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Gene: Colec12 (collectin sub-family member 12) Rattus norvegicus

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Symbol:

Colec12

Name:

collectin sub-family member 12

RGD ID:

735039

Description:

Predicted to enable low-density lipoprotein particle binding activity; pattern recognition receptor activity; and scavenger receptor activity. Predicted to be involved in defense response to bacterium and phagocytosis, recognition. Predicted to act upstream of with a positive effect on plasma membrane raft organization. Predicted to act upstream of or within immune response. Predicted to be located in membrane. Predicted to be part of collagen trimer. Orthologous to human COLEC12 (collectin subfamily member 12); PARTICIPATES IN phagocytosis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

CL-P1; collectin placenta protein 1; collectin-12; MGC114569; nurse cell scavenger receptor 2

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):	COLEC12 (collectin subfamily member 12)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Colec12 (collectin sub-family member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Colec12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	COLEC12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	COLEC12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Colec12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	COLEC12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	COLEC12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Colec12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Colec12 (collectin subfamily member 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	COLEC12 (collectin subfamily member 12)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Colec12 (collectin sub-family member 12)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	colec12 (collectin sub-family member 12)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	colec12	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	colec12	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PhylomeDB)

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	18	1,005,787 - 1,193,455 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	18	1,005,741 - 1,195,297 (+)	Ensembl				GRCr8
mRatBN7.2	18	732,950 - 920,620 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	732,950 - 920,618 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	18	960,785 - 1,142,019 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	18	1,748,614 - 1,929,841 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	18	962,684 - 1,143,918 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	18	867,048 - 1,054,047 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	867,048 - 1,052,606 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	18	910,945 - 1,096,505 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	18	996,297 - 1,188,288 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	18	629,852 - 811,837 (+)	NCBI		Celera
RGSC_v3.1	18	1,162,605 - 1,163,261 (+)	NCBI
Cytogenetic Map	18	p13	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)

substance-related disorder (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dichloroethane (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (EXP)

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

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

4,4'-diaminodiphenylmethane (EXP)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

8-Br-cAMP (ISO)

all-trans-retinoic acid (ISO)

allethrin (EXP)

arsane (ISO)

arsenic atom (ISO)

astemizole (EXP)

azathioprine (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol AF (ISO)

bisphenol F (ISO)

butanal (ISO)

Butylbenzyl phthalate (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

calcitriol (ISO)

chlorpyrifos (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

cyhalothrin (EXP)

cypermethrin (EXP)

cytarabine (ISO)

diazinon (EXP)

dimethylarsinic acid (EXP)

diquat (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

entinostat (ISO)

fenvalerate (EXP)

folic acid (ISO)

formaldehyde (ISO)

furan (EXP)

gentamycin (EXP)

inulin (ISO)

L-methionine (ISO)

lead(0) (ISO)

lipopolysaccharide (ISO)

manganese atom (ISO)

manganese(0) (ISO)

manganese(II) chloride (EXP,ISO)

melatonin (ISO)

methotrexate (ISO)

methylmercury chloride (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N-methyl-4-phenylpyridinium (EXP)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

oxaliplatin (EXP)

ozone (ISO)

panobinostat (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenylephrine (EXP)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

progesterone (ISO)

propanal (ISO)

pyrethrins (EXP)

quercetin (ISO)

rofecoxib (ISO)

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

SB 431542 (ISO)

selenium atom (ISO)

silicon dioxide (EXP,ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sodium aurothiomalate (ISO)

succimer (ISO)

sunitinib (ISO)

testosterone (EXP,ISO)

tetrachloromethane (ISO)

thapsigargin (ISO)

toluene (EXP)

topotecan (EXP)

trichostatin A (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

defense response to bacterium (ISO)

immune response (IEA,ISO)

phagocytosis, recognition (ISO,ISS)

plasma membrane raft organization (ISO)

Cellular Component

membrane (IEA)

Molecular Function

carbohydrate binding (IEA)

low-density lipoprotein particle binding (ISO,ISS)

metal ion binding (IEA)

pattern recognition receptor activity (ISO,ISS)

protein binding (ISO)

scavenger receptor activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

phagocytosis pathway (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.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	Molecular cloning of a mouse scavenger receptor with C-type lectin (SRCL)(1), a novel member of the scavenger receptor family.	Nakamura K, etal., Biochim Biophys Acta 2001 Nov 11;1522(1):53-8.
4.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
5.	GOA pipeline	RGD automated data pipeline
6.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11564734	PMID:12477932	PMID:23376485	PMID:25204797	PMID:31344978

Genomics

Comparative Map Data

Colec12
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	18	1,005,787 - 1,193,455 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	18	1,005,741 - 1,195,297 (+)	Ensembl				GRCr8
mRatBN7.2	18	732,950 - 920,620 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	732,950 - 920,618 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	18	960,785 - 1,142,019 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	18	1,748,614 - 1,929,841 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	18	962,684 - 1,143,918 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	18	867,048 - 1,054,047 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	867,048 - 1,052,606 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	18	910,945 - 1,096,505 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	18	996,297 - 1,188,288 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	18	629,852 - 811,837 (+)	NCBI		Celera
RGSC_v3.1	18	1,162,605 - 1,163,261 (+)	NCBI
Cytogenetic Map	18	p13	NCBI

COLEC12
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	18	316,737 - 500,701 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	18	316,737 - 500,722 (-)	Ensembl			hg38	GRCh38
GRCh37	18	316,737 - 500,701 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	18	309,356 - 490,685 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	18	309,355 - 490,685	NCBI
Celera	18	194,506 - 375,871 (-)	NCBI		Celera
Cytogenetic Map	18	p11.32	NCBI
HuRef	18	279,136 - 440,551 (-)	NCBI		HuRef
CHM1_1	18	318,475 - 499,849 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	18	470,846 - 654,740 (-)	NCBI		T2T-CHM13v2.0

Colec12
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	9,707,648 - 9,877,995 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	18	9,707,595 - 9,882,644 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	18	9,707,648 - 9,877,995 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	9,707,595 - 9,882,644 (+)	Ensembl			mm10	GRCm38
MGSCv37	18	9,707,646 - 9,877,993 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	18	9,707,675 - 9,877,990 (+)	NCBI		MGSCv36	mm8
Celera	18	9,737,717 - 9,907,507 (+)	NCBI		Celera
Cytogenetic Map	18	A1	NCBI
cM Map	18	4.91	NCBI

Colec12
(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_004955402	9,468,421 - 9,614,286 (+)	Ensembl
ChiLan1.0	NW_004955402	9,445,419 - 9,614,956 (+)	NCBI	ChiLan1.0	ChiLan1.0

COLEC12
(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	17	37,982,247 - 38,178,247 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	18	23,674,649 - 23,871,759 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	18	13,819,575 - 14,001,383 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	18	17,461,650 - 17,641,404 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	18	17,461,678 - 17,640,721 (+)	Ensembl			panPan2	panpan1.1

COLEC12
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	67,192,191 - 67,373,524 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	67,193,626 - 67,372,755 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	66,645,862 - 66,826,568 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	67,257,518 - 67,438,465 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	7	67,258,955 - 67,438,386 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	7	66,935,179 - 67,115,867 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	66,946,113 - 67,126,853 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	67,248,426 - 67,429,208 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Colec12
(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_024404944	63,465,877 - 63,646,996 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936550	169,084 - 350,501 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936550	169,084 - 350,209 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

COLEC12
(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	105,808,221 - 106,007,730 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	6	105,808,157 - 106,000,197 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

COLEC12
(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	18	59,701,131 - 59,884,445 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	18	59,699,348 - 59,884,461 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666050	34,490,498 - 34,675,112 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Colec12
(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_004624770	10,859,205 - 11,013,175 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624770	10,860,097 - 11,136,478 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Colec12
(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	15	34,205,609 - 34,237,754 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Colec12
1051 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	258
Count of miRNA genes:	172
Interacting mature miRNAs:	184
Transcripts:	ENSRNOT00000065494
Prediction methods:	Microtar, 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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1331781	Scl28	Serum cholesterol level QTL 28	3.995		blood HDL cholesterol amount (VT:0000184)	serum high density lipoprotein cholesterol level (CMO:0000361)	18	1	25071266	Rat
1331766	Bp236	Blood pressure QTL 236	3.022		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	31610627	Rat
6903356	Bp354	Blood pressure QTL 354	4.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	15642423	Rat
2300180	Bmd67	Bone mineral density QTL 67	4.8	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	18	1	34566578	Rat
8552968	Pigfal19	Plasma insulin-like growth factor 1 level QTL 19	11.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	18	1	26032889	Rat
9590248	Scort10	Serum corticosterone level QTL 10	19.71	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	18	1	26032889	Rat
6903347	Bp350	Blood pressure QTL 350	4.4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	31610627	Rat
2325839	Bp348	Blood pressure QTL 348		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	44930869	Rat
1331753	Bp231	Blood pressure QTL 231	3.643		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	1	54490981	Rat
1641910	Colcr3	Colorectal carcinoma resistance QTL 3	5.02	0.000007	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	18	1	25022372	Rat
2293661	Bss50	Bone structure and strength QTL 50	4.64	0.0003	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	18	1	34566578	Rat

Markers in Region

D18Mit12

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	18	1,077,851 - 1,078,087 (+)	Marker Load Pipeline
mRatBN7.2	18	805,014 - 805,250 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	938,503 - 938,738	NCBI	Rnor6.0
Rnor_5.0	18	982,400 - 982,635	UniSTS	Rnor5.0
RGSC_v3.4	18	1,069,988 - 1,070,224	RGD	RGSC3.4
RGSC_v3.4	18	1,069,989 - 1,070,224	UniSTS	RGSC3.4
Celera	18	695,687 - 695,922	UniSTS
RGSC_v3.1	18	1,069,989 - 1,070,224	RGD
RH 3.4 Map	18	27.7	RGD
RH 3.4 Map	18	27.7	UniSTS
RH 2.0 Map	18	834.3	RGD
Cytogenetic Map	18	p13	UniSTS

D18Rat114

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	18	1,111,181 - 1,111,335 (+)	Marker Load Pipeline
mRatBN7.2	18	838,348 - 838,504 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	971,826 - 971,979	NCBI	Rnor6.0
Rnor_5.0	18	1,015,723 - 1,015,876	UniSTS	Rnor5.0
RGSC_v3.4	18	1,104,768 - 1,104,921	UniSTS	RGSC3.4
RGSC_v3.4	18	1,104,767 - 1,104,921	RGD	RGSC3.4
Celera	18	729,300 - 729,459	UniSTS
RGSC_v3.1	18	1,104,768 - 1,104,921	RGD
RH 3.4 Map	18	31.5	UniSTS
RH 3.4 Map	18	31.5	RGD
RH 2.0 Map	18	840.8	RGD
SHRSP x BN Map	18	0.23	RGD
Cytogenetic Map	18	p13	UniSTS

D2Rat367

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	893,930 - 894,144 (+)	MAPPER	mRatBN7.2
mRatBN7.2	2	246,974,238 - 246,974,460 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	264,265,266 - 264,265,491	NCBI	Rnor6.0
Rnor_6.0	18	1,026,832 - 1,027,045	NCBI	Rnor6.0
Rnor_5.0	18	1,070,729 - 1,070,942	UniSTS	Rnor5.0
Rnor_5.0	2	282,393,650 - 282,393,875	UniSTS	Rnor5.0
RGSC_v3.4	18	1,161,596 - 1,161,809	UniSTS	RGSC3.4
RGSC_v3.4	2	256,054,885 - 256,055,110	UniSTS	RGSC3.4
Celera	2	238,774,849 - 238,775,080	UniSTS
Celera	18	785,146 - 785,359	UniSTS
RGSC_v3.1	18	1,161,167 - 1,161,810	RGD
SHRSP x BN Map	2	112.4598	UniSTS
SHRSP x BN Map	2	112.4598	RGD
Cytogenetic Map	18	p13	UniSTS

D18Chm30

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	838,607 - 838,796 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	972,083 - 972,267	NCBI	Rnor6.0
Rnor_6.0	18	971,885 - 972,267	NCBI	Rnor6.0
Rnor_5.0	18	1,015,782 - 1,016,164	UniSTS	Rnor5.0
Rnor_5.0	18	1,015,980 - 1,016,164	UniSTS	Rnor5.0
RGSC_v3.4	18	1,105,025 - 1,105,209	UniSTS	RGSC3.4
RGSC_v3.4	18	1,104,827 - 1,105,209	UniSTS	RGSC3.4
Celera	18	729,563 - 729,747	UniSTS
Celera	18	729,359 - 729,747	UniSTS
Cytogenetic Map	18	p13	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	162	91	90	59	85	59	6	349	185	11	141	81	92	31	16	16

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025721	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017600987	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB080968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC097495	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474073	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224233	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000018	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000065494 ⟹ ENSRNOP00000059663

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	1,005,741 - 1,193,453 (+)	Ensembl
mRatBN7.2 Ensembl	18	732,950 - 920,618 (+)	Ensembl
Rnor_6.0 Ensembl	18	867,048 - 1,052,606 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000134024 ⟹ ENSRNOP00000107802

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	1,005,755 - 1,193,447 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000151312 ⟹ ENSRNOP00000099035

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	1,112,334 - 1,195,297 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000171790 ⟹ ENSRNOP00000110484

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	1,005,755 - 1,195,297 (+)	Ensembl

RefSeq Acc Id:

NM_001025721 ⟹ NP_001020892

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	1,005,787 - 1,193,455 (+)	NCBI
mRatBN7.2	18	732,950 - 920,620 (+)	NCBI
Rnor_6.0	18	867,048 - 1,052,608 (+)	NCBI
Rnor_5.0	18	910,945 - 1,096,505 (+)	NCBI
RGSC_v3.4	18	996,297 - 1,188,288 (+)	RGD
Celera	18	629,852 - 811,837 (+)	RGD

Sequence:

show sequence

CTAGGATTGGAACTCAGAAGGCTGCCATGGGCGTGCAGTGAGTAACACTGGTGCGACTTCTCCG
GGCGGAGCGTGTCCTCGGTCACCATGAAAGACGACTTTGCAGAGGAAGAGGAGGTGCAGTCCTT
CGGTTACAAGAGGTTTGGTATTCAGGAGGGGACACAATGTACCAAATGTAAAAATAACTGGGCA
CTGAAGTTTTCGATTATATTATTATATGTTTTGTGTGCCTTACTGACCATCACAGTAGCCATTT
TGGGATATAAAGTTGTAGAGAAAATGGACACTGTCACAGATGGCATGGAGACATCTCGCCAGAC
TTACGACAACAAGCTCATTGCTGTGGAAAGTGATCTGAAGAAATTAGGGGACCAAACTGGGAAG
AAAGCTCTAAGCACCAACTCTGAGCTTTCTACCTTCAGATCAGATATTCTGGATCTCCGTCAGC
AACTTCAGGAGATCACAGAAAAAACCAGTAAGAACAAAGATATGCTAGAGAAGTTGCAAGCAAA
TGGGGACTCATTGGTTGATAGACAAAGTCAACTGAAGGAAACTCTGCAGAATAATTCTTTCCTC
ATCACCACAGTCAACAAAACTCTCCAGGCATATAATGGCTATGTCACGAATCTGCAACAAGATA
CTAGTGTGCTCCAGGGCAATCTGCAGAGCCAGATGTATTCTCAGAATGTGGTTATCATGAACCT
CAACAACCTGAACCTGACCCAGGTTCAGCAGAGGAACCTTATCACAAATCTGCAGCGATCTGTG
GATGACACGAGCCTGGCTATCCAGCAAATTAAGAATGACTTCCAAAATCTGCAACAGGTTTTCC
TTCAAGCCAAGAAGGACACCGATTGGCTAAAGGAGAAAGTACAGAGTTTGCAGACATTGGCTGC
CAACAACTCTGCCCTGGCCAAAGCCAATAATGACACCCTGGAGGATATGAATAACCAGCTCAGC
TCTTTCACAGGTCAGATGGACAACATTACCACTATCTCACAGGCTAACGAGCAGAGCATGAAAG
ACCTTCAGGACTTACACAAGGATACAGAAAATAGGACAGCTGTCAAGTTCAGCCAACTTGAGGA
ACGCTTCCAGGTCTTTGAGACAGATATTGTGAACATCATTAACAACATCAGCTACACAGCCCAT
CACCTGAGGACGCTGACCAGCAATCTGAATGATGTTAGGACCACTTGCACAGACACCTTGACCA
GACACACGGATGACCTGACCTCCTTGAATAACACACTAGTCAACATCCGCTTGGATTCTATTTC
TCTCAGGATGCAGCAAGACATGATGAGGTCAAGGTTAGACACTGAAGTAGCCAACTTATCAGTG
GTTATGGAAGAGATGAAGCTGGTTGACTCCAAGCATGGTCAGCTCATCAAGAACTTTACCATTC
TACAGGGTCCTCCTGGCCCCAGAGGTCCAAAAGGTGACAGAGGATCTCAGGGACCGCCTGGTCC
AACTGGCAACAAGGGACAGAAAGGAGAGAAGGGAGAGCCTGGTCCACCTGGCCCTGCGGGTGAG
CGAGGCACAATTGGACCAGTAGGCCCTCCTGGAGAGCGTGGCAGCAAAGGATCCAAAGGCTCAC
AGGGTCCCAAAGGATCACGTGGGTCCCCAGGAAAGCCTGGCCCTCAAGGGCCTAGTGGAGACCC
TGGACCACCAGGTCCACCAGGCAAGGATGGACTCCCTGGCCCTCAGGGCCCTCCTGGCTTCCAG
GGACTACAGGGCACTGTGGGTGAACCTGGAGTACCTGGACCTCGGGGGCTACCAGGCTTACCAG
GGGTGCCAGGCATGCCTGGGCCCAAGGGACCACCTGGCCCCCCAGGTCCCTCAGGAGCAATGGA
GCCGTTGGCTCTGCAGAATGAACCAACCCCAGCATCAGAGGTCAACGGATGTCCGCCTCACTGG
AAGAACTTCACAGATAAATGTTACTATTTTTCGGTGGAGAAAGAAATTTTTGAAGATGCTAAGC
TTTTCTGTGAAGACAAATCTTCCCATCTCGTTTTCATAAACTCAAGAGAGGAACAGCAATGGAT
AAAAAAGCAGACCATGGGGAGAGAGAGCCACTGGATCGGCCTCACAGACTCAGAGCAAGAAAGC
GAGTGGAAGTGGCTAGATGGGACACCTGTTGATTACAAAAACTGGAAAGCTGGACAACCCGACA
ACTGGGGCAGTGGCCATGGGCCTGGAGAAGACTGTGCTGGATTGATTTATGCCGGGCAGTGGAA
TGACTTCCAGTGTGATGAAATCAATAACTTCATTTGCGAAAAAGAAAGGGAGGCAGTACCATCA
TCCATATTATAACTGTGATATAATAGCAGGAACGTATTTTCTGATGCCTCTCAAAGGTGAAGAA
TACTCGTTTCTGATGCCATCACTTCTCACCAGATTGAATGGAAAAAGACCTGAAAAGTAGTTAT
TCAAAGTAAATGGATACCTACTGCACCATAACCGAAGGACTAGAGAGCTAAAATGCTCCCCAAG
TTGATACTGATTTCCAATGTGCAAATGGACTGAATCACATAGATTTTTCTCAGCCATTAACCAT
ACAATTTATGCAAATTATATCTTTCCAAATATGGAATGCTCCAATCAGAAAAAGACTATCATTG
GTTGTTGAGTTACAGGCTCTGTGTAAACAGTGTGTTTCTAAAATCCCAAATATAGAAAGAATAT
GCAGACATACACATATATAGGCCATCTTTTAGTAATAATATGAAATATACTTAAAGAGCTTTTA
AACTTCATATTTTTGTACAAAATATTTGCCTTTTACAATCATTTTACTTTTTTAAATTTTACCT
ATATAACACATAAAGCCAAAGAAAACAATAATTGTACTAATAAAATTTCAATGGAGTTTCTCTT
CAGATTTAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001020892	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH97495	(Get FASTA)	NCBI Sequence Viewer
	BAD06456	(Get FASTA)	NCBI Sequence Viewer
	EDL86660	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000059663.1
	ENSRNOP00000110484
GenBank Protein	Q4V885	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001020892 ⟸ NM_001025721

- UniProtKB:

Q76LC3 (UniProtKB/Swiss-Prot), Q4V885 (UniProtKB/Swiss-Prot), A6KND5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MKDDFAEEEEVQSFGYKRFGIQEGTQCTKCKNNWALKFSIILLYVLCALLTITVAILGYKVVEK
MDTVTDGMETSRQTYDNKLIAVESDLKKLGDQTGKKALSTNSELSTFRSDILDLRQQLQEITEK
TSKNKDMLEKLQANGDSLVDRQSQLKETLQNNSFLITTVNKTLQAYNGYVTNLQQDTSVLQGNL
QSQMYSQNVVIMNLNNLNLTQVQQRNLITNLQRSVDDTSLAIQQIKNDFQNLQQVFLQAKKDTD
WLKEKVQSLQTLAANNSALAKANNDTLEDMNNQLSSFTGQMDNITTISQANEQSMKDLQDLHKD
TENRTAVKFSQLEERFQVFETDIVNIINNISYTAHHLRTLTSNLNDVRTTCTDTLTRHTDDLTS
LNNTLVNIRLDSISLRMQQDMMRSRLDTEVANLSVVMEEMKLVDSKHGQLIKNFTILQGPPGPR
GPKGDRGSQGPPGPTGNKGQKGEKGEPGPPGPAGERGTIGPVGPPGERGSKGSKGSQGPKGSRG
SPGKPGPQGPSGDPGPPGPPGKDGLPGPQGPPGFQGLQGTVGEPGVPGPRGLPGLPGVPGMPGP
KGPPGPPGPSGAMEPLALQNEPTPASEVNGCPPHWKNFTDKCYYFSVEKEIFEDAKLFCEDKSS
HLVFINSREEQQWIKKQTMGRESHWIGLTDSEQESEWKWLDGTPVDYKNWKAGQPDNWGSGHGP
GEDCAGLIYAGQWNDFQCDEINNFICEKEREAVPSSIL

hide sequence

Ensembl Acc Id:

ENSRNOP00000059663 ⟸ ENSRNOT00000065494

Ensembl Acc Id:

ENSRNOP00000107802 ⟸ ENSRNOT00000134024

Ensembl Acc Id:

ENSRNOP00000099035 ⟸ ENSRNOT00000151312

Ensembl Acc Id:

ENSRNOP00000110484 ⟸ ENSRNOT00000171790

Protein Domains

C-type lectin Collagen-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q4V885-F1-model_v2	AlphaFold	Q4V885	1-742	view protein structure

Transcriptome

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

Promoters

RGD ID:

13700626

Promoter ID:

EPDNEW_R11150

Type:

initiation region

Name:

Colec12_1

Description:

collectin sub-family member 12

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	18	867,000 - 867,060	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:735039	AgrOrtholog
BioCyc Gene	G2FUF-8426	BioCyc
Ensembl Genes	ENSRNOG00000016366	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000065494.2	UniProtKB/Swiss-Prot
	ENSRNOT00000171790	ENTREZGENE
Gene3D-CATH	3.10.100.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7461783	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
	Collagen	UniProtKB/Swiss-Prot
	CTDL_fold	UniProtKB/Swiss-Prot
KEGG Report	rno:361289	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:114569	IMAGE-MGC_LOAD
NCBI Gene	361289	ENTREZGENE
PANTHER	MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED	UniProtKB/Swiss-Prot
Pfam	Collagen	UniProtKB/Swiss-Prot
	Lectin_C	UniProtKB/Swiss-Prot
PhenoGen	Colec12	PhenoGen
PROSITE	C_TYPE_LECTIN_1	UniProtKB/Swiss-Prot
	C_TYPE_LECTIN_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000016366	RatGTEx
SMART	CLECT	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56436	UniProtKB/Swiss-Prot
UniProt	A0ABK0KWU9_RAT	UniProtKB/TrEMBL
	A0ABK0LWB7_RAT	UniProtKB/TrEMBL
	A6KND5	ENTREZGENE, UniProtKB/TrEMBL
	COL12_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q76LC3	ENTREZGENE
UniProt Secondary	Q76LC3	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Colec12	collectin sub-family member 12			Symbol and Name status set to approved	1299863	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)