Col9a3 MGI Mouse Gene Detail - MGI:894686 - collagen, type IX, alpha 3

Symbol

Col9a3
Name

collagen, type IX, alpha 3

Feature Type

protein coding gene
IDs

MGI:894686
NCBI Gene: 12841
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr2:180239895-180263985 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 103.14 cM
Mapping Data

4 experiments

SNPs within 2kb

467 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_894686	protein coding gene	Chr2:180239583-180263985 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0026998	protein coding gene	Chr2:187129205-187154860 (+)
A/J	MGP_AJ_G0026964	protein coding gene	Chr2:179440598-179464903 (+)
AKR/J	MGP_AKRJ_G0026934	protein coding gene	Chr2:184819935-184846631 (+)
BALB/cJ	MGP_BALBcJ_G0026973	protein coding gene	Chr2:179903726-179928939 (+)
C3H/HeJ	MGP_C3HHeJ_G0026714	protein coding gene	Chr2:185170883-185196878 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0027419	protein coding gene	Chr2:192529440-192556874 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024784	protein coding gene	Chr2:170132488-170155847 (+)
CAST/EiJ	MGP_CASTEiJ_G0026173	protein coding gene	Chr2:183412331-183437687 (+)
CBA/J	MGP_CBAJ_G0026691	protein coding gene	Chr2:199534137-199558463 (+)
DBA/2J	MGP_DBA2J_G0026829	protein coding gene	Chr2:178537959-178562474 (+)
FVB/NJ	MGP_FVBNJ_G0026795	protein coding gene	Chr2:177152792-177177886 (+)
LP/J	MGP_LPJ_G0026930	protein coding gene	Chr2:187136476-187164596 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026814	protein coding gene	Chr2:202130030-202156697 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027478	protein coding gene	Chr2:184775901-184801135 (+)
PWK/PhJ	MGP_PWKPhJ_G0025909	protein coding gene	Chr2:176049198-176074414 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0025709	protein coding gene	Chr2:181267770-181298039 (+)
WSB/EiJ	MGP_WSBEiJ_G0026245	protein coding gene	Chr2:185758661-185785942 (+)

Human Ortholog

COL9A3, collagen type IX alpha 3 chain

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL9A3, collagen type IX alpha 3 chain
Synonyms

DJ885L7.4.1, EDM3, IDD, MED, STL6
Links

HGNC:2219

NCBI Gene ID: 1299

neXtProt AC: NX_Q14050

UniProt: Q14050
Chr Location

20q13.33; chr20:62816213-62841159 (+) GRCh38

MGI Vertebrate Homology

Col9a3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: COL9A3
Gene Tree

Col9a3

Diseases

3 with human COL9A3 associations

				Human Disease	Mouse Models
				multiple epiphyseal dysplasia 3 IDs multiple epiphyseal dysplasia 3 DOID:0070304 OMIM:600969
				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

6 phenotypes from 1 allele in 1 genetic background
8 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

7
Endonuclease-mediated

4
Targeted

3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

35 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

7
GO References

2

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

1053
Tissues

100
cDNA Data

69
Literature Summary

30

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA COL9A3

Xenbase col9a3

ZFIN col9a3

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All Sequences

54
RefSeq

6
UniProt

8
CCDS

CCDS17180.1

Ensembl

ENSMUSG00000027570 (Evidence)
NCBI Gene

12841

			Length	Strain/Species	Flank
genomic	12841	NCBI Gene Model \| MGI Sequence Detail	24091	C57BL/6J	± kb
transcript	NM_001378777	RefSeq \| MGI Sequence Detail	2948	ZRU/MplStud
polypeptide	NP_001365706	RefSeq \| MGI Sequence Detail	719	ZRU/MplStud

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UniProt

8 Sequences
InterPro Domains

IPR050938 Collagen and Collagen-like Structural Proteins

IPR050149 Collagen superfamily

IPR008160 Collagen triple helix repeat

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All nucleic 76

cDNA 71

Primer pair 4

Other 1

Microarray probesets 4

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MGI:2139235

Summaries

All 61

Developmental Gene Expression 30

Gene Ontology 2

Phenotypes 8
Earliest

J:17466 Abe N, et al., The complete primary structure of the long form of mouse alpha 1(IX) collagen chain and its expression during limb development. Biochim Biophys Acta. 1994 Jan 11;1204(1):61-7
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Col9a3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr22254	Chr2:180240012-180240019 (+)	121 bp
Tssr22255	Chr2:180240020-180240044 (+)	137 bp
Tssr22256	Chr2:180242832-180242834 (+)	2,938 bp
Tssr22257	Chr2:180245892-180245938 (+)	6,020 bp
Tssr22258	Chr2:180246675-180246689 (+)	6,787 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24