Col9a3 (collagen type IX alpha 3 chain)

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Gene: Col9a3 (collagen type IX alpha 3 chain) Rattus norvegicus

Analyze

Symbol:

Col9a3

Name:

collagen type IX alpha 3 chain

RGD ID:

1310255

Description:

Predicted to enable protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization; female gonad development; and male gonad development. Predicted to be part of collagen type IX trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 3; and osteochondrodysplasia. Orthologous to human COL9A3 (collagen type IX alpha 3 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; Cuprizon.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

collagen alpha-3(IX) chain; collagen, type IX, alpha 3; LOC362285; procollagen, type IX, alpha 3

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	COL9A3 (collagen type IX alpha 3 chain)	RGD	RGD
Mus musculus (house mouse):	Col9a3 (collagen, type IX, alpha 3)	RGD	RGD
Chinchilla lanigera (long-tailed chinchilla):	Col9a3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	COL9A3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	COL9A3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Col9a3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	COL9A3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	COL9A3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Col9a3 (collagen type IX alpha 3 chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	COL9A3 (collagen type IX alpha 3 chain)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Col9a3 (collagen, type IX, alpha 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	col9a3 (collagen, type IX, alpha 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	col-135	Alliance	DIOPT (InParanoid\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	col9a3	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	167,711,776 - 167,734,468 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	167,711,840 - 167,734,465 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	172,092,068 - 172,114,688 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	181,051,159 - 181,073,783 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	177,712,766 - 177,735,392 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	176,102,287 - 176,124,839 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	176,102,351 - 176,124,306 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	179,803,032 - 179,825,528 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	169,704,893 - 169,712,492 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	169,595,025 - 169,618,528 (+)	NCBI
Celera	3	164,848,089 - 164,870,750 (-)	NCBI		Celera
Cytogenetic Map	3	q43	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Autoinflammation, Immune Dysregulation, and Eosinophilia (ISO)

autosomal dominant nocturnal frontal lobe epilepsy (ISO)

benign familial infantile seizures 6 (ISO)

connective tissue disease (ISO)

developmental and epileptic encephalopathy (ISO)

developmental and epileptic encephalopathy 33 (ISO)

early infantile epileptic encephalopathy (ISO)

epilepsy (ISO)

genetic disease (ISO)

Hearing Loss (ISO)

Intervertebral Disc Disease (ISO)

multiple epiphyseal dysplasia (ISO)

multiple epiphyseal dysplasia 3 (ISO)

neuronal ceroid lipofuscinosis (ISO)

osteochondrodysplasia (ISO)

retinal detachment (ISO)

sensorineural hearing loss (ISO)

Stickler syndrome (ISO)

Stickler Syndrome, Type VI (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

5-azacytidine (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

aristolochic acid A (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

carbamazepine (ISO)

chlorpyrifos (ISO)

crocidolite asbestos (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (ISO)

etoposide (ISO)

genistein (ISO)

hydrogen peroxide (ISO)

lead diacetate (EXP)

methapyrilene (ISO)

methylmercury chloride (ISO)

microcystin-LR (EXP)

mitomycin C (ISO)

Monobutylphthalate (EXP)

panobinostat (ISO)

resveratrol (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sulforaphane (ISO)

tributylstannane (EXP)

Tributyltin oxide (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

extracellular matrix organization (IBA)

female gonad development (ISO)

male gonad development (ISO)

Cellular Component

collagen type IX trimer (IBA,ISO)

collagen-containing extracellular matrix (IBA)

extracellular space (IBA)

Molecular Function

extracellular matrix structural constituent conferring tensile strength (IBA)

protein homodimerization activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

syndecan signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
5.	COL9A3: A third locus for multiple epiphyseal dysplasia.	Paassilta P, etal., Am J Hum Genet. 1999 Apr;64(4):1036-44.
6.	GOA pipeline	RGD automated data pipeline
7.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:8660302	PMID:8889548	PMID:11145610	PMID:18448257	PMID:32964953

Genomics

Comparative Map Data

Col9a3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	167,711,776 - 167,734,468 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	167,711,840 - 167,734,465 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	172,092,068 - 172,114,688 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	181,051,159 - 181,073,783 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	177,712,766 - 177,735,392 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	176,102,287 - 176,124,839 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	176,102,351 - 176,124,306 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	179,803,032 - 179,825,528 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	169,704,893 - 169,712,492 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	169,595,025 - 169,618,528 (+)	NCBI
Celera	3	164,848,089 - 164,870,750 (-)	NCBI		Celera
Cytogenetic Map	3	q43	NCBI

COL9A3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	62,816,213 - 62,841,159 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	20	62,816,244 - 62,841,159 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	20	61,448,402 - 61,472,511 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	60,918,859 - 60,942,956 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	20	60,918,831 - 60,942,955	NCBI
Celera	20	58,124,036 - 58,148,542 (+)	NCBI		Celera
Cytogenetic Map	20	q13.33	NCBI
HuRef	20	58,166,446 - 58,190,556 (+)	NCBI		HuRef
CHM1_1	20	61,349,484 - 61,373,428 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	20	64,616,007 - 64,640,720 (+)	NCBI		T2T-CHM13v2.0

Col9a3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	180,239,895 - 180,263,985 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	180,239,583 - 180,263,982 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	180,598,102 - 180,622,192 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	180,597,790 - 180,622,189 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	180,332,927 - 180,356,890 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	180,527,652 - 180,551,593 (+)	NCBI		MGSCv36	mm8
Celera	2	184,684,058 - 184,708,019 (+)	NCBI		Celera
Cytogenetic Map	2	H4	NCBI
cM Map	2	103.14	NCBI

Col9a3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955528	1,286,314 - 1,305,863 (-)	NCBI	ChiLan1.0	ChiLan1.0

COL9A3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	20	68,597,320 - 68,622,526 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	20	59,203,959 - 59,229,221 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	20	60,496,269 - 60,522,232 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	20	60,499,089 - 60,521,871 (+)	Ensembl	panpan1.1		panPan2

COL9A3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	24	46,653,400 - 46,669,183 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	24	46,662,376 - 46,667,884 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	24	45,837,732 - 45,853,448 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	24	47,526,060 - 47,541,889 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	24	47,526,108 - 47,541,879 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	24	46,623,806 - 46,639,485 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	24	46,747,099 - 46,762,848 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	24	47,503,126 - 47,518,786 (+)	NCBI		UU_Cfam_GSD_1.0

Col9a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	194,865,544 - 194,887,279 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936514	10,319,187 - 10,340,921 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

COL9A3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	62,074,855 - 62,093,703 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	62,074,108 - 62,094,228 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

COL9A3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	1,385,108 - 1,411,960 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666050	49,238,887 - 49,266,141 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Col9a3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624741	28,591,529 - 28,610,382 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Col9a3
70 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	45
Count of miRNA genes:	39
Interacting mature miRNAs:	45
Transcripts:	ENSRNOT00000013105
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	98535255	168026850	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	98535255	168026850	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	98535255	168026850	Rat
631541	Bp81	Blood pressure QTL 81	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	124122556	169034231	Rat
2303620	Vencon4	Ventilatory control QTL 4	3.9		respiration trait (VT:0001943)	tidal volume (CMO:0000222)	3	127162703	168026850	Rat
1578656	Vnigr2	Vascular neointimal growth QTL 2	4.2		artery morphology trait (VT:0002191)	lesioned artery residual lumen area (CMO:0001417)	3	130656562	169034231	Rat
1578653	Vnigr3	Vascular neointimal growth QTL 3	3.1		artery morphology trait (VT:0002191)	artery neointimal hyperplastic lesion area (CMO:0001414)	3	130656562	169034231	Rat
9589106	Insul23	Insulin level QTL 23	13.86	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	3	131635904	169034231	Rat
2298477	Eau4	Experimental allergic uveoretinitis QTL 4		0.0011	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	3	137398739	169034231	Rat
8552952	Pigfal13	Plasma insulin-like growth factor 1 level QTL 13			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	138799500	169034231	Rat
1298068	Bp167	Blood pressure QTL 167		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	141074471	169034231	Rat
2317883	Alcrsp26	Alcohol response QTL 26	1.8	0.63	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	3	145526770	169034231	Rat
8552791	Vie2	Viral induced encephalitis QTL 2	4.1		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	3	145956084	169034231	Rat
1578666	Vnigr1	Vascular neointimal growth QTL 1	4.6		artery morphology trait (VT:0002191)	artery lumen area (CMO:0001409)	3	149040888	168026850	Rat
1300161	Rf10	Renal function QTL 10	3.57		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	3	161192952	169034231	Rat

Markers in Region

D3Mco45

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	167,725,610 - 167,725,829 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	176,116,100 - 176,116,318	NCBI	Rnor6.0
Rnor_5.0	3	179,816,789 - 179,817,007	UniSTS	Rnor5.0
RGSC_v3.4	3	169,702,831 - 169,703,623	UniSTS	RGSC3.4
RGSC_v3.4	3	169,702,831 - 169,703,049	UniSTS	RGSC3.4
Celera	3	164,856,721 - 164,856,933	UniSTS
Cytogenetic Map	3	q43	UniSTS

PMC15572P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Celera	3	164,859,644 - 164,860,278	UniSTS
Cytogenetic Map	3	q43	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		12							63	6	11
Low	2	22	15	6	18	6	3	3	11	12	25	8	3
Below cutoff	1	9	37	30	1	30	5	8		14	5	3	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108611	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003749640	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003753842	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017592314	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017602708	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BQ192353	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474066	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000123	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000013105 ⟹ ENSRNOP00000013105

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	167,711,840 - 167,734,465 (+)	Ensembl
Rnor_6.0 Ensembl	3	176,102,351 - 176,124,306 (+)	Ensembl

RefSeq Acc Id:

NM_001108611 ⟹ NP_001102081

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	167,711,842 - 167,734,468 (+)	NCBI

RefSeq Acc Id:

XM_017592314 ⟹ XP_017447803

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	167,711,776 - 167,734,468 (+)	NCBI
Rnor_6.0	3	176,102,287 - 176,124,839 (+)	NCBI

Sequence:

show sequence

CCAGCCCCTCTCCCCACCCTGCTGCCCGCTGCTCTGCGCCCGCGGCTCATAGCGCCTGCCAGCC
ATGACCGGAGCGCCTGCCCTAGCCCTGCTGCTGCTGGGGCAGCTCCTGACGGCCACCTCCGCGC
AGAAAGTGGGACCTCGAGGCCCCCCTGGTCCCCAAGGGCCTCCTGGAAAACCCGGCAAGGATGG
CATCGATGGAGAAGCTGGCCCTCCAGGTCTGCCTGGCCCTCCAGGACCCAAAGGGACCTCAGGG
AAGCCGGGGAAGCCGGGAGAGGCAGGACTGCCAGGACTGCCTGGTGTAGATGGTCTGACAGGGA
GAGATGGACCCGCAGGACCCAAAGGTGCCCCGGGAGAACGGGGAAGTCTAGGACCTCCAGGGCC
ACCAGGACTTGGAGGCAAAGGCCTCCCTGGACCTCCTGGAAACCCTGGAGTCCTCCCTGAAGGT
GCTACTGATCTGCAGTGTCCTGCCATCTGCCCTCCAGGCCCTCCAGGGCCCCCAGGAATGCCGG
GGTTCAAGGGGCCTACTGGCTACAAAGGGGAACAAGGAGAAGTCGGCAAAGATGGTGAGAAGGG
TAATCCTGGCCCCCCTGGACCTCCAGGAATCCCAGGCACTGTGGGGCTACAGGGCCCAAGAGGA
TTGCAAGGACTTCCAGGGCCACTTGGACCCCCTGGGGACCGGGGTCCCATTGGGTTTCGGGGCC
CCCCAGGGATCCCAGGAGCACCTGGGAAAGCGGGTGACAGGGGTGATAGGGGACCAGAAGGGTT
CCGTGGCCCTAAGGGTGACCTGGGCAGGCCTGGTCCCAAAGGAATCCCTGGAGTGGCTGGGCCA
GGCGGAGAACCAGGCATGCCAGGCAAGGATGGCAAGGACGGTGTGCCGGGACTTGACGGTGAGA
AGGGAGAGGCTGGTCGCACTGGTGCCCCAGGAGAAAAAGGCCCCAATGGGCTGCCGGGGCTCCC
TGGACGAGCAGGGTCCAAAGGCGAGAAGGGAGAAGTGGGTAGAACTGGGGAGCTGGGCGAGGCT
GGCCCCTCTGGAGAACCAGGTATTCCTGGAGACGTTGGTGTTCCGGGGGAGCGTGGCGAGGCTG
GTCACAGGGGCTCAGTGGGGGCCCTCGGCCCACAAGGTCCTCCTGGGGCTCCTGGCATTCGTGG
CTTCCAGGGCCAAAAAGGCAGCATAGGAGACCCTGGCCTTCCAGGCCCCCAAGGCCTACGGGGA
GATGTGGGTGACCGGGGTCCAGGAGGTGCCACAGGTCCTAAGGGAGACCAGGGCATCGCGGGTT
CTGATGGTCTTCCAGGGGACAAAGGAGAGCTGGGTCCTAATGGCCCCGTTGGACAAAAAGGAGA
GTCCGGCAGCCGAGGGGAACTGGGCCCCAAAGGCATCCAGGGCCCCAATGGTACCAGTGGGGTC
CAGGGTGTGCCTGGTCCCCCAGGTCCACTGGGCTTCCAAGGCGTGCAGGGTGTCCCAGGCATCA
CGGGGAAACCTGGAGTTCCGGGCAAGGAAGCCAGTGAACAACGCATCAGGGAGCTGTGTGGGGG
GATGATCAGTGAGCAAATTGCACAGCTGGCTGCACACCTGAGGAAGCCCTTAGCACCAGGCTCC
ATTGGCAGGCCTGGTCCAGCTGGCCCCCCAGGCCCTCCAGGCCCCCCAGGCTCCATTGGCCACC
CTGGCGCTCGGGGTCCTCCTGGATACCGTGGTCCCACTGGGGAACTAGGAGATCCTGGACCAAG
AGGAAGCCAGGGTGACAGAGGAGACAAGGGAGCAATAGGTGTAGGGTTGGATGGACCTGCTGGG
GACCAGGGCTACCGAGGGCCTCAAGGTGTGCCTGGCATCAGCAAAGATGGTCGAGATGGTGCTC
ATGGTGAGCCTGGCCTTCCTGGTGATCCTGGCCTTCCTGGAGCTGCTGGTGCTCAAGGAACCCC
GGGGATTTGCGACACCTCAGCCTGCCAAGGAGCTGTGTTAGGGGGAGGTGGGGAAAAGTCAGGT
CCTCGGAGCTCATAAGCAAGAACTAAAGTAGGAAATGACAGAGCACTCCAGCAGGCAGCAGGGA
TGAGCAGTGTGATGGCTATGGACAGGAATGGACAGTGGCTGGCTACAGTCAGCTAGTCCTTCCT
GGCCTGCTGCTTGGCCCCAAGAGCATCTATTGGCGCCACTGTCACTGTCCCATCTTCAGGATTT
ATGGCAGCCCATTCATCTGTGACAGCATACCTCAGACACAGACCTTAGGGATGGAGACTTTAAA
CCCAGCATCTGGGAGGATTGGTGTTATTGAAGAGTTTTGTACAATTCCATGAGATAAAAACACT
CAAGAGACTTGTTTACACATTTATATAAAGCCTATGACAGACTACCAATAAAGCGATCTTCTAA
CCCTTCAGATTAGTACTGGCTACAGTGTGATGAAGGCAAGGAACTTAATGTCTGCTTCACCTGC
TTTCTATTGCAAGTTAGTATAATCTTTGATGCCCAGTATTTATTCAAGGAACTACACTGTACCA
TATGTCACAATAAATAAAGCTACTCACTGGAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102081	(Get FASTA)	NCBI Sequence Viewer
	XP_017447803	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL88796	(Get FASTA)	NCBI Sequence Viewer
	EDL88797	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000013105
	ENSRNOP00000013105.7

RefSeq Acc Id:

XP_017447803 ⟸ XM_017592314

- Peptide Label:

isoform X1

- Sequence:

show sequence

MTGAPALALLLLGQLLTATSAQKVGPRGPPGPQGPPGKPGKDGIDGEAGPPGLPGPPGPKGTSG
KPGKPGEAGLPGLPGVDGLTGRDGPAGPKGAPGERGSLGPPGPPGLGGKGLPGPPGNPGVLPEG
ATDLQCPAICPPGPPGPPGMPGFKGPTGYKGEQGEVGKDGEKGNPGPPGPPGIPGTVGLQGPRG
LQGLPGPLGPPGDRGPIGFRGPPGIPGAPGKAGDRGDRGPEGFRGPKGDLGRPGPKGIPGVAGP
GGEPGMPGKDGKDGVPGLDGEKGEAGRTGAPGEKGPNGLPGLPGRAGSKGEKGEVGRTGELGEA
GPSGEPGIPGDVGVPGERGEAGHRGSVGALGPQGPPGAPGIRGFQGQKGSIGDPGLPGPQGLRG
DVGDRGPGGATGPKGDQGIAGSDGLPGDKGELGPNGPVGQKGESGSRGELGPKGIQGPNGTSGV
QGVPGPPGPLGFQGVQGVPGITGKPGVPGKEASEQRIRELCGGMISEQIAQLAAHLRKPLAPGS
IGRPGPAGPPGPPGPPGSIGHPGARGPPGYRGPTGELGDPGPRGSQGDRGDKGAIGVGLDGPAG
DQGYRGPQGVPGISKDGRDGAHGEPGLPGDPGLPGAAGAQGTPGICDTSACQGAVLGGGGEKSG
PRSS

hide sequence

RefSeq Acc Id:

ENSRNOP00000013105 ⟸ ENSRNOT00000013105

RefSeq Acc Id:	NP_001102081 ⟸ NM_001108611
- Peptide Label:	precursor
- UniProtKB:	D3ZX71 (UniProtKB/TrEMBL)

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZX71-F1-model_v2	AlphaFold	D3ZX71	1-680	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13692748

Promoter ID:

EPDNEW_R3264

Type:

initiation region

Name:

Col9a3_1

Description:

collagen type IX alpha 3 chain

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	176,102,308 - 176,102,368	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310255	AgrOrtholog
BioCyc Gene	G2FUF-46326	BioCyc
Ensembl Genes	ENSRNOG00000009531	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000013105	ENTREZGENE
	ENSRNOT00000013105.8	UniProtKB/TrEMBL
InterPro	Collagen	UniProtKB/TrEMBL
NCBI Gene	362285	ENTREZGENE
PANTHER	COLLAGEN ALPHA	UniProtKB/TrEMBL
	COLLAGEN ALPHA-1(IV) CHAIN	UniProtKB/TrEMBL
Pfam	Collagen	UniProtKB/TrEMBL
PhenoGen	Col9a3	PhenoGen
RatGTEx	ENSRNOG00000009531	RatGTEx
UniProt	D3ZX71	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-07-27	Col9a3	collagen type IX alpha 3 chain	Col9a3	collagen, type IX, alpha 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-03-20	Col9a3	collagen, type IX, alpha 3	Col9a3	procollagen, type IX, alpha 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Col9a3	procollagen, type IX, alpha 3	Col9a3_predicted	procollagen, type IX, alpha 3 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Col9a3_predicted	procollagen, type IX, alpha 3 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIA

Imported Disease Annotations - OMIM

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIA

Imported Disease Annotations - OMIM

Imported Annotations - PID (archival)