Col9a1 collagen, type IX, alpha 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col9a1provided by MGI
Official Full Name: collagen, type IX, alpha 1provided by MGI
Primary source: MGI:MGI:88465
See related: Ensembl:ENSMUSG00000026147 AllianceGenome:MGI:88465
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: Col9a-1
Summary: Predicted to be an extracellular matrix structural constituent. Acts upstream of or within chondrocyte proliferation; growth plate cartilage development; and tissue homeostasis. Predicted to be located in extracellular region. Predicted to be part of collagen type IX trimer. Predicted to be active in basement membrane and extracellular space. Is expressed in several structures, including genitourinary system; limb; respiratory system; sensory organ; and skeletal system. Used to study osteoarthritis. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 6; and osteochondrodysplasia. Orthologous to human COL9A1 (collagen type IX alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in limb E14.5 (RPKM 74.4), CNS E14 (RPKM 10.9) and 1 other tissue See more
Orthologs: human all
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Genomic context

Location:: 1 A5; 1 9.95 cM

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (24216670..24291819)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (24177589..24252738)

Chromosome 1 - NC_000067.7 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: 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 IX deficiency leads to premature vascularization and ossification of murine femoral heads through an imbalance of pro- and antiangiogenic factors.
Title: Collagen IX deficiency leads to premature vascularization and ossification of murine femoral heads through an imbalance of pro- and antiangiogenic factors.
An accelerated hypertrophic differentiation caused by a disturbed Ihh-PTHrP signaling pathway may lead to a higher bone mineral density in the vertebral bodies of newborn Col IX -/- mice and, as a result, to the early onset of disc degeneration.
Title: Absence of collagen IX accelerates hypertrophic differentiation in the embryonic mouse spine through a disturbance of the Ihh-PTHrP feedback loop.
Results show that absence of Col IX induces early developmental, structural and biomechanical alterations in both vertebral body and intervertebral disc which eventually cause severe degenerative changes in the aging spine.
Title: Early changes in morphology, bone mineral density and matrix composition of vertebrae lead to disc degeneration in aged collagen IX -/- mice.
Proteomic analysis of interaction partners of collagen alpha1 IX in the articular cartilage of mice.
Title: Comparative proteomic analysis of normal and collagen IX null mouse cartilage reveals altered extracellular matrix composition and novel components of the collagen IX interactome.
They test the hypothesis that aged Col9a1(-/-) mice would reduce joint pain by adopting locomotor behaviors that reduce both the magnitude and daily frequency of joint loading.
Title: Locomotor activity and gait in aged mice deficient for type IX collagen.
Loss of type IX collagen and COMP leads to matrix aberrations that may make cartilage more susceptible to degeneration.
Title: Combined role of type IX collagen and cartilage oligomeric matrix protein in cartilage matrix assembly: cartilage oligomeric matrix protein counteracts type IX collagen-induced limitation of cartilage collagen fibril growth in mouse chondrocyte cultures.
Col9a1(-/-) mice present behavioral changes consistent with anatomic signs of osteoarthritis and intervertebral disc degeneration.
Title: Decreased physical function and increased pain sensitivity in mice deficient for type IX collagen.
all long bones are shorter and broader in newborn Col9a1-/- mice
Title: Collagen IX-deficiency seriously compromises growth cartilage development in mice.
mineralized bone matrix deficient of short collagen IX may become susceptible to osteoclastic bone resorption, possibly through a novel non-cell-autonomous mechanism
Title: Trabecular bone deterioration in col9a1+/- mice associated with enlarged osteoclasts adhered to collagen IX-deficient bone.
A deletion mutation for type IX collagen is associated with connective tissue changes characteristic of musculoskeletal degeneration in bony and cartilaginous tissue regions
Title: Early-onset degeneration of the intervertebral disc and vertebral end plate in mice deficient in type IX collagen.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

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

Targeted (1) 1 citation
Endonuclease-mediated (2)

General gene information

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Markers

D17511 (e-PCR)
- UniSTS:158781

Col9a1 (e-PCR), detects polymorphism
- UniSTS:265067

17.MMHAP18FRF8.seq (e-PCR)
- UniSTS:123334

Col9a1 (e-PCR), detects polymorphism
- UniSTS:478962

UniSTS:478964 (e-PCR)
- UniSTS:478964

Col9a1 (e-PCR), detects polymorphism
- UniSTS:478964

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables carbohydrate 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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within bone morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cartilage development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chondrocyte proliferation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within growth plate cartilage development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within growth plate cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within tissue homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type IX trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IX trimer	ISO Inferred from Sequence Orthology more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
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(IX) chain

Names: alpha 1 type IX collagen; procollagen, type IX, 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_001290691.1 → NP_001277620.1 collagen alpha-1(IX) chain isoform 2 precursor

See identical proteins and their annotated locations for NP_001277620.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK011547, AK017395, AK160749, BY144829

Consensus CDS

CCDS69871.1

UniProtKB/TrEMBL

Q9D0D2

Related

ENSMUSP00000085687.3, ENSMUST00000088349.3

Conserved Domains (1) summary

pfam01391
Location:267 → 324

Collagen; Collagen triple helix repeat (20 copies)
NM_007740.3 → NP_031766.3 collagen alpha-1(IX) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_031766.3

Status: VALIDATED

Description

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

Source sequence(s)

AK004383, AK017395, AK031071, CX207941, L12215

Consensus CDS

CCDS35527.1

UniProtKB/TrEMBL

G3X995

Related

ENSMUSP00000051579.9, ENSMUST00000054588.15

Conserved Domains (2) summary

pfam01391
Location:508 → 565

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:50 → 244

TSPN; Thrombospondin N-terminal -like domains

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_000067.7 Reference GRCm39 C57BL/6J

Range

24216670..24291819

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006495649.3 → XP_006495712.1 collagen alpha-1(IX) chain isoform X1

Conserved Domains (2) summary

pfam01391
Location:319 → 350

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:50 → 244

TSPN; Thrombospondin N-terminal -like domains
XM_036157312.1 → XP_036013205.1 collagen alpha-1(IX) chain isoform X2

Conserved Domains (2) summary

smart00210
Location:50 → 244

TSPN; Thrombospondin N-terminal -like domains

pfam01391
Location:496 → 552

Collagen; Collagen triple helix repeat (20 copies)