary

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Official Symbol: Col6a1provided by RGD
Official Full Name: collagen type VI alpha 1 chainprovided by RGD
Primary source: RGD:1565398
See related: EnsemblRapid:ENSRNOG00000001249 AllianceGenome:RGD:1565398
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1565398
Summary: Predicted to enable collagen binding activity and platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in endodermal cell differentiation; extracellular matrix organization; and gonad development. Predicted to act upstream of or within cellular response to amino acid stimulus. Predicted to be located in extracellular region and sarcolemma. Predicted to be part of collagen type IX trimer. Predicted to be active in basement membrane and extracellular space. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL6A1 (collagen type VI alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Uterus (RPKM 2562.2), Lung (RPKM 786.5) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Col6a1 in Genome Data Viewer

Location:: 20p12

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (11905690..11924111)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (11906105..11924599)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (12657913..12676370)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These findings indicate that Col VI provided a characteristic microenvironment in the GOR and that NG2-Col VI interactions may regulate the differentiation of osteoblast lineages prior to terminal maturation.
Title: Distribution of type VI collagen in association with osteoblast lineages in the groove of Ranvier during rat postnatal development.

Submit: New GeneRIF Correction

General gene information

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Markers

RH129493 (e-PCR)
- UniSTS:212797

UniSTS:531308 (e-PCR)
- UniSTS:531308

Col6a1 (e-PCR), detects polymorphism
- UniSTS:531308

RH129051 (e-PCR)
- UniSTS:212359

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables collagen binding	ISO Inferred from Sequence Orthology more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables platelet-derived growth factor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within 2-oxoglutarate metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adipose tissue development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within apoptotic nuclear changes	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within autophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within basement membrane organization	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within bone mineralization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within caveola assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to amino acid stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collagen fibril organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collagen metabolic process	ISO Inferred from Sequence Orthology more info
involved_in endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within energy homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within energy reserve metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within extracellular matrix assembly	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within fat cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glycolytic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hair follicle development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within homeostasis of number of cells	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within insulin receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within insulin-like growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb joint morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung alveolus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mitochondrial depolarization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mitochondrial transmembrane transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mitochondrion organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organismal locomotion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within muscle cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within muscle cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within muscle organ development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within muscle structure development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within muscle system process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within myelination in peripheral nervous system	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ossification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within peripheral nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein tetramerization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within reactive oxygen species metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within reduction of food intake in response to dietary excess	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell size	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of collagen fibril organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within respiratory system process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to UV	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to bleomycin	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to decreased oxygen levels	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to lipid	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to mechanical stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to muscle activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to pain	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to peptide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to polyamine macromolecule	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to reactive oxygen species	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to toxic substance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to wounding	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of mechanical stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within single fertilization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle fiber development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle fiber differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle organ development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle tissue growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle tissue regeneration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skin development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tissue remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within transmission of nerve impulse	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tricarboxylic acid cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within uterus development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in basement membrane	ISO Inferred from Sequence Orthology more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	ISO Inferred from Sequence Orthology more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
is_active_in intracellular vesicle	ISO Inferred from Sequence Orthology more info
is_active_in lysosome	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
is_active_in myofibril	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info
is_active_in sarcoplasmic reticulum	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: collagen alpha-1(VI) chain

Names: collagen, type VI, alpha 1; procollagen, type VI, alpha 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.