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Gene: Clec4f (C-type lectin domain family 4, member F) Rattus norvegicus

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Symbol:

Clec4f

Name:

C-type lectin domain family 4, member F

RGD ID:

621062

Description:

Predicted to enable galactose binding activity; glycolipid binding activity; and pattern recognition receptor activity. Involved in positive regulation of gene expression. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC4F (C-type lectin domain family 4 member F); INTERACTS WITH 3H-1,2-dithiole-3-thione; aflatoxin B1; ammonium chloride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; C-type lectin 13; C-type lectin domain family 4 member F; C-type lectin superfamily member 13; Clecsf13; Kclr; Kupffer cell receptor; MGC112607

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):	CLEC4F (C-type lectin domain family 4 member F)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Clec4f (C-type lectin domain family 4, member f)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Clec4f (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CLEC4F (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CLEC4F (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Clec4f (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CLEC4F (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CLEC4F (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Clec4f (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Clec4f (C-type lectin domain family 4 member F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CLEC4F (C-type lectin domain family 4 member F)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Clec4f (C-type lectin domain family 4, member f)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:ch73-86n18.1	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Danio rerio (zebrafish):	si:ch211-133n4.7	Alliance	DIOPT (Ensembl Compara\|PhylomeDB)
Caenorhabditis elegans (roundworm):	clec-149	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	clec-149	Alliance	DIOPT (OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	tfc	Alliance	DIOPT (OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	lectin-37Da	Alliance	DIOPT (PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	dcsignlg	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	LOC100494969	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	LOC101735287	Alliance	DIOPT (OrthoFinder\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	LOC100494969	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|SonicParanoid)

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	117,686,686 - 117,696,407 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	117,686,686 - 117,696,438 (-)	Ensembl				GRCr8
mRatBN7.2	4	116,129,023 - 116,138,744 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	116,129,023 - 116,138,775 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	121,607,811 - 121,617,529 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	117,382,983 - 117,392,701 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	115,996,525 - 116,006,244 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	115,322,300 - 115,332,021 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	115,322,291 - 115,332,052 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	179,911,569 - 179,921,290 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	117,839,863 - 117,849,584 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	105,121,362 - 105,131,083 (-)	NCBI		Celera
RGSC_v3.1	4	118,084,343 - 118,094,065 (-)	NCBI
Cytogenetic Map	4	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Experimental Liver Cirrhosis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

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

3H-1,2-dithiole-3-thione (EXP)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (EXP)

ammonium chloride (EXP)

amphetamine (EXP)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

buspirone (EXP)

cadmium dichloride (EXP)

carbon nanotube (ISO)

chrysene (ISO)

clofibrate (ISO)

cocaine (EXP)

decabromodiphenyl ether (EXP)

Echimidine (EXP)

ethanol (EXP)

flutamide (EXP)

fumonisin B1 (ISO)

Heliotrine (EXP)

hexachlorobenzene (EXP)

Lasiocarpine (EXP)

manganese(II) chloride (EXP)

methapyrilene (ISO)

N-nitrosodiethylamine (EXP,ISO)

nefazodone (EXP)

nickel atom (ISO)

nimesulide (EXP)

nitrofen (EXP)

okadaic acid (ISO)

paracetamol (ISO)

perfluorooctanoic acid (EXP)

phenobarbital (ISO)

pirinixic acid (EXP,ISO)

potassium dichromate (ISO)

pravastatin (EXP,ISO)

resveratrol (EXP,ISO)

rotenone (EXP)

senecionine (EXP,ISO)

Senkirkine (EXP)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

streptozocin (EXP)

tetrachloromethane (ISO)

theophylline (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (EXP,ISO)

triphenyl phosphate (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

endocytosis (IEA)

immune response (IBA)

NK T cell activation (ISO)

positive regulation of gene expression (HMP)

Cellular Component

external side of plasma membrane (IBA)

membrane (IEA)

plasma membrane (ISO)

Molecular Function

carbohydrate binding (IBA,IEA,TAS)

galactose binding (ISO)

glycolipid binding (ISO)

pattern recognition receptor activity (IBA)

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 and sequencing of a cDNA for a carbohydrate binding receptor unique to rat Kupffer cells.	Hoyle GW and Hill RL, J Biol Chem 1988 Jun 5;263(16):7487-92.
3.	Structure of the gene for a carbohydrate-binding receptor unique to rat kupffer cells.	Hoyle GW and Hill RL, J Biol Chem 1991 Jan 25;266(3):1850-7.
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Transcriptomic Analysis of Rat Macrophages.	Pridans C, etal., Front Immunol. 2021 Feb 1;11:594594. doi: 10.3389/fimmu.2020.594594. eCollection 2020.
7.	GOA pipeline	RGD automated data pipeline
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:12672702	PMID:23762286

Genomics

Comparative Map Data

Clec4f
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	117,686,686 - 117,696,407 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	117,686,686 - 117,696,438 (-)	Ensembl				GRCr8
mRatBN7.2	4	116,129,023 - 116,138,744 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	116,129,023 - 116,138,775 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	121,607,811 - 121,617,529 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	117,382,983 - 117,392,701 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	115,996,525 - 116,006,244 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	115,322,300 - 115,332,021 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	115,322,291 - 115,332,052 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	179,911,569 - 179,921,290 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	117,839,863 - 117,849,584 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	105,121,362 - 105,131,083 (-)	NCBI		Celera
RGSC_v3.1	4	118,084,343 - 118,094,065 (-)	NCBI
Cytogenetic Map	4	q34	NCBI

CLEC4F
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	70,808,643 - 70,825,235 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	70,808,643 - 70,820,599 (-)	Ensembl			hg38	GRCh38
GRCh37	2	71,035,775 - 71,047,731 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	70,889,283 - 70,901,240 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	70,947,432 - 70,959,387	NCBI
Celera	2	70,886,456 - 70,898,414 (-)	NCBI		Celera
Cytogenetic Map	2	p13.3	NCBI
HuRef	2	70,772,576 - 70,784,093 (-)	NCBI		HuRef
CHM1_1	2	70,965,099 - 70,977,053 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	70,819,694 - 70,836,320 (-)	NCBI		T2T-CHM13v2.0

Clec4f
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	83,621,524 - 83,633,098 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	83,621,524 - 83,633,169 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	83,644,542 - 83,656,116 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	83,644,542 - 83,656,187 (-)	Ensembl			mm10	GRCm38
MGSCv37	6	83,594,536 - 83,606,110 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	83,610,200 - 83,621,774 (-)	NCBI		MGSCv36	mm8
Celera	6	85,626,646 - 85,638,216 (-)	NCBI		Celera
Cytogenetic Map	6	C3	NCBI
cM Map	6	35.94	NCBI

Clec4f
(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_004955424	14,367,192 - 14,381,350 (+)	Ensembl
ChiLan1.0	NW_004955424	14,365,348 - 14,379,664 (+)	NCBI	ChiLan1.0	ChiLan1.0

CLEC4F
(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	12	55,568,918 - 55,580,564 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	55,572,862 - 55,584,508 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	70,872,242 - 70,883,547 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	71,985,988 - 71,997,123 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	71,985,814 - 71,997,123 (-)	Ensembl			panPan2	panpan1.1

CLEC4F
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	69,170,393 - 69,179,578 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	69,170,437 - 69,179,914 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	69,057,978 - 69,067,000 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	70,192,860 - 70,202,052 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	70,192,908 - 70,202,376 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	69,911,411 - 69,920,436 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	70,172,783 - 70,181,815 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	70,472,208 - 70,481,400 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Clec4f
(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_024406292	13,553,601 - 13,565,458 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936491	15,005,413 - 15,017,952 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936491	15,005,474 - 15,018,031 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLEC4F
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	71,677,918 - 71,696,346 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	3	71,683,898 - 71,696,357 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

CLEC4F
(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	14	36,293,963 - 36,304,590 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666045	75,716,850 - 75,727,779 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clec4f
(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_004624762	2,567,794 - 2,584,493 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624762	2,567,854 - 2,584,329 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Clec4f
(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	62,593,955 - 62,603,904 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Clec4f
70 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	141
Count of miRNA genes:	96
Interacting mature miRNAs:	101
Transcripts:	ENSRNOT00000017643
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
1582232	Gluco25	Glucose level QTL 25	3.6	0.0023	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	86583980	149763391	Rat
631689	Scl4	Serum cholesterol level QTL 4	1.9	0.008	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	96731383	141731383	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	39431983	123203361	Rat
1578655	Bmd11	Bone mineral density QTL 11	11		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	4	92406430	137406430	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	27730518	170099664	Rat
1357342	Bw40	Body weight QTL 40		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	4	74233320	119233320	Rat
631556	Bp135	Blood pressure QTL 135		0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	80212111	119233320	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	26234499	134199155	Rat
70167	Bw22	Body weight QTL 22	3.1		body mass (VT:0001259)	body weight (CMO:0000012)	4	74233320	119233320	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
731165	Uae21	Urinary albumin excretion QTL 21	2.4	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	108206096	153206096	Rat
1549832	Bss3	Bone structure and strength QTL 3	11		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	4	111383604	156383604	Rat
70177	Xhs1	X-ray hypersensitivity QTL 1	25.1		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	82944895	154403548	Rat
6909128	Pancm4	Pancreatic morphology QTL 4	11.35		pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	4	27862204	126119996	Rat
61476	Aia3	Adjuvant induced arthritis QTL 3	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	75939858	140508796	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	65060960	127749483	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	45429897	149763204	Rat
1578670	Bss14	Bone structure and strength QTL 14	16.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	4	88883695	133883695	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	40490442	117737312	Rat
70201	Gcr1	Gastric cancer resistance QTL 1	2.7		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	4	103834277	148834277	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	57613339	151163960	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	12212457	182430611	Rat
1578662	Bss15	Bone structure and strength QTL 15	19.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	4	88883695	133883695	Rat
2302049	Pia32	Pristane induced arthritis QTL 32	5.1	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	107346299	152346299	Rat
6478763	Anxrr46	Anxiety related response QTL 46		0.07428	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	112427331	157427331	Rat
6478760	Anxrr45	Anxiety related response QTL 45		0.06717	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	112427331	157427331	Rat
1331802	Srn5	Serum renin concentration QTL 5	3.045		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	4	117559384	162559384	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
2306545	Iddm39	Insulin dependent diabetes mellitus QTL 39			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	78687630	123687630	Rat
7207480	Bss105	Bone structure and strength QTL 105	8.1		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	4	111383604	156383604	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
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	74169813	134199155	Rat
634334	Xhs3	X-ray hypersensitivity QTL 3	10		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	86058928	131411333	Rat
61406	Scwia1	Streptococcal cell wall induced arthritis QTL 1	2.3		joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	4	75939858	140508796	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	45429897	149763204	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5889999	148002343	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
631662	Hcar2	Hepatocarcinoma resistance QTL 2	3.1	0.0003	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	84349032	129349032	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	45429709	157555683	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	63245026	129846354	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
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	57664252	127749483	Rat
2306899	Bp338	Blood pressure QTL 338		0.071	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	82336765	127336765	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	65495851	159259805	Rat
2293840	Kiddil9	Kidney dilation QTL 9	2.9		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	4	113634167	149763391	Rat
12798519	Anxrr54	Anxiety related response QTL 54	2.54	0.05	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	116184844	161184844	Rat
12798523	Anxrr56	Anxiety related response QTL 56	2.83	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	86583980	131583980	Rat

Markers in Region

RH132980

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	4	117,686,865 - 117,687,571 (+)	Marker Load Pipeline
mRatBN7.2	4	116,129,202 - 116,129,908 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	115,322,480 - 115,323,185	NCBI	Rnor6.0
Rnor_5.0	4	179,911,749 - 179,912,454	UniSTS	Rnor5.0
RGSC_v3.4	4	117,840,043 - 117,840,748	UniSTS	RGSC3.4
Celera	4	105,121,542 - 105,122,247	UniSTS
RH 3.4 Map	4	674.9	UniSTS
Cytogenetic Map	4	q34	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
6	8	41	59	83	86	57	91	57	6	270	157	11	33	43	55	29	9	9

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053753	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC111232	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC098661	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	J03734	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M55532	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000017643 ⟹ ENSRNOP00000017643

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	4	117,686,686 - 117,696,438 (-)	Ensembl
mRatBN7.2 Ensembl	4	116,129,023 - 116,138,775 (-)	Ensembl
Rnor_6.0 Ensembl	4	115,322,291 - 115,332,052 (-)	Ensembl

RefSeq Acc Id:

NM_053753 ⟹ NP_446205

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	117,686,686 - 117,696,407 (-)	NCBI
mRatBN7.2	4	116,129,023 - 116,138,744 (-)	NCBI
Rnor_6.0	4	115,322,300 - 115,332,021 (-)	NCBI
Rnor_5.0	4	179,911,569 - 179,921,290 (-)	NCBI
RGSC_v3.4	4	117,839,863 - 117,849,584 (-)	RGD
Celera	4	105,121,362 - 105,131,083 (-)	RGD

Sequence:

show sequence

TGGGCTCCCAGGACAGACCTTAGAATCGTGGGGCAAGAGCAGTGCAGGAGGATGAAGGAGGCGG
AACTGAACAGAGATGTGGCTAAATTCTGCACTGACAACCAGTGTGTCATCCTACAGCCCCAAGG
ACTGGGGCCTAAGTCAGCTGCTCCCATGGCTCCCAGGACACTGAGGCACGTCCAGGCCATTGTG
GCACTAGTGGTGGTGACTGTGTTCTTCTCTCTCCTTGCTCTTTTTGTGGTGGTTTTACAGCCTT
GGAGACAGAAGCAGAATGAGGATCATCCTGTCAAAGCCGGGCTTCATGGAGGCAACTACTCTGG
ATCTGACAATTGTTCCCAATTTGTCCGGAGGGCAGAAATGCAAGAGGCTATCCAGAGTCTCAGG
GCCTCTGGGAATTCTAGCAGCTGTCACAAGGAGATACAGACCCTGAAGTACCAGATGGACAATG
TTAGTTCTCAGGTGCAGTTGCTTGGGGGCCATCTGGAGGAAGCCAATGCTGACATCCAGCAGGC
AAAGGATGTGCTGAAGGGCACTGGGGCCTTGGCCTCGGAGACCCAGGCACTGAGAAGCTCCTTG
GAGGTCGCCAGTGCGGATATCCATAGTCTGAGAGGCGATTTGGAAAAGGCAAATGCCATGACTT
CCCAGACCCAAGGTCTCTTAAAGAGCAGCACAGACAACACCAGTGCTGAGCTCCATGTGCTGGG
CAGAGGCCTGGAGGAAGCCCAGTCTGAGATCCAGGCTTTGAGGGGAAGTCTGCAGAGTTCAAAT
GACCTCGGCTCCCGGACTCAGAACTTTCTCCAGCACAGTATGGACAACATTAGTGCTGAAATCC
AGGCCATGAGAGATGGTATGCAAAGAGCTGGCGAGGAGATGACCTCATTAAAGAAAGATCTAGA
AACACTTACTGCTCAGATTCAAAATGCAAATGGCCACCTGGAGCAGACAGATACCCAGATCCAG
GGGCTAAAAGCTCAGTTGAAAAGCACCAGTTCCTTGAACTCCCAGATTGAGGTGGTCAATGGCA
AATTGAAAGACTCCAGCAGAGAGTTACAGACACTGAGAAGGGACCTGAGTGATGTCTCAGCTTT
GAAGTCCAACGTCCAGATGTTACAGAGCAATCTTCAGAAGGCCAAGGCAGAGGTACAGAGTTTG
AAAACAGGTCTGGAGGCTACCAAAACTCTCGCTGCCAAGATTCAGGGACAACAGAGTGACCTGG
AGGCCCTGCAGAAAGCTGTGGCTGCACACACGCAGGGGCAGAAGACTCAGAATCAGGTTCTCCA
GCTGATCATGCAGGACTGGAAGTACTTCAATGGAAAGTTTTATTACTTTTCTCGTGACAAGAAG
TCATGGCATGAGGCCGAGAATTTCTGTGTGTCCCAGGGAGCACACCTGGCTTCGGTGACCTCTC
AGGAGGAGCAGGCATTCCTGGTACAGATCACAAATGCTGTGGACCATTGGATTGGGCTCACTGA
TCAGGGCACAGAGGGCAACTGGCGCTGGGTGGATGGGACACCATTCGATTATGTCCAGAGCAGA
AGGTTTTGGAGGAAAGGCCAGCCTGACAACTGGAGACACGGAAACGGAGAGCGTGAAGACTGTG
TTCATCTGCAGCGGATGTGGAACGACATGGCCTGTGGGACCGCCTACAACTGGGTGTGCAAGAA
GTCTACAGATTGGTCTGTGGCCAGAACGGACCAGAGCTGAGTCTCTCCCCCCTGAGACTCCTAT
AGCCTTGAACTCTCCTCAGGACTTCTTGTGTCCTGTGTTGCCATTGTCTCGCCATTTAAAACAT
GCTTGCCTCCTTAAAGATAAGCCCTGCATGCTAGTGTCCCCTTAGTGCCCCAACAGGTCTGCCT
AGATAAGCCCTCAATAAACACTCATTGAATGG

hide sequence

Protein Sequences


Protein RefSeqs	NP_446205	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40892	(Get FASTA)	NCBI Sequence Viewer
	AAA41472	(Get FASTA)	NCBI Sequence Viewer
	AAH98661	(Get FASTA)	NCBI Sequence Viewer
	EDL91155	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000017643
	ENSRNOP00000017643.2
GenBank Protein	P10716	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_446205 ⟸ NM_053753

- UniProtKB:

Q4KMB0 (UniProtKB/Swiss-Prot), P10716 (UniProtKB/Swiss-Prot), A6IAN7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MKEAELNRDVAKFCTDNQCVILQPQGLGPKSAAPMAPRTLRHVQAIVALVVVTVFFSLLALFVV
VLQPWRQKQNEDHPVKAGLHGGNYSGSDNCSQFVRRAEMQEAIQSLRASGNSSSCHKEIQTLKY
QMDNVSSQVQLLGGHLEEANADIQQAKDVLKGTGALASETQALRSSLEVASADIHSLRGDLEKA
NAMTSQTQGLLKSSTDNTSAELHVLGRGLEEAQSEIQALRGSLQSSNDLGSRTQNFLQHSMDNI
SAEIQAMRDGMQRAGEEMTSLKKDLETLTAQIQNANGHLEQTDTQIQGLKAQLKSTSSLNSQIE
VVNGKLKDSSRELQTLRRDLSDVSALKSNVQMLQSNLQKAKAEVQSLKTGLEATKTLAAKIQGQ
QSDLEALQKAVAAHTQGQKTQNQVLQLIMQDWKYFNGKFYYFSRDKKSWHEAENFCVSQGAHLA
SVTSQEEQAFLVQITNAVDHWIGLTDQGTEGNWRWVDGTPFDYVQSRRFWRKGQPDNWRHGNGE
REDCVHLQRMWNDMACGTAYNWVCKKSTDWSVARTDQS

hide sequence

Ensembl Acc Id:

ENSRNOP00000017643 ⟸ ENSRNOT00000017643

Protein Domains

C-type lectin

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P10716-F1-model_v2	AlphaFold	P10716	1-550	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693183

Promoter ID:

EPDNEW_R3707

Type:

multiple initiation site

Name:

Clec4f_1

Description:

C-type lectin domain family 4, member F

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	4	115,332,020 - 115,332,080	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621062	AgrOrtholog
BioCyc Gene	G2FUF-43999	BioCyc
Ensembl Genes	ENSRNOG00000013137	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000017643	ENTREZGENE
	ENSRNOT00000017643.5	UniProtKB/Swiss-Prot
Gene3D-CATH	1.20.5.170	UniProtKB/Swiss-Prot
	3.10.100.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7384948	IMAGE-MGC_LOAD
InterPro	C-type_lectin-like	UniProtKB/Swiss-Prot
	C-type_lectin-like/link_sf	UniProtKB/Swiss-Prot
	C-type_lectin/snaclec_domain	UniProtKB/Swiss-Prot
	C-type_lectin_CS	UniProtKB/Swiss-Prot
	CD209-like_CTLD	UniProtKB/Swiss-Prot
	CTDL_fold	UniProtKB/Swiss-Prot
KEGG Report	rno:114598	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:112607	IMAGE-MGC_LOAD
NCBI Gene	114598	ENTREZGENE
PANTHER	MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED	UniProtKB/Swiss-Prot
Pfam	Lectin_C	UniProtKB/Swiss-Prot
PhenoGen	Clec4f	PhenoGen
PROSITE	C_TYPE_LECTIN_1	UniProtKB/Swiss-Prot
	C_TYPE_LECTIN_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000013137	RatGTEx
SMART	CLECT	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56436	UniProtKB/Swiss-Prot
	Tropomyosin	UniProtKB/Swiss-Prot
UniProt	A6IAN7	ENTREZGENE, UniProtKB/TrEMBL
	CLC4F_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q4KMB0	ENTREZGENE
UniProt Secondary	Q4KMB0	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2011-06-08	Clec4f	C-type lectin domain family 4, member F	Clec4f	C-type lectin domain family 4, member f	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Clec4f	C-type lectin domain family 4, member f	Clecsf13	C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13	Symbol and Name updated	1299863	APPROVED
2005-01-20	Clecsf13	C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13	Kclr	Kupffer cell receptor	Symbol and Name updated	1299863	APPROVED
2002-08-07	Kclr	Kupffer cell receptor			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_protein	protein has 550 amino acids	633038
gene_transcript	has 18 contiguous, homologous sequences which have 14 residues in length	633038

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