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Gene: Col9a1 (collagen type IX alpha 1 chain) Rattus norvegicus

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Symbol:

Col9a1

Name:

collagen type IX alpha 1 chain

RGD ID:

1309425

Description:

Predicted to enable carbohydrate binding activity and protein homodimerization activity. Involved in chondrocyte differentiation. Predicted to be located in extracellular region. Predicted to be part of collagen type IX trimer. 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); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; alpha-Zearalanol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

collagen alpha-1(IX) chain; collagen, type IX, alpha 1; LOC305104; procollagen, type IX, alpha 1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	9	34,081,364 - 34,164,552 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	9	34,003,905 - 34,164,543 (+)	Ensembl				GRCr8
mRatBN7.2	9	26,585,034 - 26,668,222 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	26,585,034 - 26,668,213 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	9	35,095,083 - 35,178,680 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	40,212,633 - 40,295,468 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	38,523,127 - 38,606,738 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	30,419,001 - 30,502,307 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	30,419,001 - 30,502,298 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	9	29,243,190 - 29,326,425 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	9	22,907,157 - 22,990,836 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	9	24,120,894 - 24,204,338 (+)	NCBI		Celera
RGSC_v3.1	9	22,900,690 - 22,991,448 (+)	NCBI
Cytogenetic Map	9	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

connective tissue disease (ISO)

Desbuquois dysplasia (ISO)

dilated cardiomyopathy (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

Hearing Loss (ISO)

Marfan syndrome (ISO)

Marshall syndrome (ISO)

multiple epiphyseal dysplasia (ISO)

multiple epiphyseal dysplasia 6 (ISO)

myopia (ISO)

optic atrophy (ISO)

osteoarthritis (ISS)

osteochondrodysplasia (ISO)

retinal disease (ISO)

retinitis pigmentosa 1 (ISO)

sensorineural hearing loss (ISO)

Stickler syndrome (ISO)

Stickler Syndrome, Type IV (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

4,4'-sulfonyldiphenol (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-Zearalanol (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

carbamazepine (ISO)

carmustine (ISO)

CGP 52608 (ISO)

chlorpyrifos (EXP,ISO)

clobetasol (ISO)

cobalt dichloride (EXP)

Cuprizon (EXP)

cytarabine (ISO)

dexamethasone (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

folic acid (ISO)

lead diacetate (EXP)

lipopolysaccharide (ISO)

N-Nitrosopyrrolidine (ISO)

paracetamol (ISO)

perfluorooctanoic acid (EXP)

phenobarbital (EXP)

phenylmercury acetate (ISO)

Ptaquiloside (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

SB 431542 (ISO)

sodium arsenite (EXP,ISO)

sunitinib (ISO)

T-2 toxin (ISO)

testosterone (ISO)

thioacetamide (EXP)

trichloroethene (EXP)

triclosan (ISO)

triticonazole (EXP)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ morphogenesis (IEA)

bone morphogenesis (ISO)

cartilage development (ISO)

chondrocyte differentiation (IEP)

chondrocyte proliferation (ISO)

growth plate cartilage development (ISO)

skeletal system development (ISO)

tissue homeostasis (ISO)

Cellular Component

collagen type IX trimer (IEA,ISO)

Molecular Function

carbohydrate binding (IEA,ISO)

metal ion binding (IEA)

protein binding (ISO)

protein homodimerization activity (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

syndecan signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Establishment of bone morphogenetic protein 2 responsive chondrogenic cell line.	Aikawa T, etal., J Bone Miner Res. 1996 Apr;11(4):544-53.
2.	A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity.	Czarny-Ratajczak M, etal., Am J Hum Genet. 2001 Nov;69(5):969-80. Epub 2001 Sep 14.
3.	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.
4.	New Altered Non-Fibrillar Collagens in Human Dilated Cardiomyopathy: Role in the Remodeling Process.	Gil-Cayuela C, etal., PLoS One. 2016 Dec 9;11(12):e0168130. doi: 10.1371/journal.pone.0168130. eCollection 2016.
5.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
6.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
7.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
8.	PID Annotation Import Pipeline	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9.	GOA pipeline	RGD automated data pipeline
10.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
12.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:2465149	PMID:8197187	PMID:8266829	PMID:8660302	PMID:8889548	PMID:11680679	PMID:18191556	PMID:18448257	PMID:18467703

Genomics

Comparative Map Data

Col9a1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	9	34,081,364 - 34,164,552 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	9	34,003,905 - 34,164,543 (+)	Ensembl				GRCr8
mRatBN7.2	9	26,585,034 - 26,668,222 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	26,585,034 - 26,668,213 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	9	35,095,083 - 35,178,680 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	40,212,633 - 40,295,468 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	38,523,127 - 38,606,738 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	30,419,001 - 30,502,307 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	30,419,001 - 30,502,298 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	9	29,243,190 - 29,326,425 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	9	22,907,157 - 22,990,836 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	9	24,120,894 - 24,204,338 (+)	NCBI		Celera
RGSC_v3.1	9	22,900,690 - 22,991,448 (+)	NCBI
Cytogenetic Map	9	q21	NCBI

COL9A1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	70,215,061 - 70,303,084 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	70,216,040 - 70,303,084 (-)	Ensembl			hg38	GRCh38
GRCh37	6	70,924,764 - 71,012,787 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	70,982,529 - 71,069,494 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	6	70,982,947 - 71,049,621	NCBI
Celera	6	71,314,154 - 71,401,187 (-)	NCBI		Celera
Cytogenetic Map	6	q13	NCBI
HuRef	6	68,124,097 - 68,211,118 (-)	NCBI		HuRef
CHM1_1	6	71,092,075 - 71,179,110 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	71,395,620 - 71,483,638 (-)	NCBI		T2T-CHM13v2.0

Col9a1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	24,216,670 - 24,291,819 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	24,216,691 - 24,291,765 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	1	24,177,589 - 24,252,738 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	24,177,610 - 24,252,684 (+)	Ensembl			mm10	GRCm38
MGSCv37	1	24,184,449 - 24,259,577 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	1	24,131,975 - 24,206,620 (+)	NCBI		MGSCv36	mm8
Celera	1	24,015,215 - 24,090,378 (+)	NCBI		Celera
Cytogenetic Map	1	A5	NCBI
cM Map	1	9.95	NCBI

Col9a1
(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 Ensembl	NW_004955488	5,296,895 - 5,384,940 (-)	Ensembl
ChiLan1.0	NW_004955488	5,296,895 - 5,384,940 (-)	NCBI	ChiLan1.0	ChiLan1.0

COL9A1
(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-v2	5	90,204,374 - 90,403,331 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	88,129,574 - 88,326,674 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	68,051,446 - 68,138,715 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	71,349,471 - 71,436,370 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	71,349,471 - 71,436,370 (-)	Ensembl			panPan2	panpan1.1

COL9A1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	32,763,782 - 32,847,456 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	32,764,496 - 32,847,574 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	32,622,570 - 32,712,754 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	12	33,302,925 - 33,393,116 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	12	33,303,461 - 33,386,418 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	12	32,833,854 - 32,924,027 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	12	32,875,246 - 32,965,256 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	12	32,987,732 - 33,078,117 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Col9a1
(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_024404946	68,018,968 - 68,102,662 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936618	2,176,240 - 2,260,000 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936618	2,176,328 - 2,260,000 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

COL9A1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	50,403,361 - 50,498,332 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	1	50,403,355 - 50,498,356 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	56,676,805 - 56,773,217 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

COL9A1
(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	17	4,570,766 - 4,761,678 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	4,674,162 - 4,761,924 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666058	10,581,860 - 10,773,875 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Col9a1
(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_female_1.0 Ensembl	NW_004624819	9,571,265 - 9,663,820 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624819	9,571,250 - 9,664,541 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Col9a1
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	4	101,513,526 - 101,602,414 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Col9a1
716 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	73
Count of miRNA genes:	65
Interacting mature miRNAs:	66
Transcripts:	ENSRNOT00000018116
Prediction methods:	Microtar, 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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2303170	Bp332	Blood pressure QTL 332	3.73	0.027	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	9	6714888	84474983	Rat
631211	Bw4	Body weight QTL4	5.31		retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	9	5346479	50346479	Rat
2303559	Gluco54	Glucose level QTL 54	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	9	8750492	53750492	Rat
1300180	Bw14	Body weight QTL 14	3.776		body mass (VT:0001259)	body weight (CMO:0000012)	9	31250432	68875676	Rat
61450	Ciaa3	CIA Autoantibody QTL 3	6.5		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	9	29567664	74567664	Rat
70186	Niddm26	Non-insulin dependent diabetes mellitus QTL 26	3.87		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	9	29567664	83835942	Rat
9589055	Scfw5	Subcutaneous fat weight QTL 5	5.55	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	9	496645	45496645	Rat
1641911	Alcrsp13	Alcohol response QTL 13			response to alcohol trait (VT:0010489)	brain neurotensin receptor 1 density (CMO:0002068)	9	6214995	51214995	Rat
1354650	Despr5	Despair related QTL 5	4.01	0.0017	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	9	8750492	53750492	Rat
1300124	Cm4	Cardiac mass QTL 4	3.55		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	9	1	41763315	Rat
7207805	Bmd88	Bone mineral density QTL 88	4		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	9	31250432	65651574	Rat
61425	Cia15	Collagen induced arthritis QTL 15	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	9	5346479	50416711	Rat
9589158	Gluco65	Glucose level QTL 65	6.82	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	9	496645	45496645	Rat
1600365	Mcs20	Mammary carcinoma susceptibility QTL 20	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	9	21031430	49025574	Rat
7411592	Foco8	Food consumption QTL 8	7.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	496645	45496645	Rat
1298088	Edpm11	Estrogen-dependent pituitary mass QTL 11	2.5		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	9	6214995	51214995	Rat
1598823	Memor16	Memory QTL 16	1.9		exploratory behavior trait (VT:0010471)	difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	9	31456061	57460683	Rat

Markers in Region

RH129101

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	9	26,667,953 - 26,668,173 (+)	MAPPER	mRatBN7.2
Rnor_6.0	9	30,502,039 - 30,502,258	NCBI	Rnor6.0
Rnor_5.0	9	29,326,157 - 29,326,376	UniSTS	Rnor5.0
RGSC_v3.4	9	22,990,568 - 22,990,787	UniSTS	RGSC3.4
Celera	9	24,204,070 - 24,204,289	UniSTS
Cytogenetic Map	9	q13	UniSTS

RH143643

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	9	26,665,445 - 26,665,646 (+)	MAPPER	mRatBN7.2
Rnor_6.0	9	30,499,531 - 30,499,731	NCBI	Rnor6.0
Rnor_5.0	9	29,323,649 - 29,323,849	UniSTS	Rnor5.0
RGSC_v3.4	9	22,988,060 - 22,988,260	UniSTS	RGSC3.4
Celera	9	24,201,562 - 24,201,762	UniSTS
RH 3.4 Map	9	248.49	UniSTS
Cytogenetic Map	9	q13	UniSTS

UniSTS:478964

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	9	26,605,362 - 26,606,963 (+)	MAPPER	mRatBN7.2
Rnor_6.0	9	30,439,333 - 30,440,933	NCBI	Rnor6.0
Rnor_5.0	9	29,263,476 - 29,265,076	UniSTS	Rnor5.0
RGSC_v3.4	9	22,927,716 - 22,929,316	UniSTS	RGSC3.4
Celera	9	24,141,274 - 24,142,874	UniSTS
Cytogenetic Map	9	q13	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	8	54	129	34	41	18	12	18	6	201	86	9	114	75	83	23	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001100842	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039083449	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BQ191679	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473987	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DY313373	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DY316977	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000009	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	S67620	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000018116 ⟹ ENSRNOP00000018116

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	9	34,081,364 - 34,164,543 (+)	Ensembl
mRatBN7.2 Ensembl	9	26,585,034 - 26,668,213 (+)	Ensembl
Rnor_6.0 Ensembl	9	30,419,001 - 30,502,298 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000115769 ⟹ ENSRNOP00000081771

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	9	34,101,513 - 34,164,543 (+)	Ensembl
mRatBN7.2 Ensembl	9	26,605,218 - 26,668,213 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000150022 ⟹ ENSRNOP00000103106

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	9	34,003,905 - 34,164,543 (+)	Ensembl

RefSeq Acc Id:

NM_001100842 ⟹ NP_001094312

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	34,081,364 - 34,164,552 (+)	NCBI
mRatBN7.2	9	26,585,034 - 26,668,222 (+)	NCBI
Rnor_6.0	9	30,419,001 - 30,502,307 (+)	NCBI
Rnor_5.0	9	29,243,190 - 29,326,425 (+)	NCBI
Celera	9	24,120,894 - 24,204,338 (+)	NCBI

Sequence:

show sequence

CCCCTGGCTGGGCCTGGGCTTACTGGCTGTTTCTCTCCACCCCTTTCCTTTGCTTCAGCTTAAA
GAGTTATTACATGCCATCAGTTCACTCTTTTTGCTTTTAGCCCTAAGAGGGGCAAGAAGGAGCA
AGCTTGGGGCCAAATCTCAGAGCCAGAGAAGGATAGAGAAGGGGTGTTGGGGAGTAGGGACTCC
CCTCCAACCCCCTCATGGTGACTCTTATAAACCCAAGAGAACCCACTGGGAAAATGAAGAACTT
CTGGAAAATTCCACTTTTCTTCTTTGCATGCAGTTTTCTGGGACCCTGTGTATCTGCAACTCCT
AAGCGTCGTGCAAGATTTCCTGCCAATTCTGTTTCTCATGGTGGAAGTGAACTGTGTCCCAAGA
TCAGGATTGGCCAGGATGACTTGCCAGGATTTGACCTGATTTCTCAGTTCCAAATTGAGAAGGC
TGCATCTCGAAGGACTATCCAGAGGGTGGTGGGGTCCACAGCGTTACAAGTGGCTTACAAGCTG
GGAAGTAATGTAGACTTCAGGATTCCAACAAGGCATTTGTATCCCAGTGGACTGCCTGAAGAAT
ATTCCTTTTTAACTACTTTCCGGATGACTGGAAGCACACTTGAAAAGCAATGGAACATTTGGCA
GATCCAGGATTCCTCAGGGAGGGAGCAAGTTGGCGTGAAGATAAATGGCCAAACAAAGTCTGTC
GCGTTTTCATACAAGGGACTGGACGGGAGTCTCCAAACGGCAGCCTTCTTGAATTTGCAGTCCT
TGTTTGACTCCCGTTGGCATAAGCTCATGATTGGCGTGGAGAGAACAAGAGCTACTCTTTTTAT
TGACTGCATCCAGATCGATTCCTTACCTATAAAGCCGAGAGCCCAGATCGATGCTGATGGCTTT
GCTGTGCTGGGAAAACTTGTGGACAATCCTCAGGTTTCTGTTCCCTTTGAACTCCAGTGGATGC
TGATTCACTGTGACCCCCTGAGACCCCGGAGAGAGACGTGCCATGAACTGCCAGTCAGAATCAC
AACCAGCCAGACCACCGATGAGAGAGGTCCTCCGGGTGAGCAGGGGCCTCCGGGGCCTCCCGGG
CCTCCTGGAGTTCCGGGCATAGATGGTATTGATGGTGACCGAGGTCCAAAGGGTCCCCCCGGAC
CTCCGGGTCCTCCTGGAGACCCGGGCAAGCCAGGAGCACCAGGCAAGCCAGGCACTCCAGGAGC
TGATGGATTAACAGGACCTGATGGGTCCCCGGGCTCCGTTGGACCAAGGGGACAAAAAGGAGAA
CCTGGTGTGCCTGGGTCTCGTGGATTTCCAGGCCGTGGCATTCCAGGACCCCCTGGCCCTCCTG
GGACCACAGGACTTCCTGGAGAACTTGGCCGAGTAGGCCCTGCTGGCGACCCTGGGAAAAGAGG
ACCACCTGGTCCTCCTGGACCCCCAGGACCTAGTGGAACAATTGGATTTCATGATGGAGACCCA
TTGTGCCCCAATTCCTGCCCACCAGGTCGCTCTGGCTATCCAGGCCTACCAGGCATGAGAGGCC
ACAAAGGGGCGAAAGGAGAAATTGGCGAGCCAGGAAGACAAGGACACAAGGGTGAAGAGGGTGA
CCAGGGGGAACTGGGAGAAGTTGGAGCTCAAGGACCTCCAGGAGCTCAAGGTCTGAGAGGCATC
ACTGGCATAGTTGGAGACAAAGGAGAAAAAGGTGCTCGGGGATTCGATGGAGATCCTGGGCCTC
AGGGCGTTCCAGGTGCAGCTGGTGATCAAGGGCAGCGAGGACCTCCAGGAGAAACAGGTCCTAA
GGGAGACAGGGGCATTCAAGGTTCCCGAGGAATTCCTGGATCCCCGGGTCCAAAAGGAGACACG
GGCTTGCCAGGTGTCGATGGTCGAGACGGAATCCCGGGAATGCCTGGAACAAAGGGTGAAGCAG
GAAAGCCTGGACCTCCCGGTGATGCGGGATTGCAGGGTTTACCGGGTGTACCTGGGATTCCTGG
TGCAAAAGGTGTGGCCGGCGAAAAGGGTAACACGGGTCCTCCGGGGAAGCCTGGTCAGTTGGGA
AGTTCAGGAAAACCAGGCCAACAAGGACCGCCGGGAGAGGTTGGACCTCGGGGACCCAGGGGCC
TTCCAGGCAGCAGAGGCCCGGTAGGACCAGAAGGCTCTCCAGGCATACCAGGGAAACTGGGACC
TCTTGGCAGCCCTGGCCTTCCTGGCTTGCCTGGGCCCCCTGGACTTCCTGGAATGAAAGGAGAC
AGGGGTGTATTTGGTGAACCAGGTCCCAAGGGCGAACAGGGTGCCTCTGGTGAAGAAGGTGAAG
CAGGAGTAAGGGGTGACCTTGGAGATATGGGACAACCTGGCCCAAAGGGATCAGTGGGTAACCC
TGGGGAGCCCGGCCTGAGGGGACCTGAAGGAATCAGAGGGCTTCCTGGAGTGGAAGGACCAAGA
GGACCACCTGGACCCCGAGGTGTGCAAGGAGAACAGGGTGCCACTGGACTGCCTGGTATCCAGG
GACCTCCGGGCAGAGCGCCGACGGACCAGCACATCAAGCAGGTTTGCATGAGAGTTGTGCAAGA
GCATTTTGCAGAAATGGCAGCTAGCCTCAAGAGACCAGACACAGGAGCTTCTGGTCTTCCTGGG
AGGCCTGGTCCCCCAGGGCCTCCCGGCCCTCCAGGAGAGAATGGTTTCCCTGGTCAGATGGGAA
TCCGTGGCCTTCCAGGCATTAAGGGTCCCCCTGGTGCTCTTGGCTTAAGGGGACCTAAAGGTGA
CTTGGGAGAAAAAGGAGAACGTGGTCCTCCAGGAAGAGGTCCTAAGGGTTTGCCTGGAGCTATC
GGTCTCCCAGGTGATCCAGGCCCTGCCAGCTATGGGAAAAATGGCCGAGATGGAGAGCAAGGTC
CCCCAGGAGTGGCAGGAATTCCTGGTGTGCCTGGGCCCCCAGGTCCTCCAGGCCCTCCTGGTTT
CTGTGAGCCAGCCTCTTGCACCCTTCAGGCAGGTCAAAGAGCATTTAGCAAAGGGCCTGACAAG
TGAAAGCCTTCGTGTTCTAGACTCCCCTATACACACCGTGCCTGGTAGAGGAGCATGTGGGAGA
AACAATATATCCAACAGTGGGGCAACGACTAAAAGGTTTCACCTCAGACATCACTACACACGTG
CTATATGACAATCGGATTTAGAAGAACTGGTGCTATTCCGTTAAGTCTTGTTCCTTCAGGAGCG
TCATCAGACAAAAGTCAAATTCAATTTCTCTTTAGGCAAATTTATAAATCCTCCTCCTGGGCTT
TTGGATTTTAGTGTGCTATGAGTGCATATATGATGTATTGTGGGCCACTGTGCCAACAACAGCA
GCAGCAGCAGCAAACTGTTCAGTTTACCTCACTTGCTGTCATTGTTTTTATTTCAATTAAGATA
TTGACCTGAGATTTGAACAATCAGTTGTGTCAAGTACTGCTAAGGAACAAAACCCACTACATTC
AACAAAATTGGTGCTTAAAATCTTCATCAGGGCCGTGTCACAGAAGTGGTCTCTATAGATGGTG
GTTCTCATCTTTATTCTGAATTTGTGAATATACTGCGCCCCAAACGCACTCGCATTGTAAGATC
CACGTGAAAGCAAAGAAGTGATACCCCAACGTGCATATGTTTTGTGGCTGACATTATTTATTTT
AAAAGTTTGAGATAACATGTCTGGTTGTACCAAAGAAGAAATAAACATGATTTCATAATCTTTT
GTACGTTCTAAGATAAGTCGTCATGTTAAATGTGGTTGCATGTTAATCGAACTTGTTTAGATTC
ATTAAATTTTTGACTTATTGCTACTTTTAAAAATGTAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039083449 ⟹ XP_038939377

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	34,101,547 - 34,164,548 (+)	NCBI
mRatBN7.2	9	26,605,217 - 26,668,218 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001094312	(Get FASTA)	NCBI Sequence Viewer
	XP_038939377	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB29306	(Get FASTA)	NCBI Sequence Viewer
	EDM18615	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000018116
	ENSRNOP00000081771
GenBank Protein	P20850	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_001094312 ⟸ NM_001100842
- Peptide Label:	precursor
- UniProtKB:	F1LQ93 (UniProtKB/TrEMBL)
- Sequence:	show sequence MVTLINPREPTGKMKNFWKIPLFFFACSFLGPCVSATPKRRARFPANSVSHGGSELCPKIRIGQ DDLPGFDLISQFQIEKAASRRTIQRVVGSTALQVAYKLGSNVDFRIPTRHLYPSGLPEEYSFLT TFRMTGSTLEKQWNIWQIQDSSGREQVGVKINGQTKSVAFSYKGLDGSLQTAAFLNLQSLFDSR WHKLMIGVERTRATLFIDCIQIDSLPIKPRAQIDADGFAVLGKLVDNPQVSVPFELQWMLIHCD PLRPRRETCHELPVRITTSQTTDERGPPGEQGPPGPPGPPGVPGIDGIDGDRGPKGPPGPPGPP GDPGKPGAPGKPGTPGADGLTGPDGSPGSVGPRGQKGEPGVPGSRGFPGRGIPGPPGPPGTTGL PGELGRVGPAGDPGKRGPPGPPGPPGPSGTIGFHDGDPLCPNSCPPGRSGYPGLPGMRGHKGAK GEIGEPGRQGHKGEEGDQGELGEVGAQGPPGAQGLRGITGIVGDKGEKGARGFDGDPGPQGVPG AAGDQGQRGPPGETGPKGDRGIQGSRGIPGSPGPKGDTGLPGVDGRDGIPGMPGTKGEAGKPGP PGDAGLQGLPGVPGIPGAKGVAGEKGNTGPPGKPGQLGSSGKPGQQGPPGEVGPRGPRGLPGSR GPVGPEGSPGIPGKLGPLGSPGLPGLPGPPGLPGMKGDRGVFGEPGPKGEQGASGEEGEAGVRG DLGDMGQPGPKGSVGNPGEPGLRGPEGIRGLPGVEGPRGPPGPRGVQGEQGATGLPGIQGPPGR APTDQHIKQVCMRVVQEHFAEMAASLKRPDTGASGLPGRPGPPGPPGPPGENGFPGQMGIRGLP GIKGPPGALGLRGPKGDLGEKGERGPPGRGPKGLPGAIGLPGDPGPASYGKNGRDGEQGPPGVA GIPGVPGPPGPPGPPGFCEPASCTLQAGQRAFSKGPDK hide sequence

Ensembl Acc Id:

ENSRNOP00000018116 ⟸ ENSRNOT00000018116

RefSeq Acc Id:	XP_038939377 ⟸ XM_039083449
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5ZSW9 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000081771 ⟸ ENSRNOT00000115769

Ensembl Acc Id:

ENSRNOP00000103106 ⟸ ENSRNOT00000150022

Protein Domains

Thrombospondin-like N-terminal

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P20850-F1-model_v2	AlphaFold	P20850	1-325	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1309425	AgrOrtholog
BioCyc Gene	G2FUF-27960	BioCyc
Ensembl Genes	ENSRNOG00000012920	Ensembl, ENTREZGENE
Ensembl Transcript	ENSRNOT00000018116	ENTREZGENE
	ENSRNOT00000115769	ENTREZGENE
InterPro	Collagen	UniProtKB/Swiss-Prot
	Collagen_superfamily	UniProtKB/Swiss-Prot
NCBI Gene	305104	ENTREZGENE
PANTHER	COLLAGEN ALPHA	UniProtKB/Swiss-Prot
	COLLAGEN TRIPLE HELIX REPEAT	UniProtKB/Swiss-Prot
Pfam	Collagen	UniProtKB/Swiss-Prot
PhenoGen	Col9a1	PhenoGen
RatGTEx	ENSRNOG00000012920	RatGTEx
UniProt	A0A8I5ZSW9	ENTREZGENE, UniProtKB/TrEMBL
	A0ABK0LEM3_RAT	UniProtKB/TrEMBL
	A6JJB7_RAT	UniProtKB/TrEMBL
	CO9A1_RAT	UniProtKB/Swiss-Prot
	F1LQ93	ENTREZGENE, UniProtKB/TrEMBL
	P20850	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-07-27	Col9a1	collagen type IX alpha 1 chain	Col9a1	collagen, type IX, alpha 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-25	Col9a1	collagen, type IX, alpha 1	Col9a1	procollagen, type IX, alpha 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Col9a1	procollagen, type IX, alpha 1	Col9a1_predicted	procollagen, type IX, alpha 1 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Col9a1_predicted	procollagen, type IX, alpha 1 (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)

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Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - PID (archival)

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Imported Disease Annotations - OMIM

Imported Annotations - PID (archival)