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Gene: Clec11a (C-type lectin domain containing 11A) Rattus norvegicus

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Symbol:

Clec11a

Name:

C-type lectin domain containing 11A

RGD ID:

3627

Description:

Predicted to enable growth factor activity. Predicted to be involved in ossification and positive regulation of cell population proliferation. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human CLEC11A (C-type lectin domain containing 11A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; amitrole.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

C-type lectin domain family 11 member A; C-type lectin domain family 11, member A; lymphocyte secreted C-type lectin; osteolectin; Scgf; stem cell growth factor

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	1	103,938,029 - 103,941,170 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	103,935,185 - 103,946,784 (-)	Ensembl				GRCr8
mRatBN7.2	1	94,800,456 - 94,809,002 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	94,801,496 - 94,804,633 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	100,186,898 - 100,190,039 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	108,659,538 - 108,662,679 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	101,949,972 - 101,953,113 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	100,290,374 - 100,293,515 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	100,289,295 - 100,293,558 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	101,354,449 - 101,364,335 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	94,785,179 - 94,788,320 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	89,064,393 - 89,067,534 (-)	NCBI		Celera
RGSC_v3.1	1	94,864,111 - 94,866,313 (-)	NCBI
Cytogenetic Map	1	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

anemia (ISO)

carotid stenosis (ISO)

malignant mesothelioma (ISO)

osteoporosis (ISO)

Plasmodium falciparum malaria (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2-methylcholine (ISO)

5-fluorouracil (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

all-trans-retinoic acid (ISO)

amitrole (EXP)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

asbestos (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

buta-1,3-diene (ISO)

Butylbenzyl phthalate (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

chlorpyrifos (ISO)

cisplatin (ISO)

copper atom (EXP)

copper(0) (EXP)

DDE (ISO)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

dicyclanil (ISO)

dioxygen (EXP)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

folic acid (ISO)

formaldehyde (EXP)

furan (EXP)

methapyrilene (ISO)

methimazole (EXP)

methoxychlor (EXP)

naphthalene (ISO)

niclosamide (ISO)

oxaliplatin (EXP)

paclitaxel (ISO)

paracetamol (EXP,ISO)

resveratrol (ISO)

Salinomycin (ISO)

SB 431542 (ISO)

temozolomide (ISO)

tetrachloromethane (ISO)

thapsigargin (ISO)

titanium dioxide (ISO)

topotecan (EXP)

trichostatin A (ISO)

triclosan (ISO)

Triptolide (ISO)

triptonide (ISO)

tunicamycin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

ossification (IBA,IEA)

positive regulation of cell population proliferation (ISO,ISS)

signal transduction (IEA)

Cellular Component

cytoplasm (IEA)

extracellular region (IEA,ISO,ISS)

extracellular space (IBA)

Molecular Function

carbohydrate binding (IEA,NAS)

growth factor activity (IBA,IEA,ISO,ISS)

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 MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	Isolation and characterization of a cDNA for human mouse, and rat full-length stem cell growth factor, a new member of C-type lectin superfamily.	Mio H, etal., Biochem Biophys Res Commun 1998 Aug 10;249(1):124-30.
4.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	A negative feedback system between oocyte bone morphogenetic protein 15 and granulosa cell kit ligand: its role in regulating granulosa cell mitosis.	Otsuka F and Shimasaki S, Proc Natl Acad Sci U S A 2002 Jun 11;99(12):8060-5.
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9442024	PMID:11920266	PMID:12477932	PMID:15234225	PMID:16502470

Genomics

Comparative Map Data

Clec11a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	103,938,029 - 103,941,170 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	103,935,185 - 103,946,784 (-)	Ensembl				GRCr8
mRatBN7.2	1	94,800,456 - 94,809,002 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	94,801,496 - 94,804,633 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	100,186,898 - 100,190,039 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	108,659,538 - 108,662,679 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	101,949,972 - 101,953,113 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	100,290,374 - 100,293,515 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	100,289,295 - 100,293,558 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	101,354,449 - 101,364,335 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	94,785,179 - 94,788,320 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	89,064,393 - 89,067,534 (-)	NCBI		Celera
RGSC_v3.1	1	94,864,111 - 94,866,313 (-)	NCBI
Cytogenetic Map	1	q22	NCBI

CLEC11A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	50,723,364 - 50,725,708 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	50,723,286 - 50,725,719 (+)	Ensembl			hg38	GRCh38
GRCh37	19	51,226,621 - 51,228,965 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	55,918,417 - 55,920,793 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	19	48,277,720 - 48,280,096 (+)	NCBI		Celera
Cytogenetic Map	19	q13.33	NCBI
HuRef	19	47,561,665 - 47,564,041 (+)	NCBI		HuRef
CHM1_1	19	51,228,387 - 51,230,763 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	53,812,175 - 53,814,519 (+)	NCBI		T2T-CHM13v2.0

Clec11a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	43,953,190 - 43,956,383 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	43,952,111 - 43,956,326 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	7	44,303,766 - 44,306,959 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	44,302,687 - 44,306,902 (-)	Ensembl			mm10	GRCm38
MGSCv37	7	51,559,136 - 51,562,329 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	7	44,172,296 - 44,174,936 (-)	NCBI		MGSCv36	mm8
Celera	7	39,761,572 - 39,764,765 (-)	NCBI		Celera
Cytogenetic Map	7	B3	NCBI
cM Map	7	28.83	NCBI

Clec11a
(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_004955559	514,134 - 517,787 (-)	Ensembl
ChiLan1.0	NW_004955559	515,341 - 517,521 (-)	NCBI	ChiLan1.0	ChiLan1.0

CLEC11A
(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	20	56,765,704 - 56,792,874 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	58,686,688 - 58,713,994 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	47,682,806 - 47,690,389 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	56,582,922 - 56,588,580 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	56,586,183 - 56,588,580 (+)	Ensembl			panPan2	panpan1.1

CLEC11A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	106,078,055 - 106,080,473 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	106,078,291 - 106,080,517 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	105,652,800 - 105,655,696 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	106,590,156 - 106,593,051 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	106,590,157 - 106,592,405 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	106,262,618 - 106,265,513 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	105,904,171 - 105,907,067 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	106,744,763 - 106,747,659 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Clec11a
(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_024409349	22,599,551 - 22,602,592 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936889	476,133 - 478,711 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936889	476,439 - 478,620 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLEC11A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	55,496,746 - 55,506,550 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	6	55,502,892 - 55,505,690 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	51,402,246 - 51,404,981 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLEC11A
(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	6	43,780,151 - 43,782,780 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666073	23,796,046 - 23,798,420 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clec11a
(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_004624832	3,929,949 - 3,932,370 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624832	3,929,949 - 3,934,088 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Clec11a
(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	2	155,222,074 - 155,226,394 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Clec11a
53 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	96
Count of miRNA genes:	68
Interacting mature miRNAs:	79
Transcripts:	ENSRNOT00000025949
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	87889942	132889942	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	51941022	208479811	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	39728272	132889942	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	102780511	182384005	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	51940904	168768703	Rat
2300324	Fetw1	Fetal weight QTL 1	12.1	0.005	fetal growth trait (VT:0004201)	fetal body weight (CMO:0002080)	1	92963855	109494029	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	101228864	146228864	Rat
1331800	Scl25	Serum cholesterol level QTL 25	3.013		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	87785026	142582336	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	83019780	128019780	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	66404680	111404680	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34184556	172281316	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	66009857	160501508	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34565911	208798288	Rat
631519	Pia11	Pristane induced arthritis QTL 11	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	93903998	191260518	Rat
1302788	Scl19	Serum cholesterol QTL 19	4.6	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	66400974	132889942	Rat
1549903	Bp267	Blood pressure QTL 267			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	84107164	115183752	Rat
2313083	Bmd74	Bone mineral density QTL 74	4	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	91302413	136302413	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	51511344	153680016	Rat
724567	Tcas6	Tongue tumor susceptibility QTL 6	6.85		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	1	102359314	153680016	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	99645382	182701046	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	99645382	221502378	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	86622262	131622262	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	66077886	111077886	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	103779152	223964440	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	98879955	208479939	Rat
738022	Anxrr13	Anxiety related response QTL 13	4.6	0.00039	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)	1	92683681	137683681	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	86993904	131993904	Rat
152025249	Scl82	Serum cholesterol level QTL 82	4.77		blood cholesterol amount (VT:0000180)		1	52891222	109116986	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	92683681	137683681	Rat
7411712	Strs4	Sensitivity to stroke QTL 4	8.7		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	1	87558587	132558587	Rat
737977	Bp160	Blood pressure QTL 160		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	97582336	142582336	Rat
2293142	Bp314	Blood pressure QTL 314			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	101594089	146594089	Rat
61433	Cia2	Collagen induced arthritis QTL 2	5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	100345976	145345976	Rat
724529	Cm16	Cardiac mass QTL 16	2.7		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	1	96717367	160111531	Rat

Markers in Region

RH133756

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	94,801,649 - 94,801,843 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	100,290,532 - 100,290,725	NCBI	Rnor6.0
Rnor_5.0	1	101,355,643 - 101,355,836	UniSTS	Rnor5.0
RGSC_v3.4	1	94,785,337 - 94,785,530	UniSTS	RGSC3.4
Celera	1	89,064,551 - 89,064,744	UniSTS
RH 3.4 Map	1	905.8	UniSTS
Cytogenetic Map	1	q22	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	12	67	149	91	90	59	67	59	6	330	167	11	128	80	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001012459	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC090344	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000025949 ⟹ ENSRNOP00000025949

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	103,938,033 - 103,946,784 (-)	Ensembl
mRatBN7.2 Ensembl	1	94,801,496 - 94,804,633 (-)	Ensembl
Rnor_6.0 Ensembl	1	100,289,295 - 100,293,558 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000113316 ⟹ ENSRNOP00000087157

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	103,938,033 - 103,945,702 (-)	Ensembl
mRatBN7.2 Ensembl	1	94,801,496 - 94,804,633 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000130520 ⟹ ENSRNOP00000108820

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	103,937,850 - 103,941,032 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000141755 ⟹ ENSRNOP00000108012

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	103,935,185 - 103,941,170 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000143798 ⟹ ENSRNOP00000101032

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	103,938,033 - 103,943,914 (-)	Ensembl

RefSeq Acc Id:

NM_001012459 ⟹ NP_001012477

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	103,938,029 - 103,941,170 (-)	NCBI
mRatBN7.2	1	94,801,492 - 94,804,633 (-)	NCBI
Rnor_6.0	1	100,290,374 - 100,293,515 (-)	NCBI
Rnor_5.0	1	101,354,449 - 101,364,335 (-)	NCBI
RGSC_v3.4	1	94,785,179 - 94,788,320 (-)	RGD
Celera	1	89,064,393 - 89,067,534 (-)	RGD

Sequence:

show sequence

GAAGGTTCAAGGGGCTAGTGATCTGCCCACCAGACTGGGACACTTGCTAGTTCTATACCCCAAC
CCTACCCCAGGCTTTCTGATCTCTACTAGTCTGGGCGCTGGGAAGTCCAGCTGGATGCAGGCAG
CCTGGCTCTTGGGGGCCCTACTGGTCCCTCACCTTTTGAGTTTTGGCCATGGAGCCCGAGGTCA
TGGGAAGGAATGGGAAGGAGTCTGGGGAGGTGCCCTGGAGGAGGAGCGAGATCGGGAGTCACTG
ATGTTGAAGAATCTCCAGGAGGCCCTAGGGCTGCCCACTGGGGTGGGAAATAAGGATAATCTTG
CTGAAAACTCTGAAGGCAAAGAGGTCTGGGAGGCCACGGAGACTCAAGGGGAAGAAGAGGAAGA
GGAAACCACCACAACACCTTCTTCTAGCCCCACTCCTTTCCCCAGCCCTTCTCCTACATCAGAG
GACACAGTCACTTACATCCTGGGCCGCTTGGCCAGCCTCGATGCAGGCCTACACCAATTGCACA
TCCGTCTGCATGTTTTGGACACCCGTGTGGTTGAGCTGACCCAGGGGCTGCGGCGGCTGCGGGA
TGCCGCGAGTGACACCCGCGACTCAGTGCAAGCTCTGAAGGAGGTACAGGTCCGTTCTGAGCAG
GAGCACGGCCGCTTGGAGGGCTGCCTGAAGGGCCTGCGCCTAGGCCACAAATGCTTCCTGCTCT
CGCGAGACTTCGAGACACAGGCGGCGGCGCAAGCGCGGTGTAAGGCGCGAGGTGGGAGTTTAGC
GCAGCCTGCGGACCGCCAGCAAATGGATGCTCTAAGCCGGTACTTACGAGCTGCTCTTGCCCCC
TACAACTGGCCAGTGTGGCTGGGAGTGCACGACCGGCGCTCGGAGGGGCTCTACCTTTTCGAGA
ACGGCCAGCGCGTGTCATTCTTCGCCTGGCACCGCGCACTCAGCCCGGAGTCCGGCGCCCAGCC
TAGTGCGGCATCCCATCCACTTAGCCCGGATCAGCCCAATGGCGGCATCCTGGAGAACTGCGTG
GCCCAGGCCTCAGACGACGGCTCCTGGTGGGACCATGACTGTGAGCGGCGCCTCTACTTCGTCT
GCGAGTTCCCTTTCTAGAGAGCAGGTCTCTGCCGCGGAGCTCTAGCGCACATTCTGCACCGTAC
ACCGCGCACCCTACTGTTAGGGGTCTGGGGTCGCTCAGAGATTAAGCAAGACCATGGATACATT
TTAATAAGAAGAGGCTTTTAATTTTAGATACTGGCACCCAGACTGATTGGGGCCAAGGTCTACA
CCTGAGATCGCTTCCAAGATGCAAGCCCTAGCTATTATCAGCCCAGAGCTTATAAAGGCAAATC
CCACAAGATTGCATGTAGCCTGATGACATGGAGGCAGGGGCTTAAATTTTAACATATATGTCTT
GTAGTTGTCCTAGTCATCCTTTGAGCAGAGGAAGCAAGATTGATTACAAAAGCAGAGATAGCAG
TTAGTCGTACAACTAAATTTGCTAGAACAGCAAATTTTACAAGACCAATCAATTTCAAAATAGT
CTTCAATATCTGGGAGAAAGGGGAAGTGGACTGCTAGTGTACAGCCTGCACAAGCTAGGAGCTT
TCGTCTTAGAGCCATATTTGCTTTGGTCTCTCAAGCGTAGTGAGTCTAAACTTCTAAATGTAAT
GTTGAATACCTACGGTGTACATTCTGCACCCTGTACCCTACACTGCGCCCTACATCCCACTCTG
TACACCTTTCATTCTACAACCTACATAGTGCAACCTGCACCTTGAACCCTCCTTGGGCCAGAAG
TGCCACCAATCCTGGCTGGTCCCCTACCCCCACCCTGAGAGATAGCCTGTACAACTTCTCCATG
TCCCCCCACCTGTCTTTGAAACTTCAAGGTCCCAACTAGGCCCGGTGCCAATAAATCCTTTTAA
AATATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001012477	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH90344	(Get FASTA)	NCBI Sequence Viewer
	EDM07506	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000025949
	ENSRNOP00000025949.3
GenBank Protein	O88201	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_001012477 ⟸ NM_001012459
- Peptide Label:	precursor
- UniProtKB:	Q5EAN4 (UniProtKB/Swiss-Prot), O88201 (UniProtKB/Swiss-Prot), A6JAM8 (UniProtKB/TrEMBL), A0A8I6A7X7 (UniProtKB/TrEMBL)
- Sequence:	show sequence MQAAWLLGALLVPHLLSFGHGARGHGKEWEGVWGGALEEERDRESLMLKNLQEALGLPTGVGNK DNLAENSEGKEVWEATETQGEEEEEETTTTPSSSPTPFPSPSPTSEDTVTYILGRLASLDAGLH QLHIRLHVLDTRVVELTQGLRRLRDAASDTRDSVQALKEVQVRSEQEHGRLEGCLKGLRLGHKC FLLSRDFETQAAAQARCKARGGSLAQPADRQQMDALSRYLRAALAPYNWPVWLGVHDRRSEGLY LFENGQRVSFFAWHRALSPESGAQPSAASHPLSPDQPNGGILENCVAQASDDGSWWDHDCERRL YFVCEFPF hide sequence

Ensembl Acc Id:

ENSRNOP00000025949 ⟸ ENSRNOT00000025949

Ensembl Acc Id:

ENSRNOP00000087157 ⟸ ENSRNOT00000113316

Ensembl Acc Id:

ENSRNOP00000108012 ⟸ ENSRNOT00000141755

Ensembl Acc Id:

ENSRNOP00000108820 ⟸ ENSRNOT00000130520

Ensembl Acc Id:

ENSRNOP00000101032 ⟸ ENSRNOT00000143798

Protein Domains

C-type lectin

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-O88201-F1-model_v2	AlphaFold	O88201	1-328	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689995

Promoter ID:

EPDNEW_R519

Type:

multiple initiation site

Name:

Clec11a_1

Description:

C-type lectin domain containing 11A

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	1	100,293,559 - 100,293,619	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3627	AgrOrtholog
BioCyc Gene	G2FUF-59777	BioCyc
Ensembl Genes	ENSRNOG00000019138	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000025949	ENTREZGENE
	ENSRNOT00000025949.7	UniProtKB/Swiss-Prot
Gene3D-CATH	3.10.100.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7304238	IMAGE-MGC_LOAD
InterPro	C-type_lectin-like	UniProtKB/Swiss-Prot
	C-type_lectin-like/link_sf	UniProtKB/Swiss-Prot
	C-type_lectin_CS	UniProtKB/Swiss-Prot
	CLec_Tetranectin-domain	UniProtKB/Swiss-Prot
	CTDL_fold	UniProtKB/Swiss-Prot
KEGG Report	rno:29313	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:105670	IMAGE-MGC_LOAD
NCBI Gene	29313	ENTREZGENE
PANTHER	C-TYPE LECTIN DOMAIN FAMILY 11 MEMBER A	UniProtKB/Swiss-Prot
	TETRANECTIN-RELATED	UniProtKB/Swiss-Prot
Pfam	Lectin_C	UniProtKB/Swiss-Prot
PhenoGen	Clec11a	PhenoGen
PROSITE	C_TYPE_LECTIN_1	UniProtKB/Swiss-Prot
	C_TYPE_LECTIN_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000019138	RatGTEx
SMART	CLECT	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56436	UniProtKB/Swiss-Prot
UniProt	A0A8I6A7X7	ENTREZGENE, UniProtKB/TrEMBL
	A0ABK0LD36_RAT	UniProtKB/TrEMBL
	A0ABK0LUC6_RAT	UniProtKB/TrEMBL
	A0ABK0LUT5_RAT	UniProtKB/TrEMBL
	A6JAM8	ENTREZGENE, UniProtKB/TrEMBL
	CLC11_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q5EAN4	ENTREZGENE
UniProt Secondary	Q5EAN4	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-03-29	Clec11a	C-type lectin domain containing 11A	Clec11a	C-type lectin domain family 11, member A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-06-08	Clec11a	C-type lectin domain family 11, member A	Clec11a	C-type lectin domain family 11, member a	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Clec11a	C-type lectin domain family 11, member a	Scgf	stem cell growth factor	Symbol and Name updated	1299863	APPROVED
2002-06-10	Scgf	stem cell growth factor			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_homology	90.4% amino acid similarity to the human protein	69976

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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