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Gene: Clec9a (C-type lectin domain containing 9A) Rattus norvegicus

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Symbol:

Clec9a

Name:

C-type lectin domain containing 9A

RGD ID:

1562513

Description:

Predicted to enable carbohydrate binding activity. Predicted to be involved in positive regulation of cytokine production and receptor-mediated endocytosis. Predicted to be located in membrane. Predicted to be active in cell surface. Orthologous to human CLEC9A (C-type lectin domain containing 9A); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; amphetamine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

C-type lectin domain family 9 member A; C-type lectin domain family 9, member A; LOC502901; RGD1562513; similar to RIKEN cDNA 9830005G06

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	4	164,546,323 - 164,561,380 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	164,546,311 - 164,561,380 (+)	Ensembl				GRCr8
mRatBN7.2	4	162,859,742 - 162,875,742 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	162,860,308 - 162,875,352 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	169,095,117 - 169,110,174 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	164,878,072 - 164,893,129 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	163,512,123 - 163,527,180 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	163,173,593 - 163,189,532 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	163,174,487 - 163,189,530 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	211,817,581 - 211,833,518 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	166,683,644 - 166,698,701 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	151,545,704 - 151,560,761 (+)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-estradiol (EXP)

17beta-estradiol 3-benzoate (EXP)

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

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

amphetamine (EXP)

arsenite(3-) (ISO)

Benzo[k]fluoranthene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

crocidolite asbestos (ISO)

Dibutyl phosphate (ISO)

diquat (ISO)

epoxiconazole (ISO)

furan (EXP)

Indeno[1,2,3-cd]pyrene (ISO)

indole-3-methanol (EXP)

N-acetyl-L-cysteine (EXP)

N-nitrosodiethylamine (EXP)

pregnenolone 16alpha-carbonitrile (ISO)

sodium arsenite (ISO)

testosterone (EXP)

thalidomide (ISO)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

endocytosis (IEA)

positive regulation of cytokine production (ISO,ISS)

receptor-mediated endocytosis (IBA,IEA,ISO,ISS)

Cellular Component

cell surface (IBA,ISO,ISS)

membrane (IEA)

Molecular Function

carbohydrate binding (IEA)

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.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:18408006	PMID:18497879	PMID:20544345

Genomics

Comparative Map Data

Clec9a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	164,546,323 - 164,561,380 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	164,546,311 - 164,561,380 (+)	Ensembl				GRCr8
mRatBN7.2	4	162,859,742 - 162,875,742 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	162,860,308 - 162,875,352 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	169,095,117 - 169,110,174 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	164,878,072 - 164,893,129 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	163,512,123 - 163,527,180 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	163,173,593 - 163,189,532 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	163,174,487 - 163,189,530 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	211,817,581 - 211,833,518 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	166,683,644 - 166,698,701 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	151,545,704 - 151,560,761 (+)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

CLEC9A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	10,030,682 - 10,066,031 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	10,030,678 - 10,066,031 (+)	Ensembl			hg38	GRCh38
GRCh37	12	10,183,281 - 10,218,630 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	10,074,543 - 10,109,832 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	12	10,074,542 - 10,109,832	NCBI
Celera	12	15,344,658 - 15,379,948 (+)	NCBI		Celera
Cytogenetic Map	12	p13.2	NCBI
HuRef	12	9,926,163 - 9,961,453 (+)	NCBI		HuRef
CHM1_1	12	10,152,590 - 10,187,902 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	9,917,091 - 9,952,444 (+)	NCBI		T2T-CHM13v2.0

Clec9a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	129,385,825 - 129,401,727 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	129,385,825 - 129,401,726 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	129,408,862 - 129,424,764 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	129,408,862 - 129,424,763 (+)	Ensembl			mm10	GRCm38
MGSCv37	6	129,358,881 - 129,372,723 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	129,374,555 - 129,390,455 (+)	NCBI		MGSCv36	mm8
Celera	6	131,130,782 - 131,144,677 (+)	NCBI		Celera
Cytogenetic Map	6	F3	NCBI
cM Map	6	63.3	NCBI

Clec9a
(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_004955413	7,788,019 - 7,808,824 (-)	Ensembl
ChiLan1.0	NW_004955413	7,787,663 - 7,808,761 (-)	NCBI	ChiLan1.0	ChiLan1.0

CLEC9A
(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	10	15,518,669 - 15,553,858 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	15,515,427 - 15,550,616 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	10,076,013 - 10,110,891 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	10,324,732 - 10,359,899 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	10,324,732 - 10,359,899 (+)	Ensembl			panPan2	panpan1.1

Clec9a
(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_024404945	97,352,608 - 97,367,607 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936902	484,456 - 499,052 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936902	484,390 - 499,052 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLEC9A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	5	61,876,050 - 61,885,307 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	64,708,460 - 64,716,423 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLEC9A
(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	11	9,913,571 - 9,941,215 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	9,927,436 - 9,941,537 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666089	2,001,394 - 2,016,037 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clec9a
(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	6	18,169,837 - 18,184,546 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Clec9a
624 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	795
Count of miRNA genes:	314
Interacting mature miRNAs:	394
Transcripts:	ENSRNOT00000055843, ENSRNOT00000071268
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
6478754	Anxrr43	Anxiety related response QTL 43		0.14035	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	146370897	184426481	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	134095016	179095016	Rat
1582237	Kidm34	Kidney mass QTL 34	4	0.0001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	4	149763204	169799698	Rat
6478693	Anxrr32	Anxiety related response QTL 32		0.00092	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	146370897	184426481	Rat
6478757	Anxrr44	Anxiety related response QTL 44		0.01087	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
1358364	Sradr4	Stress Responsive Adrenal Weight QTL 4	4.92		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	131384565	176384565	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	27730518	170099664	Rat
61451	Ciaa4	CIA Autoantibody QTL 4	3.1		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	4	123870974	168870974	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	140059299	181024663	Rat
6478700	Anxrr33	Anxiety related response QTL 33		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146370897	184426481	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	140059299	184426481	Rat
10053718	Scort25	Serum corticosterone level QTL 25	2.15	0.0097	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	157292416	184426481	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	60916264	184426481	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	94638356	168870820	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	106848959	168870974	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	127263297	172263297	Rat
6478778	Anxrr51	Anxiety related response QTL 51		0.25384	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	126334185	171334185	Rat
10401796	Kidm48	Kidney mass QTL 48			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	147299608	184426481	Rat
6478718	Anxrr34	Anxiety related response QTL 34		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146370897	184426481	Rat
6478782	Anxrr52	Anxiety related response QTL 52		0.02091	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	123870974	168870974	Rat
634347	Hcar8	Hepatocarcinoma resistance QTL 8	5.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	124700988	169700988	Rat
6478720	Alc23	Alcohol consumption QTL 23		0.00509	drinking behavior trait (VT:0001422)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	155834926	184426481	Rat
6478785	Anxrr53	Anxiety related response QTL 53		0.01397	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	60916264	174095838	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	100752691	179366077	Rat
1581566	Eae21	Experimental allergic encephalomyelitis QTL 21	6.2		body mass (VT:0001259)	maximum body weight loss to initial body weight ratio (CMO:0001400)	4	137447185	182447185	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	4	137430611	182430611	Rat
6478728	Anxrr36	Anxiety related response QTL 36		0.01061	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	60916264	184426481	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	86709649	168870974	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	134199006	168870974	Rat
634342	Cia24	Collagen induced arthritis QTL 24	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	148121375	176967367	Rat
6478733	Anxrr37	Anxiety related response QTL 37		0.00095	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	123870974	168870974	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	140059299	184426481	Rat
6478737	Anxrr38	Anxiety related response QTL 38		0.00159	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
2293659	Bmd35	Bone mineral density QTL 35	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	4	160623982	184426481	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	12212457	182430611	Rat
6478748	Anxrr42	Anxiety related response QTL 42		0.28008	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146370897	184426481	Rat
12798525	Anxrr57	Anxiety related response QTL 57	3.21	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	148834094	168870974	Rat

Markers in Region

RH130333

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	162,875,078 - 162,875,286 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	163,189,257 - 163,189,464	NCBI	Rnor6.0
Rnor_5.0	4	211,833,243 - 211,833,450	UniSTS	Rnor5.0
RGSC_v3.4	4	166,698,428 - 166,698,635	UniSTS	RGSC3.4
Celera	4	151,560,488 - 151,560,695	UniSTS
RH 3.4 Map	4	1014.4	UniSTS
Cytogenetic Map	4	q42	UniSTS

RH133930

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	162,875,601 - 162,875,805 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	163,189,780 - 163,189,983	NCBI	Rnor6.0
Rnor_5.0	4	211,833,766 - 211,833,969	UniSTS	Rnor5.0
RGSC_v3.4	4	166,698,951 - 166,699,154	UniSTS	RGSC3.4
Celera	4	151,561,011 - 151,561,214	UniSTS
RH 3.4 Map	4	1013.4	UniSTS
Cytogenetic Map	4	q42	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	50	121	91	90	59	75	59	6	307	158	11	100	66	86	31	15	15

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109354	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GU357486	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000088108 ⟹ ENSRNOP00000071858

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	4	164,546,311 - 164,561,380 (+)	Ensembl
mRatBN7.2 Ensembl	4	162,860,308 - 162,875,352 (+)	Ensembl
Rnor_6.0 Ensembl	4	163,174,487 - 163,189,530 (+)	Ensembl

RefSeq Acc Id:

NM_001109354 ⟹ NP_001102824

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	164,546,323 - 164,561,380 (+)	NCBI
mRatBN7.2	4	162,860,294 - 162,875,352 (+)	NCBI
Rnor_6.0	4	163,174,473 - 163,189,530 (+)	NCBI
Rnor_5.0	4	211,817,581 - 211,833,518 (+)	NCBI
RGSC_v3.4	4	166,683,644 - 166,698,701 (+)	RGD
Celera	4	151,545,704 - 151,560,761 (+)	RGD

Sequence:

show sequence

TCCATTTTTTTTGTACCAGCCTACTCCTGACTACTAAAGAAGTTCTTTGTGTTGGGCTCCTATG
TTGACTGCTTTACCTCTCCAAGCACCTTCAGCATGCATGAGGAAGAAATATACACCTCTCTTCA
GTGGGACATTCCAACCTCAGAGGCCTCTCAGAAGTGTCCATCCCTTAGCAAATGTCCAGGAACA
TGGTGTATTGTGACGGTGATTTCCTGTGTGGTCTGTGTGGGCTTACTAGCAGCATCCATTTTCT
TGGGCATCAAGTTCTCCCAGGTGTCCTCTCTTGTAATGGAGCAGCGGGAAAGGCTCATCCGACA
GGACACAGCATTGCTGAACCTCACAGAGTGGCAGAGGAACCATACACTGCAGTTAAAAAGCTGC
CAAGCCTCACTACAAAGATCTCTCCGTTCAGGCAGTAACTGCAACCCTTGTCCACCGAACTGGA
TTCAGAATGGAAAAAGTTGTTACTATGCCTTTGACCGCTGGGAAACGTGGAACAACAGTAAGAA
GAGTTGTTTAAAAGAGGGCGATAGTCTCCTTCAAATAGACAGCAAAGAAGAAATGGAGTTTATC
AACCTCAGTATATGGAAGCTCAAAGGAGGATATGAATACTGGGTGGGAGTGTTTCAAGATGGAC
CCAGTGGATCTTGGTTTTGGGAAGATGGCTCTTCTCCTCTCTCTGACTTGTTGCCAACAGACAG
ACAGCTATCAGCCAGCCAGATCTGTGGATACCTCAAAGACCATACTCTCATCTCGGATAACTGC
AGTAACTGGAAATATTTTATCTGTGAGAAGAAGGCATTTGGATCCTGCATCTGAAAGATACAAC
TCAAAGCTACCTGCTACACAAGTGTTCGAAAGAGGTCAGAGAGCAAATGCAGGAGGAGGTTGGT
GTGAGGCCTACAAAGGCAAACTTGCTTTTTCATATGAACTTGGCAATATTCTATAATGCTTTGA
AAATTTCAGTTGACCTTGTCCATTGTACCCAGGAGAAAATTGATTTAGGGCTACAGAAGACCTG
ACTCATTGAGAACAAGGAAGAGAAAATCATTTCCCGTCTGTTTGAAAGTCCAAAGTGACTATCC
ATACCGCACAGACATCTAGCTGTCTTTGTAGGAGTTTTTACAGTAATCCCTGGTTTGCTTTTTT
TTTTAGTAAACAATTCTACCTACTATACTTACAACTGACCAAGGATCACAGAATTTCTTTACTG
AGAGCTTTTCTTCAGATCAGCTTCCAGTCATGGTGTATCATAAGATTACACACTGAGAGGAGAG
AGATGGAATTCTAAATGGTAGTGTTACCAGCAATCACATACTAGGGGGACTTAGGTGCTAGATA
AAAATGAGCAGAATGGGGCCTCCAGTATTGGTAATATTCTTCTGAGACTCAAGGCCTAGGAGGC
TGAAACTCACGGATATAGAGATTTACAGTTTCTAACCCTTGGAGCTAGGGGATTATTGCTCTAG
GATCTGAATGCTCAGGTTAAAGGCTTATAGCTTTTCGTTTTAATCAGTACTGACTCCAGATCTT
GACAGCTTTCACAATCCCTGACCTTTAGCTGTAGCCTTAGACAGCAGTCAGTAGCAGCAGGCAG
CTCCCACTGGTCTTATAATTCTTGGATGGCTGTAGGGTGATGGGCATTAACTCTGCAGTGACCA
CTATTACAGTCCTCTGATCTAGAATGTGGGAATCTCTCGTCAGCCTCTGTTGGCTGTTAGTGTT
GCAGCTCTCAGTATAGATTTTCTGTGATCCTTGGTCCTAAAGACTGCAGCTCCTTGACACTCTT
TCAGGTCCCCAAGCCCATGTTTCTCCTCTCTGGTTTGCCACACAGCCTTCTGTGTTTATTCAGA
CTTGAGTTTCTGCCTTCTTTCTTCTTGTCTCTGACTCTACCATTCCTTGGCATCTCTCTGATTC
TTCTGCCCCACGCTTTCTGTCATGGCCCCTCTCTGGAATTCTTCAGCTGTTCTTTTGTCTCTCG
ACTGCCACTGCCACTGCCACAGTGGCTGCTGTCACCACCAGAGCCGCTCGCTTGCTTGCCTTTG
CAACCATCTTGTGCTTCTGCGTCTTCTCTTTGTGTTAACGGCTCAGGCCACTCCTCTAATGATG
CAGAGCAAAAGAGCCAAGAGAAAGGGCCATTCAGGAAGTCTTTTATTGGTCCTAATGTTGCAGC
TTCAGGAGTGTCAGAGGAGGGGGTGTTCTGGCTGACTCTAAAGCTGAACCAAACAGGTTATTTT
ATAGATAAGAAGGAGGTGTGATAAGGGTGTGTGTCCCTTCACAGCAGCCCTTCAAGGACTGTGT
TTGTACCATCACAGCACAGACTACTGTTTAGACAGTCACAGGTCTTTCCCTAGGGCCGTGATCG
GAAATGCGCCCCCTCTGGCCTGAGAGAGAACAGCTGCAGGATCTCTGGGTCTGTGTTGTTTGCC
AAGACTTCTCTTTCCATAGGCTGTTTTGGTGGTGTGAGCAGTTCCGACTGGAGCCTGTCTTCAG
TCATGGAGTGGTGTATTCTTCAGCTTCTTTACCTCAGAGTAAAATGGCCAAACTGCTGGACTGT
CATTGAGGGCAGTCTGGCCAGTTGTTTGTAAACAGGCTGCTTGGTTGGTAGCTTAAATCATTCA
TTCCCAGACATTAAAAGTGTGCTTACAATAAATACTTAATAAAACCCCACTGTATTACAAGTCT
AATAGCATTTGACAGTACTTAATAAAAATGAACATTTAGCGGGATTTAACTTCTGCCCCAAAGC
TGTAGAATCATTGAATCCCTCTCATCTGTCTCAGAAGGAAACAGGGTTCTACTCTCTGTGGATT
GTGCTTTTCAGACTGCAGAGTTCTGCTGGGAAAGAAACTATTAGAATTTCACGTAGGTAAAGGA
ATAGGCTAGACATCTGCACGTCCCGTTGTGTAGGCGGGACCTCCCATCTTATTGCTCACGAATC
AAACGGCTCTGTCTGCACTGACAGGATGAACTACCTAGCACTTCTAACTGACGGTCCCCGTGCC
TCAACTTCCCTGCTATAAAACTGTAATATGATTCACTTCAAAATATCGCTTAAGAATGTCATCC
AAATGCTACACGCTAACTATAGAAAATGGTATTTTAGGCAGGAAAGGGAAAATTAAAATGTGTG
ACATCTACCAGAAGAAAAATTTGCAAATGATCGTTATCATGTTCCCATGACATAGATATTTCGT
GTGTCATCTCTGTCATACTGCATAGCATGCTCTTAATAAATATTTGCTAAATTC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102824	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	ADK94896	(Get FASTA)	NCBI Sequence Viewer
	D4AD02	(Get FASTA)	NCBI Sequence Viewer
	EDM01742	(Get FASTA)	NCBI Sequence Viewer
	EDM01743	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000071858
	ENSRNOP00000071858.1

RefSeq Acc Id:

NP_001102824 ⟸ NM_001109354

- UniProtKB:

D9Z4I7 (UniProtKB/Swiss-Prot), D4AD02 (UniProtKB/Swiss-Prot), A6IM47 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MHEEEIYTSLQWDIPTSEASQKCPSLSKCPGTWCIVTVISCVVCVGLLAASIFLGIKFSQVSSL
VMEQRERLIRQDTALLNLTEWQRNHTLQLKSCQASLQRSLRSGSNCNPCPPNWIQNGKSCYYAF
DRWETWNNSKKSCLKEGDSLLQIDSKEEMEFINLSIWKLKGGYEYWVGVFQDGPSGSWFWEDGS
SPLSDLLPTDRQLSASQICGYLKDHTLISDNCSNWKYFICEKKAFGSCI

hide sequence

Ensembl Acc Id:

ENSRNOP00000071858 ⟸ ENSRNOT00000088108

Protein Domains

C-type lectin

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4AD02-F1-model_v2	AlphaFold	D4AD02	1-241	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:1562513	AgrOrtholog
BioCyc Gene	G2FUF-42785	BioCyc
Ensembl Genes	ENSRNOG00000051690	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000088108	ENTREZGENE
	ENSRNOT00000088108.2	UniProtKB/Swiss-Prot
Gene3D-CATH	3.10.100.10	UniProtKB/Swiss-Prot
InterPro	C-type_lectin-like	UniProtKB/Swiss-Prot
	C-type_lectin-like/link_sf	UniProtKB/Swiss-Prot
	CLEC9A	UniProtKB/Swiss-Prot
	CTDL_fold	UniProtKB/Swiss-Prot
	NKR-like_CTLD	UniProtKB/Swiss-Prot
KEGG Report	rno:502901	UniProtKB/Swiss-Prot
NCBI Gene	502901	ENTREZGENE
PANTHER	C-TYPE LECTIN DOMAIN FAMILY 9 MEMBER A	UniProtKB/Swiss-Prot
	PTHR47727	UniProtKB/Swiss-Prot
Pfam	Lectin_C	UniProtKB/Swiss-Prot
PhenoGen	Clec9a	PhenoGen
PROSITE	C_TYPE_LECTIN_1	UniProtKB/Swiss-Prot
	C_TYPE_LECTIN_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000051690	RatGTEx
SMART	CLECT	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56436	UniProtKB/Swiss-Prot
UniProt	A6IM47	ENTREZGENE, UniProtKB/TrEMBL
	CLC9A_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	D9Z4I7	ENTREZGENE
UniProt Secondary	D9Z4I7	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-03-29	Clec9a	C-type lectin domain containing 9A	Clec9a	C-type lectin domain family 9, member A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-06-08	Clec9a	C-type lectin domain family 9, member A	Clec9a	C-type lectin domain family 9, member a	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-29	Clec9a	C-type lectin domain family 9, member a	RGD1562513_predicted	similar to RIKEN cDNA 9830005G06 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1562513_predicted	similar to RIKEN cDNA 9830005G06 (predicted)	LOC502901	similar to RIKEN cDNA 9830005G06	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC502901	similar to RIKEN cDNA 9830005G06			Symbol and Name status set to provisional	70820	PROVISIONAL

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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