Col9a2 MGI Mouse Gene Detail - MGI:88466 - collagen, type IX, alpha 2

Symbol

Col9a2
Name

collagen, type IX, alpha 2
Synonyms

Col9a-2

Feature Type

protein coding gene
IDs

MGI:88466
NCBI Gene: 12840
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr4:120896763-120912522 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 56.78 cM
Mapping Data

2 experiments

SNPs within 2kb

521 from dbSNP Build 142
Strain Annotations

18
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88466	protein coding gene	Chr4:120896582-120912522 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0028719	protein coding gene	Chr4:122342894-122358823 (+)
A/J	MGP_AJ_G0028679	protein coding gene	Chr4:117509749-117525668 (+)
AKR/J	MGP_AKRJ_G0028632	protein coding gene	Chr4:120103602-120119522 (+)
BALB/cJ	MGP_BALBcJ_G0028702	protein coding gene	Chr4:118124421-118141390 (+)
C3H/HeJ	MGP_C3HHeJ_G0028417	protein coding gene	Chr4:121631978-121648674 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0029143	protein coding gene	Chr4:126947945-126963880 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026420	protein coding gene	Chr4:111554601-111570858 (+)
CAST/EiJ	MGP_CASTEiJ_G0027848	protein coding gene	Chr4:119005366-119028430 (+)
CBA/J	MGP_CBAJ_G0028384	protein coding gene	Chr4:130388937-130404842 (+)
DBA/2J	MGP_DBA2J_G0028531	protein coding gene	Chr4:118086145-118101904 (+)
FVB/NJ	MGP_FVBNJ_G0028497	protein coding gene	Chr4:116612195-116628042 (+)
LP/J	MGP_LPJ_G0028631	protein coding gene	Chr4:122463525-122479441 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028525	protein coding gene	Chr4:135196196-135212110 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029180	protein coding gene	Chr4:121177438-121193382 (+)
PWK/PhJ	MGP_PWKPhJ_G0027571	protein coding gene	Chr4:115037984-115060857 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0027397	protein coding gene	Chr4:117595332-117613433 (+)
WSB/EiJ	MGP_WSBEiJ_G0027928	protein coding gene	Chr4:121194666-121210598 (+)

Human Ortholog

COL9A2, collagen type IX alpha 2 chain

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL9A2, collagen type IX alpha 2 chain
Synonyms

DJ39G22.4, EDM2, MED, STL5
Links

HGNC:2218

NCBI Gene ID: 1298

neXtProt AC: NX_Q14055

UniProt: Q14055
Chr Location

1p34.2; chr1:40300489-40317813 (-) GRCh38

MGI Vertebrate Homology

Col9a2 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: COL9A2
Gene Tree

Col9a2

Diseases

3 with human COL9A2 associations

				Human Disease	Mouse Models
				multiple epiphyseal dysplasia 2 IDs multiple epiphyseal dysplasia 2 DOID:0070298 OMIM:600204
				osteochondrodysplasia IDs osteochondrodysplasia DOID:2256 DOID:1764 ICD10CM:Q78.9 ICD9CM:756.4 MESH:D010009 NCI:C34466 NCI:C84978 UMLS_CUI:C0008449 UMLS_CUI:C0029422
				Stickler syndrome IDs Stickler syndrome DOID:0080046 OMIM:PS108300 ORDO:828

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

15 phenotypes from 1 allele in 1 genetic background
19 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

17
Chemically induced (other)

2
Endonuclease-mediated

2
Gene trapped

7
Radiation induced

1
Targeted

5
Genomic Mutations

4 involving Col9a2
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

53 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

10
GO References

4

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

903
Tissues

75
cDNA Data

54
Literature Summary

23

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase col9a2

ZFIN col9a2

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All Sequences

43
RefSeq

2
UniProt

3
CCDS

CCDS18599.1

Ensembl

ENSMUSG00000028626 (Evidence)
NCBI Gene

12840

			Length	Strain/Species	Flank
genomic	12840	NCBI Gene Model \| MGI Sequence Detail	15760	C57BL/6J	± kb
transcript	NM_007741	RefSeq \| MGI Sequence Detail	2746	ZRU/MplStud
polypeptide	Q07643	UniProt \| EBI \| MGI Sequence Detail	688	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000005723 collagen alpha-2(IX) chain

(term hierarchy)
InterPro Domains

IPR050938 Collagen and Collagen-like Structural Proteins

IPR050149 Collagen superfamily

IPR008160 Collagen triple helix repeat
GlyGen

Q07643 2 sites

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All nucleic 62

Genomic 3

cDNA 54

Primer pair 4

Other 1

Microarray probesets 3

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MGD-MRK-2084, MGD-MRK-2086, MGI:2140269

Summaries

All 70

Developmental Gene Expression 23

Gene Ontology 4

Phenotypes 19
Earliest

J:717 Elima K, et al., Specific hybridization probes for mouse alpha 2(IX) and alpha 1(X) collagen mRNAs. Biochim Biophys Acta. 1992 Feb 28;1130(1):78-80
Latest

J:353621 Patel VN, et al., Specific 3-O-sulfated heparan sulfate domains regulate salivary gland basement membrane metabolism and epithelial differentiation. Nat Commun. 2024 Aug 31;15(1):7584

TSS for Col9a2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr38812	Chr4:120896753-120896877 (+)	52 bp
Tssr38813	Chr4:120896878-120896894 (+)	123 bp
Tssr38814	Chr4:120896898-120896909 (+)	141 bp
Tssr38815	Chr4:120898956-120898968 (+)	2,199 bp
Tssr38816	Chr4:120910227-120910240 (+)	13,471 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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