Col11a1 collagen, type XI, alpha 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col11a1provided by MGI
Official Full Name: collagen, type XI, alpha 1provided by MGI
Primary source: MGI:MGI:88446
See related: Ensembl:ENSMUSG00000027966 AllianceGenome:MGI:88446
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: cho; C530001D20Rik
Summary: This gene encodes the alpha-1 subunit of type XI collagen, one of the low abundance fibrillar collagens that is essential for normal embryonic skeletal development and the cohesive properties of cartilage. The encoded protein, in association with the alpha-1 subunit of type II collagen, forms a heterotrimeric type XI procollagen that undergoes proteolytic processing. Mice lacking the encoded protein develop severe chondrodysplasia and die at birth. [provided by RefSeq, Dec 2015]
Expression: Biased expression in limb E14.5 (RPKM 65.0), CNS E14 (RPKM 14.0) and 3 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F3; 3 49.35 cM

Exon count:: 69

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (113823933..114014405)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (114030479..114220756)

Chromosome 3 - NC_000069.7 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?

Collagen XI regulates the acquisition of collagen fibril structure, organization and functional properties in tendon.
Title: Collagen XI regulates the acquisition of collagen fibril structure, organization and functional properties in tendon.
genetically abnormal cartilage matrix properties due to mutation were not additive to load-induced cartilage damage
Title: Collagen XI mutation lowers susceptibility to load-induced cartilage damage in mice.
Taken together, these results indicate that the transcription factor Sp1 upregulates the proximal promoter activity of the mouse Col11a1 gene in chondrocytes.
Title: Sp1 upregulates the proximal promoter activity of the mouse collagen α1(XI) gene (Col11a1) in chondrocytes.
these results indicate that the transcription factor NF-Y regulates the proximal promoter activity of mouse Col11a1 gene in chondrocytes
Title: Nuclear factor Y (NF-Y) regulates the proximal promoter activity of the mouse collagen α1(XI) gene (Col11a1) in chondrocytes.
Lef1 is an activator of the Col11a1 promoter and that Col11a1 suppresses terminal osteoblast differentiation
Title: Collagen 11a1 is indirectly activated by lymphocyte enhancer-binding factor 1 (Lef1) and negatively regulates osteoblast maturation.
the cho mutation leads to osteoarthritis through a mechanism that does not initially involve mechanical factors.
Title: Osteoarthritis-like changes and decreased mechanical function of articular cartilage in the joints of mice with the chondrodysplasia gene (cho).
Stickler syndrome and Marshall syndrome mutations in COL11A1 cause hearing loss via dominant negative effects upon wild-type fibrillar collagen polypeptides in the extracellular matrices of the cochlea.
Title: Auditory function associated with Col11a1 haploinsufficiency in chondrodysplasia (cho) mice.
The expression patterns suggest essential roles for Col11a1 and Col11a2 in the basilar or tectorial membranes.
Title: Col11a1 and Col11a2 mRNA expression in the developing mouse cochlea: implications for the correlation of hearing loss phenotype with mutant type XI collagen genotype.

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Variation

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Alleles

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

Endonuclease-mediated (4)
Spontaneous (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH134389 (e-PCR)
- UniSTS:217671

Col11a1 (e-PCR), detects polymorphism
- UniSTS:277876

NoName (e-PCR)
- UniSTS:548515

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables heparan sulfate binding	IEA Inferred from Electronic Annotation more info
enables heparan sulfate binding	ISO Inferred from Sequence Orthology more info
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cartilage condensation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chondrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within collagen fibril organization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in detection of mechanical stimulus involved in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in detection of mechanical stimulus involved in sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endodermal cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within proteoglycan metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within tendon development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within tendon development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation more info
involved_in visual perception	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of collagen trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type XI trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type XI trimer	ISO Inferred from Sequence Orthology more info
part_of collagen type XI trimer	NAS Non-traceable Author Statement more info	PubMed
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 collagen-containing extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in collagen-containing extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-1(XI) chain

Names: a1(XI) collagen; pro-alpha1(XI) collagen; procollagen, type XI, 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_007729.3 → NP_031755.2 collagen alpha-1(XI) chain preproprotein

See identical proteins and their annotated locations for NP_031755.2

Status: REVIEWED

Source sequence(s)

AC156386, AK140136, AK157734

Consensus CDS

CCDS17778.1

UniProtKB/Swiss-Prot

Q61245, Q64047, Q80WR4

Related

ENSMUSP00000089793.6, ENSMUST00000092155.12

Conserved Domains (3) summary

pfam01391
Location:839 → 898

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:37 → 228

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1576 → 1802

COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

113823933..114014405

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006500969.2 → XP_006501032.1 collagen alpha-1(XI) chain isoform X1

Conserved Domains (3) summary

pfam01391
Location:851 → 910

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:37 → 228

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1585 → 1814

COLFI; Fibrillar collagen C-terminal domain
XM_006500971.2 → XP_006501034.1 collagen alpha-1(XI) chain isoform X3

Conserved Domains (3) summary

pfam01391
Location:766 → 825

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:37 → 228

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1500 → 1729

COLFI; Fibrillar collagen C-terminal domain
XM_006500970.2 → XP_006501033.1 collagen alpha-1(XI) chain isoform X2

Conserved Domains (3) summary

pfam01391
Location:800 → 859

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:37 → 228

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1534 → 1763

COLFI; Fibrillar collagen C-terminal domain
XM_030252409.1 → XP_030108269.1 collagen alpha-1(XI) chain isoform X4

Conserved Domains (2) summary

pfam01391
Location:616 → 665

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:813 → 1042

COLFI; Fibrillar collagen C-terminal domain