Sparcl1 (SPARC like 1) - Rat Genome Database

Name: Sparcl1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Sparcl1 (SPARC like 1) Rattus norvegicus

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Symbol:

Sparcl1

Name:

SPARC like 1

RGD ID:

2531

Description:

Predicted to enable calcium ion binding activity; collagen binding activity; and extracellular matrix binding activity. Involved in regulation of synapse organization. Is active in extracellular matrix of synaptic cleft and glutamatergic synapse. Orthologous to human SPARCL1 (SPARC like 1); INTERACTS WITH (+)-pilocarpine; 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

Ecm2; Extracellular matrix protein 2; matrix glycoprotein Sc1; Sc1; SPARC-like 1; SPARC-like 1 (hevin); SPARC-like 1 (mast9, hevin); SPARC-like protein 1

RGD Orthologs

Alliance Orthologs

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):	SPARCL1 (SPARC like 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Sparcl1 (SPARC-like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Sparcl1 (SPARC like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SPARCL1 (SPARC like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HSD17B11 (hydroxysteroid 17-beta dehydrogenase 11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Sparcl1 (SPARC like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SPARCL1 (SPARC like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SPARCL1 (SPARC like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Sparcl1 (SPARC like 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SPARCL1 (SPARC like 1)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Sparcl1 (SPARC-like 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	sparcl1 (SPARC-like 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	ost-1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	SPARC	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|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
GRCr8	14	5,937,484 - 5,968,532 (+)	NCBI		GRCr8
mRatBN7.2	14	5,632,816 - 5,663,866 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	5,632,569 - 5,663,865 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	5,601,783 - 5,632,794 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	6,902,017 - 6,933,024 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	5,600,631 - 5,631,801 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	6,994,261 - 7,025,309 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	6,994,190 - 7,025,308 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	6,985,394 - 7,016,296 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	6,766,347 - 6,797,581 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	6,766,346 - 6,797,580 (+)	NCBI
Celera	14	5,771,812 - 5,802,805 (+)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant polycystic kidney disease (ISO)

corneal dystrophy (ISO)

endometriosis (ISO)

epilepsy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-pilocarpine (EXP)

1,2,4-trimethylbenzene (EXP)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (EXP,ISO)

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

2,4-dibromophenyl 2,4,5-tribromophenyl ether (ISO)

2,6-dinitrotoluene (EXP)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3-chloropropane-1,2-diol (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3-methylcholanthrene (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

7,12-dimethyltetraphene (EXP)

acetamide (EXP)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

bleomycin A2 (EXP)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

calcitriol (ISO)

cantharidin (ISO)

carbon nanotube (ISO)

casticin (ISO)

CGP 52608 (ISO)

chitosan (ISO)

choline (ISO)

chrysene (ISO)

cocaine (EXP)

copper atom (EXP)

copper(0) (EXP)

cordycepin (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dichloroacetic acid (ISO)

diuron (EXP)

doxorubicin (ISO)

epoxiconazole (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

fentin chloride (EXP)

folic acid (ISO)

formaldehyde (ISO)

genistein (EXP)

indole-3-methanol (EXP)

indometacin (ISO)

inulin (ISO)

L-ascorbic acid (ISO)

L-methionine (ISO)

Lasiocarpine (ISO)

lead(0) (ISO)

leflunomide (EXP)

lithium atom (EXP)

lithium hydride (EXP)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

miconazole (ISO)

N-nitrosodiethylamine (ISO)

nitrofen (EXP)

O-methyleugenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

pioglitazone (ISO)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

progesterone (ISO)

rotenone (EXP)

sodium arsenate (ISO)

sodium arsenite (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

trimellitic anhydride (ISO)

troglitazone (ISO)

undecane (EXP)

valproic acid (ISO)

vancomycin (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

regulation of synapse organization (EXP,IDA)

signal transduction (IEA)

synaptic membrane adhesion (IEA,ISO)

Cellular Component

collagen-containing extracellular matrix (IEA)

extracellular matrix of synaptic cleft (IDA)

extracellular space (IBA,IEA)

glutamatergic synapse (EXP,IDA,IEA,ISO)

Molecular Function

calcium ion binding (IBA,IEA)

collagen binding (IBA)

extracellular matrix binding (IBA)

protein binding (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.	Molecular cloning of SC1: a putative brain extracellular matrix glycoprotein showing partial similarity to osteonectin/BM40/SPARC.	Johnston IG, etal., Neuron 1990 Jan;4(1):165-76.
3.	Control of excitatory CNS synaptogenesis by astrocyte-secreted proteins Hevin and SPARC.	Kucukdereli H, etal., Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):E440-9. doi: 10.1073/pnas.1104977108. Epub 2011 Jul 25.
4.	Localization of the extracellular matrix protein SC1 to synapses in the adult rat brain.	Lively S, etal., Neurochem Res. 2007 Jan;32(1):65-71. doi: 10.1007/s11064-006-9226-4. Epub 2006 Dec 7.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	GOA pipeline	RGD automated data pipeline
8.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
10.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
11.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Additional References at PubMed

PMID:16502470	PMID:18335312	PMID:21937915	PMID:22588386	PMID:23376485	PMID:26771491	PMID:27068509	PMID:35820448	PMID:37534667

Genomics

Comparative Map Data

Sparcl1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	5,937,484 - 5,968,532 (+)	NCBI		GRCr8
mRatBN7.2	14	5,632,816 - 5,663,866 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	5,632,569 - 5,663,865 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	5,601,783 - 5,632,794 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	6,902,017 - 6,933,024 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	5,600,631 - 5,631,801 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	6,994,261 - 7,025,309 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	6,994,190 - 7,025,308 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	6,985,394 - 7,016,296 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	6,766,347 - 6,797,581 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	6,766,346 - 6,797,580 (+)	NCBI
Celera	14	5,771,812 - 5,802,805 (+)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

SPARCL1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	87,473,335 - 87,529,376 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	87,473,335 - 87,531,061 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	88,394,487 - 88,450,528 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	88,613,511 - 88,669,530 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	88,751,668 - 88,807,685	NCBI
Celera	4	85,683,694 - 85,739,861 (-)	NCBI		Celera
Cytogenetic Map	4	q22.1	NCBI
HuRef	4	84,140,423 - 84,196,598 (-)	NCBI		HuRef
CHM1_1	4	88,371,316 - 88,427,455 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	90,802,350 - 90,858,405 (-)	NCBI		T2T-CHM13v2.0

Sparcl1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	104,226,974 - 104,261,954 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	104,226,977 - 104,261,599 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	104,079,108 - 104,114,088 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	104,079,111 - 104,113,733 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	104,508,127 - 104,543,107 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	104,319,413 - 104,354,006 (-)	NCBI		MGSCv36	mm8
Celera	5	101,385,822 - 101,420,665 (-)	NCBI		Celera
Cytogenetic Map	5	E5	NCBI
cM Map	5	50.55	NCBI

Sparcl1
(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_004955474	2,370,237 - 2,391,285 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955474	2,352,662 - 2,387,237 (+)	NCBI	ChiLan1.0	ChiLan1.0

SPARCL1
(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	3	85,482,960 - 85,539,823 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	85,745,304 - 85,802,172 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	79,769,085 - 79,825,430 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	90,495,769 - 90,551,960 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	90,498,810 - 90,521,665 (-)	Ensembl	panpan1.1		panPan2

HSD17B11
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	32	10,821,332 - 10,854,541 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	32	10,794,617 - 10,854,193 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	32	31,099,926 - 31,132,979 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	32	10,873,296 - 10,906,759 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	32	10,845,726 - 10,906,673 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	32	10,954,508 - 10,987,556 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	32	10,782,541 - 10,815,990 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	32	29,139,474 - 29,172,518 (+)	NCBI		UU_Cfam_GSD_1.0

Sparcl1
(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_024405285	2,115,830 - 2,154,939 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936905	535,355 - 574,734 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936905	535,589 - 574,719 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SPARCL1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	131,386,973 - 131,431,200 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	131,386,804 - 131,431,427 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	140,599,058 - 140,643,513 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SPARCL1
(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	7	35,858,402 - 35,914,776 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	7	35,857,559 - 35,915,115 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	14,558,006 - 14,615,157 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Sparcl1
(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_004624872	3,981,072 - 3,997,533 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624872	3,981,166 - 4,015,843 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Sparcl1
312 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	26
Count of miRNA genes:	25
Interacting mature miRNAs:	26
Transcripts:	ENSRNOT00000020357
Prediction methods:	Miranda, Rnahybrid
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
1300114	Srn2	Serum renin concentration QTL 2	3.27		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	14	3813074	21217635	Rat
70195	Mcs8	Mammary carcinoma susceptibility QTL 8	4.28		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	14	3813074	24531477	Rat
2293089	Iddm31	Insulin dependent diabetes mellitus QTL 31	4.7		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	14	3813074	18274691	Rat
2300183	Bmd60	Bone mineral density QTL 60	5.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	14	1	26541967	Rat
724541	Niddm53	Non-insulin dependent diabetes mellitus QTL 53		0.001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	3813074	9088978	Rat
1331740	Bw26	Body weight QTL 26	3.028		body mass (VT:0001259)	body weight (CMO:0000012)	14	3813074	30767156	Rat
634352	Apr6	Acute phase response QTL 6	3.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	14	1	41131407	Rat
71115	Niddm15	Non-insulin dependent diabetes mellitus QTL 15	4.8		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	14	1217606	11030812	Rat
619619	Rf4	Renal disease susceptibility QTL 4	4.1	0.002	urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	14	1	32754612	Rat
2300159	Bmd61	Bone mineral density QTL 61	5.3	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	14	1	26541967	Rat
70204	Niddm20	Non-insulin dependent diabetes mellitus QTL 20	5.1	0.000008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	1217606	16960180	Rat

Markers in Region

D14Wox22

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	5,663,514 - 5,663,677 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	7,024,958 - 7,025,120	NCBI	Rnor6.0
Rnor_5.0	14	7,015,945 - 7,016,107	UniSTS	Rnor5.0
RGSC_v3.4	14	6,797,230 - 6,797,392	UniSTS	RGSC3.4
Celera	14	5,802,454 - 5,802,616	UniSTS
Cytogenetic Map	14	p22	UniSTS

AW529913

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	5,650,920 - 5,651,114 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	7,012,366 - 7,012,559	NCBI	Rnor6.0
Rnor_5.0	14	7,003,353 - 7,003,546	UniSTS	Rnor5.0
RGSC_v3.4	14	6,784,638 - 6,784,831	UniSTS	RGSC3.4
Celera	14	5,789,860 - 5,790,053	UniSTS
RH 3.4 Map	14	115.7	UniSTS
Cytogenetic Map	14	p22	UniSTS

D21S1917

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	19	10,198,146 - 10,198,193 (+)	MAPPER	mRatBN7.2
mRatBN7.2	14	5,647,345 - 5,647,929 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	7,008,791 - 7,009,374	NCBI	Rnor6.0
Rnor_6.0	19	10,615,050 - 10,615,096	NCBI	Rnor6.0
Rnor_5.0	19	10,609,857 - 10,609,903	UniSTS	Rnor5.0
Rnor_5.0	14	6,999,778 - 7,000,361	UniSTS	Rnor5.0
RGSC_v3.4	14	6,781,063 - 6,781,646	UniSTS	RGSC3.4
RGSC_v3.4	19	10,637,206 - 10,637,252	UniSTS	RGSC3.4
Celera	19	10,084,530 - 10,084,576	UniSTS
Celera	14	5,786,285 - 5,786,868	UniSTS
Cytogenetic Map	14	p22	UniSTS

SPARCL1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	5,658,228 - 5,658,324 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	7,019,673 - 7,019,768	NCBI	Rnor6.0
Rnor_5.0	14	7,010,660 - 7,010,755	UniSTS	Rnor5.0
RGSC_v3.4	14	6,791,945 - 6,792,040	UniSTS	RGSC3.4
Celera	14	5,797,169 - 5,797,264	UniSTS
Cytogenetic Map	14	p22	UniSTS

RH133331

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	5,663,520 - 5,663,724 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	7,024,964 - 7,025,167	NCBI	Rnor6.0
Rnor_5.0	14	7,015,951 - 7,016,154	UniSTS	Rnor5.0
RGSC_v3.4	14	6,797,236 - 6,797,439	UniSTS	RGSC3.4
Celera	14	5,802,460 - 5,802,663	UniSTS
RH 3.4 Map	14	116.4	UniSTS
Cytogenetic Map	14	p22	UniSTS

RH137752

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	5,643,506 - 5,643,685 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	7,004,952 - 7,005,130	NCBI	Rnor6.0
Rnor_5.0	14	6,995,939 - 6,996,117	UniSTS	Rnor5.0
RGSC_v3.4	14	6,777,224 - 6,777,402	UniSTS	RGSC3.4
Celera	14	5,782,446 - 5,782,624	UniSTS
RH 3.4 Map	14	88.2	UniSTS
Cytogenetic Map	14	p22	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	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012946	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC122637	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC061755	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474022	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223918	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U27562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000020357 ⟹ ENSRNOP00000020357

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	5,632,569 - 5,663,865 (+)	Ensembl
Rnor_6.0 Ensembl	14	6,994,190 - 7,025,308 (+)	Ensembl

RefSeq Acc Id:

NM_012946 ⟹ NP_037078

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	5,937,484 - 5,968,532 (+)	NCBI
mRatBN7.2	14	5,632,816 - 5,663,866 (+)	NCBI
Rnor_6.0	14	6,994,261 - 7,025,309 (+)	NCBI
Rnor_5.0	14	6,985,394 - 7,016,296 (+)	NCBI
RGSC_v3.4	14	6,766,347 - 6,797,581 (+)	RGD
Celera	14	5,771,812 - 5,802,805 (+)	RGD

Sequence:

show sequence

TCTGCGCTGCCTGCGAACGTCTGCAGCACGGAGCCAGCGAGGGAGGGAGATCCAGGAATCCGCA
GCAGAAACCATGACATCCTGCGACACCCTGTGGTGCCAACCTCCAAGCTCTCATCTGTCACTCT
AGACCCTGACGGGCTGGCAGAGCGGCAGAATTTCAACCCCAGTACACTTGAATGGGCTTCCAGG
CAAAGCAGTCAAGCTAACGAGGAAGGGGGTGGAAGAGCTCCTCTTGGGCGTTTGTCAAACTTTT
ACCTCCTGGCTGTGTGCAAAGAGGGGATTGAACTTCAGCTTCAAGCTACCCAGGCTGTGGATCC
AGCCACCTCTCAGCAGGTCTAGCCAGCATGAAGGCCGTGCTTCTCCTCCTGTATGCCTTGGGGA
TCGCTGCTGCAGTCCCGACAACGTTTCTCTCTGATCATTCCAACCCAACTTCCGCAACACTGCC
GACACTGGAAGATGCTACAGTCCCCACTGTCCCAGCTGAAGCTGCAGCAGACATAGAAAAGCAC
CCCAACCATAAGGCTGAAAAACCTTCAGCACTGAACTCAGAAGAGGAAGCCCATGAACAGTCGA
CAGAGCAGGACAAAACCTACAGCTTCGAGGTGGACCTGAAGGATGAGGAGGATGGGGATGGGGA
TTTAAGTGTAGATCCGACGGAAAGAACGCTAGATCTACAGGAAGGGACAAGCGAACCGCAGCAG
AAAAGGCTCCCGGAGAACGCCGATTTCCCTGCTACTGTGTCCACTCCCTTTGTGGATTCTGACC
AACCTGCAAATATCACAAAGGGAGAGGAGAGTCAGGAGCAACCTGTAAGTGACTCGCACCAGCA
ACAGGACGAGAGCGGCAAGCAGACCCAAGACTCGATGACTGAAGAAAGCCACAAACAAGATCCG
GGTATTCCCAATGAAGAAAAGGAAGAAGAGGAAGATCCAGAAGACGTTGGTGCACCCAGTGATA
ACCAAGAGGAAGAAAAAGAACCACCCGAGGAGCAGCCTACCAGCAAGTGGGAAGGAAACGGAGA
CCAATCTGAAGACATCTTACAAGAGTCCAGTCAGCCAACTCAGATAAGCAAGACAAAGAATGAT
TTCGAGCAAGGAAGCCAAGGGCAAGAGGGTGACTCTAATGCAGAAGGGGAGGACAAGGCAGCAG
GCAGCAAGGAACACCTTCCGCATACGGAGTGGCAGGGCCAAGAAGGGAGAGCTGGCCTTGACGC
TATTGGCAACCGGAAGGACACAGATGAAGAAAAGGCTGTTTCCACGGAACCTACCGATGCTGCC
GTCGTGCCTAGGAACCACGGAGCCAGTGATAACGGGGGCGGGGATGACTCTAAGCATGGTGCAA
GCGATGACTACTTCATCCCCAGCCAGGAATTCCTAGAGGCTGAAAGAATGCATTCCCTCTCCTA
TTACCTCAAATACGGAGAGGAGACGCCGGACGAGAGCGAGAACCGAAGTGAGGCTGGAGACAAC
CAAGGGGCCAAGAAAGCTGAGAGCTCACCAAATGCTGAACCGTCCGATGAGGGCAACTCAAGGG
GGCACAGTGCTGATTCTTGCATGAACTTCCAGTGTAAAAGGGGACACACTTGCAAAACGGATCA
ACACGGAAAACCCCACTGTGTTTGCCAAGATCCAGAGACGTGTCCCCCTGCAAAAATCCTCGAC
CAAGCTTGTGGCACTGACAACCAGACCTACGCCAGCTCCTGTCACCTGTTTGCTACCAAGTGCA
TGCTGGAAGGGACCAAAAAGGGACACCAGCTGCAGTTGGATTACTTTGGAGCTTGCAAATCTAT
TCCTGCTTGTACGGACTTCGAAGTGGCTCAGTTTCCGCTGCGGATGAGAGACTGGCTCAAAAAC
ATCCTCATGCAGCTTTACGAACCAAACCCCAAACATGGCGGCTACCTAAATGAAAAGCAAAGAA
GCAAAGTCAAGAAAATTTACCTGGATGAAAAGAGACTCTTGGCTGGAGACCACCCCATTGAACT
TCTCTTAAGGGACTTCAAGAAAAACTACCACATGTATGTGTATCCTGTGCACTGGCAGTTTAAC
GAATTGGATCAGCATCCTGCGGACAGGATCTTGACACATTCTGAACTTGCGCCTCTGCGAGCTT
CCCTGGTGCCCATGGAGCACTGCATAACGCGCTTCTTTGAGGAGTGTGACCCCAACAAGGACAA
GCATATCACCTTGAAGGAATGGGGCCACTGCTTTGGAATTAAAGAAGAAGACATAGATGAAAAC
CTCCTCTTTTGAATTAAGACTCCAGAGAATCGAAACTTTCCATCAGCCCTGCTTGCTTTAACCA
CTTCCGCGTAGGAGCCGCCATGACACTCTACATTCCTATGTAGCAAAACGTGTTTGCATGTAAG
AGAAGACAATGATAGTAATTGCTTCTTAGAAATATATATATATATATTAACTTAGTAAATAAAA
CTTTAAAATTAAGTAGAGTCGATGTCTAAAAGACTGTCCTGCCTGGGGACAGTTACCCATGGTA
ATGTCACCCTGTGCATCTGCGTTTGTAATTGATAATTACAAACTATTAAAAACAGCGTTTGTAC
TGTCCATGACACCTGATGCATGCTAAGGAAGTGGGATATTGTTCTTTCGAGATTAATATACCTT
ATTGTCAGTATCCTGATGTCCTAATAAAAAGTCTATGAAACCTCAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_037078	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA68708	(Get FASTA)	NCBI Sequence Viewer
	AAH61755	(Get FASTA)	NCBI Sequence Viewer
	EDL99503	(Get FASTA)	NCBI Sequence Viewer
	EDL99504	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000020357.6
GenBank Protein	P24054	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_037078 ⟸ NM_012946
- Peptide Label:	precursor
- UniProtKB:	A6K5T4 (UniProtKB/TrEMBL), Q6P7A8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MKAVLLLLYALGIAAAVPTTFLSDHSNPTSATLPTLEDATVPTVPAEAAADIEKHPNHKAEKPS ALNSEEEAHEQSTEQDKTYSFEVDLKDEEDGDGDLSVDPTERTLDLQEGTSEPQQKRLPENADF PATVSTPFVDSDQPANITKGEESQEQPVSDSHQQQDESGKQTQDSMTEESHKQDPGIPNEEKEE EEDPEDVGAPSDNQEEEKEPPEEQPTSKWEGNGDQSEDILQESSQPTQISKTKNDFEQGSQGQE GDSNAEGEDKAAGSKEHLPHTEWQGQEGRAGLDAIGNRKDTDEEKAVSTEPTDAAVVPRNHGAS DNGGGDDSKHGASDDYFIPSQEFLEAERMHSLSYYLKYGEETPDESENRSEAGDNQGAKKAESS PNAEPSDEGNSRGHSADSCMNFQCKRGHTCKTDQHGKPHCVCQDPETCPPAKILDQACGTDNQT YASSCHLFATKCMLEGTKKGHQLQLDYFGACKSIPACTDFEVAQFPLRMRDWLKNILMQLYEPN PKHGGYLNEKQRSKVKKIYLDEKRLLAGDHPIELLLRDFKKNYHMYVYPVHWQFNELDQHPADR ILTHSELAPLRASLVPMEHCITRFFEECDPNKDKHITLKEWGHCFGIKEEDIDENLLF hide sequence

Ensembl Acc Id:

ENSRNOP00000020357 ⟸ ENSRNOT00000020357

Protein Domains

EF-hand Follistatin-like Kazal-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P24054-F1-model_v2	AlphaFold	P24054	1-634	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699175

Promoter ID:

EPDNEW_R9700

Type:

initiation region

Name:

Sparcl1_1

Description:

SPARC like 1

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	14	6,994,235 - 6,994,295	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2531	AgrOrtholog
BioCyc Gene	G2FUF-16499	BioCyc
Ensembl Genes	ENSRNOG00000015093	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000020357.7	UniProtKB/TrEMBL
Gene3D-CATH	3.30.60.30	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF-hand	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:5600008	IMAGE-MGC_LOAD
InterPro	EF-hand-dom_pair	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_Hand_1_Ca_BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_hand_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Fol_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Follistatin/Osteonectin_EGF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Kazal_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Kazal_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Osteonectin_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SPARC-like_p1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SPARC/Testican_Ca-bd-dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25434	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72541	IMAGE-MGC_LOAD
NCBI Gene	25434	ENTREZGENE
PANTHER	SPARC OSTEONECTIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SPARC-LIKE PROTEIN 1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	FOLN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Kazal_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SPARC_Ca_bdg	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Sparcl1	PhenoGen
PIRSF	SPARC-like_p1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	EF_HAND_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EF_HAND_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	KAZAL_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	OSTEONECTIN_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	OSTEONECTIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000015093	RatGTEx
SMART	FOLN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	KAZAL	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	EGF/Laminin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF100895	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF47473	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC228820
UniProt	A6K5T4	ENTREZGENE, UniProtKB/TrEMBL
	G3V7X5_RAT	UniProtKB/TrEMBL
	P24054	ENTREZGENE
	Q6P7A8	ENTREZGENE, UniProtKB/TrEMBL
	SPRL1_RAT	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-12-09	Sparcl1	SPARC like 1	Sparcl1	SPARC-like 1 (hevin)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-18	Sparcl1	SPARC-like 1 (hevin)	Sparcl1	SPARC-like 1 (mast9, hevin)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Sparcl1	SPARC-like 1 (mast9, hevin)		SPARC-like 1	Name updated	1299863	APPROVED
2002-11-06	Sparcl1	SPARC-like 1	Ecm2	Extracellular matrix protein 2	Symbol and Name updated	625702	APPROVED
2002-06-10	Ecm2	Extracellular matrix protein 2			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in brain and neurons during development and in adult	1298897
gene_homology	has high similarity to extracellular matrix glycoprotein osteonectin/BM40/SPARC	1298897
gene_physical_interaction	binds calcium	1298897
gene_product	secreted glycoprotein	1298897

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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