Col6a1 collagen, type VI, alpha 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col6a1provided by MGI
Official Full Name: collagen, type VI, alpha 1provided by MGI
Primary source: MGI:MGI:88459
See related: Ensembl:ENSMUSG00000001119 AllianceGenome:MGI:88459
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Col6a-1
Summary: Predicted to enable collagen binding activity and platelet-derived growth factor binding activity. Acts upstream of or within cellular response to amino acid stimulus. Located in extracellular matrix and sarcolemma. Is expressed in several structures, including alimentary system; brain; genitourinary system; heart and pericardium; and sensory organ. Used to study Bethlem myopathy and Ullrich congenital muscular dystrophy. 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: Broad expression in subcutaneous fat pad adult (RPKM 393.3), ovary adult (RPKM 227.8) and 16 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 39.71 cM

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (76544626..76561878, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (76708792..76726044, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lack of COL6/collagen VI causes megakaryocyte dysfunction by impairing autophagy and inducing apoptosis.
Title: Lack of COL6/collagen VI causes megakaryocyte dysfunction by impairing autophagy and inducing apoptosis.
Non-canonical Fzd7 signaling contributes to breast cancer mesenchymal-like stemness involving Col6a1.
Title: Non-canonical Fzd7 signaling contributes to breast cancer mesenchymal-like stemness involving Col6a1.
Type VI collagen and its cleavage product, endotrophin, cooperatively regulate the adipogenic and lipolytic capacity of adipocytes.
Title: Type VI collagen and its cleavage product, endotrophin, cooperatively regulate the adipogenic and lipolytic capacity of adipocytes.
Col6a1(-/-) mice have decreased level of plasma adiponectin.
Title: Role of adiponectin in the metabolism of skeletal muscles in collagen VI-related myopathies.
Collagen VI Deficiency is associated with alveolar and airway abnormalities in the Lung.
Title: Collagen VI Deficiency Results in Structural Abnormalities in the Mouse Lung.
Ex vivo muscle preparations from ColVI null mice revealed altered neuromuscular transmission, with electrophysiological defects and decreased safety factor (i.e., the excess current generated in response to a nerve impulse over that required to reach the action potential threshold).
Title: Collagen VI is required for the structural and functional integrity of the neuromuscular junction.
These data indicated an inhibitory role of ColVI in ENCC migration and suggested that ColVI suppression in the intestine might represent a novel therapeutic strategy for aganglionic colonic diseases.
Title: Collagen VI suppresses fibronectin-induced enteric neural crest cell migration by downregulation of focal adhesion proteins.
Col6a1-/- neural cultures displayed an increased incidence of spontaneous apoptosis and higher vulnerability to oxidative stress, accompanied by altered regulation of autophagy with increased p62 protein levels and decreased LC3 lipidation. Analysis of brain sections confirmed increased apoptosis and abnormal regulation of autophagy in the CNS of collagen VI-deficient animals.
Title: Lack of collagen VI promotes neurodegeneration by impairing autophagy and inducing apoptosis during aging.
This study demonstrates that Col6a1-Cre driver mice are as useful as Twist2-Cre driver mice for functional analyses of GALT-resident mesenchymal cells, including MCi cells.
Title: Targeted deletion of RANKL in M cell inducer cells by the Col6a1-Cre driver.
Confocal laser scanning microscopy co-localised perlecan with type VI collagen as pericellular components of intervertebral disc (IVD) cells and translamellar cross-bridges in ovine and murine IVDs.
Title: Pericellular colocalisation and interactive properties of type VI collagen and perlecan in the intervertebral disc.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Col6a1 (e-PCR), detects polymorphism
- UniSTS:141371

AI747156 (e-PCR)
- UniSTS:180058

NoName (e-PCR)
- UniSTS:236390

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

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

Col6a1 (e-PCR), detects polymorphism
- UniSTS:259059

Homology

Homologs of the Col6a1 gene: The Col6a1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 488 organisms have orthologs with human gene Col6a1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables collagen binding	ISO Inferred from Sequence Orthology more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables platelet-derived growth factor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to amino acid stimulus	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	ISO Inferred from Sequence Orthology more info	PubMed
located_in extracellular space	HDA more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info	PubMed
located_in sarcolemma	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: collagen alpha-1(VI) chain

Names: 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.

mRNA and Protein(s)

NM_009933.4 → NP_034063.1 collagen alpha-1(VI) chain precursor

See identical proteins and their annotated locations for NP_034063.1

Status: VALIDATED

Source sequence(s)

EF437374, X66405

Consensus CDS

CCDS23952.1

UniProtKB/Swiss-Prot

Q04857

UniProtKB/TrEMBL

B0LAD9

Related

ENSMUSP00000001147.5, ENSMUST00000001147.5

Conserved Domains (2) summary

pfam01391
Location:271 → 328

Collagen; Collagen triple helix repeat (20 copies)

cd01480
Location:823 → 1008

vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...