Col6a6 collagen, type VI, alpha 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col6a6provided by MGI
Official Full Name: collagen, type VI, alpha 6provided by MGI
Primary source: MGI:MGI:2444259
See related: Ensembl:ENSMUSG00000043719 AllianceGenome:MGI:2444259
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: E330019B14; E330026B02Rik
Summary: Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in cell adhesion. Located in extracellular region. Is expressed in several structures, including genitourinary system; intraembryonic coelom; liver; lung; and musculoskeletal system. Orthologous to human COL6A6 (collagen type VI alpha 6 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in subcutaneous fat pad adult (RPKM 3.9), limb E14.5 (RPKM 3.2) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 F1; 9 56.99 cM

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (105566616..105705413, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (105689417..105828246, complement)

Chromosome 9 - NC_000075.7 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?

Immunoelectron microscopy of skeletal muscle localized the collagen VI alpha 6 chain to the reticular lamina of muscle fibers
Title: Differential and restricted expression of novel collagen VI chains in mouse.
discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix
Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).
analysis of collagen VI chains alpha4, alpha5, and alpha6with high homology to the alpha3 chain
Title: Three novel collagen VI chains with high homology to the alpha3 chain.

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Variation

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Alleles

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

Endonuclease-mediated (2)

General gene information

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Markers

D9Dcr83 (e-PCR), detects polymorphism
- UniSTS:499045

D9Dcr84 (e-PCR), detects polymorphism
- UniSTS:499046

D9Dcr85 (e-PCR), detects polymorphism
- UniSTS:499047

D9Dcr86 (e-PCR), detects polymorphism
- UniSTS:499048

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

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
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info	PubMed
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: collagen alpha-6(VI) chain

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_001102607.1 → NP_001096077.1 collagen alpha-6(VI) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_001096077.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK087828, AM748261, AM748262

Consensus CDS

CCDS52906.1

UniProtKB/Swiss-Prot

A6H587, A6H588, A6H589, A6H590, Q8C6K9

UniProtKB/TrEMBL

E9Q6A6

Related

ENSMUSP00000096040.4, ENSMUST00000098441.10

Conserved Domains (6) summary

pfam01391
Location:1539 → 1643

Collagen; Collagen triple helix repeat (20 copies)

smart00327
Location:1186 → 1344

VWA; von Willebrand factor (vWF) type A domain

COG2304
Location:434 → 633

YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]

cd01450
Location:1963 → 2141

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam00092
Location:621 → 789

VWA; von Willebrand factor type A domain

cl00057
Location:25 → 179

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_172927.3 → NP_766515.2 collagen alpha-6(VI) chain isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1, that results in an isoform (2) with a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC119951, AK054356

Consensus CDS

CCDS23468.1

UniProtKB/TrEMBL

B9EK79

Related

ENSMUSP00000060840.5, ENSMUST00000060896.5

Conserved Domains (3) summary

COG2304
Location:434 → 633

YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]

pfam00092
Location:621 → 789

VWA; von Willebrand factor type A domain

cl00057
Location:25 → 179

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...