Colec12 (collectin sub-family member 12)

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

Analyze

Symbol:

Colec12

Name:

collectin sub-family member 12

RGD ID:

735039

Description:

Predicted to have low-density lipoprotein particle binding activity; pattern recognition receptor activity; and scavenger receptor activity. Predicted to be involved in several processes, including cellular response to exogenous dsRNA; positive regulation of cell adhesion molecule production; and toll-like receptor 3 signaling pathway. Predicted to localize to collagen trimer and integral component of membrane. 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

Also known as:

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

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	18	732,950 - 920,620 (+)	NCBI
Rnor_6.0 Ensembl	18	867,048 - 1,052,606 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	867,048 - 1,054,047 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	910,945 - 1,096,505 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	996,297 - 1,188,288 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	1,162,605 - 1,163,261 (+)	NCBI
Celera	18	629,852 - 811,837 (+)	NCBI		Celera
Cytogenetic Map	18	p13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Experimental Liver Cirrhosis (ISO)

Neurodevelopmental Disorders (ISO)

substance-related disorder (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (EXP,ISO)

2,3,7,8-tetrachlorodibenzodioxine (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)

astemizole (EXP)

azathioprine (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

calcitriol (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

cytarabine (ISO)

diazinon (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

entinostat (ISO)

folic acid (ISO)

formaldehyde (ISO)

furan (EXP)

L-methionine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

lipopolysaccharide (ISO)

manganese(II) chloride (EXP)

melatonin (ISO)

methotrexate (ISO)

methylmercury chloride (ISO)

N-methyl-4-phenylpyridinium (EXP)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

oxaliplatin (EXP)

panobinostat (ISO)

paracetamol (ISO)

phenylephrine (EXP)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

progesterone (ISO)

propanal (ISO)

quercetin (ISO)

rofecoxib (ISO)

SB 431542 (ISO)

selenium atom (ISO)

silicon dioxide (EXP,ISO)

silver atom (ISO)

silver(0) (ISO)

sodium aurothiomalate (ISO)

succimer (ISO)

sunitinib (ISO)

testosterone (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

cellular response to exogenous dsRNA (ISO)

defense response to bacterium (ISO)

immune response (ISO)

phagocytosis, recognition (ISO,ISS)

positive regulation of cell adhesion molecule production (ISO)

toll-like receptor 3 signaling pathway (ISO)

Cellular Component

collagen trimer (IEA)

integral component of membrane (IEA)

Molecular Function

carbohydrate binding (IEA)

low-density lipoprotein particle binding (ISO,ISS)

metal ion binding (IEA)

pattern recognition receptor activity (ISO,ISS)

scavenger receptor activity (ISO)

signaling receptor activity (IBA)

Molecular Pathway Annotations Click to see Annotation Detail View

phagocytosis pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	MGD data from the GO Consortium
3.	Nakamura K, etal., Biochim Biophys Acta 2001 Nov 11;1522(1):53-8.
4.	Pipeline to import KEGG annotations from KEGG into RGD
5.	RGD automated data pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	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
mRatBN7.2	18	732,950 - 920,620 (+)	NCBI
Rnor_6.0 Ensembl	18	867,048 - 1,052,606 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	867,048 - 1,054,047 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	910,945 - 1,096,505 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	996,297 - 1,188,288 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	1,162,605 - 1,163,261 (+)	NCBI
Celera	18	629,852 - 811,837 (+)	NCBI		Celera
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.p13 Ensembl	18	316,737 - 500,722 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	18	316,737 - 500,701 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	18	316,737 - 500,701 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	18	309,356 - 490,685 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	18	309,355 - 490,685	NCBI
Celera	18	194,506 - 375,871 (-)	NCBI
Cytogenetic Map	18	p11.32	NCBI
HuRef	18	279,136 - 440,551 (-)	NCBI		HuRef
CHM1_1	18	318,475 - 499,849 (-)	NCBI		CHM1_1

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		mm39
GRCm39 Ensembl	18	9,707,595 - 9,882,644 (+)	Ensembl
GRCm38	18	9,707,648 - 9,877,995 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	9,707,595 - 9,882,644 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	9,707,646 - 9,877,993 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	18	9,707,675 - 9,877,990 (+)	NCBI			mm8
Celera	18	9,737,717 - 9,907,507 (+)	NCBI		Celera
Cytogenetic Map	18	A1	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
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
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	panpan1.1		panPan2
Mhudiblu_PPA_v0	18	13,819,575 - 14,001,383 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

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 Ensembl	7	67,193,626 - 67,372,755 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	7	67,192,191 - 67,373,524 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

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
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	105,808,212 - 106,007,730 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	105,808,157 - 106,000,197 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

COLEC12
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	18	59,701,131 - 59,884,445 (-)	NCBI
ChlSab1.1 Ensembl	18	59,699,348 - 59,884,461 (-)	Ensembl

Colec12
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624770	10,860,097 - 11,136,478 (-)	NCBI

Position Markers

D18Mit12

Rat Assembly	Chr	Position (strand)	Source	JBrowse
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
RGSC_v3.1	18	1,069,989 - 1,070,224	RGD
Celera	18	695,687 - 695,922	UniSTS
RH 3.4 Map	18	27.7	UniSTS
RH 3.4 Map	18	27.7	RGD
RH 2.0 Map	18	834.3	RGD
Cytogenetic Map	18	p13	UniSTS

D18Rat114

Rat Assembly	Chr	Position (strand)	Source	JBrowse
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
RGSC_v3.1	18	1,104,768 - 1,104,921	RGD
Celera	18	729,300 - 729,459	UniSTS
RH 3.4 Map	18	31.5	RGD
RH 3.4 Map	18	31.5	UniSTS
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
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
RGSC_v3.1	18	1,161,167 - 1,161,810	RGD
Celera	18	785,146 - 785,359	UniSTS
Celera	2	238,774,849 - 238,775,080	UniSTS
SHRSP x BN Map	2	112.4598	RGD
SHRSP x BN Map	2	112.4598	UniSTS
Cytogenetic Map	18	p13	UniSTS

D18Chm30

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	971,885 - 972,267	NCBI	Rnor6.0
Rnor_6.0	18	972,083 - 972,267	NCBI	Rnor6.0
Rnor_5.0	18	1,015,980 - 1,016,164	UniSTS	Rnor5.0
Rnor_5.0	18	1,015,782 - 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

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
9590248	Scort10	Serum corticosterone level QTL 10	19.71	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	18	1	25999214	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	25999214	Rat
61388	Bp2	Blood pressure QTL 2	3.23		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	1	35097280	Rat
2300180	Bmd67	Bone mineral density QTL 67	4.8	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	18	1	38195967	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	38195967	Rat
9589153	Insul31	Insulin level QTL 31	7.15	0.05	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	18	1	38753381	Rat

miRNA Target Status

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.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	39	8	6	13	6	6	6	65	29	34	11	6
Low	1	4	49	35	6	35	2	5	9	6	6		2
Below cutoff											1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025721	(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
	JACYVU010000298	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000065494 ⟹ ENSRNOP00000059663

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	867,048 - 1,052,606 (+)	Ensembl

RefSeq Acc Id:

NM_001025721 ⟹ NP_001020892

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
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

RefSeq Acc Id:

XM_017600987 ⟹ XP_017456476

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	18	1,005,061 - 1,054,047 (+)	NCBI

Sequence:

show sequence

GAGAGCAAGAGTGCATATGGAGGAAGAACAGATTCCAGCTTTGATGTTACCCATTACCTGTGTT
ACCCATATACTTCCTACACAACACTGTTTCTACTATCAATGGCAGAGAACCTGTCATTAACTAA
GGTTAATCCTGCTCAGTTGTGTGCCCTATCATCATTTTGTTAGTCCTTAAGCTGCCTCAAAGTG
ACACTGTCTAAAGCAGCAACACTAGAGGCAAGTGGGGAGCCATGGGTTTTCATGTTGCCCTCTG
ACTTGTCCAGTTGAGCCTGCGAGTACTAAATGTGGAGAACAAATTGGTGGTGGATAGTTGACAT
TGACAGTGTCTGAAAGGTCTCAAGAGGTGTGTTTCACATTCCTTCCCCAGCCCTATCACCAGTC
CTACCACTACCAGAGAGCCAGCTTCTGGTGGAGCATCCCAGCTGAGCTGGAGGCTGGTGCACAC
TGAGGATCTGATTGTTGACATTCATGCACCTGTCCCAGGATGCCTACATCCTGGCCTCTAGGCC
AAGGAGAGGGTGTCATTCTGTCACTCCTCACCTGCAAGGACAGGCACAAAGGTATTCAGGAGGG
GACACAATGTACCAAATGTAAAAATAACTGGGCACTGAAGTTTTCGATTATATTATTATATGTT
TTGTGTGCCTTACTGACCATCACAGTAGCCATTTTGGGATATAAAGTTGTAGAGAAAATGGACA
CTGTCACAGATGGCATGGAGACATCTCGCCAGACTTACGACAACAAGCTCATTGCTGTGGAAAG
TGATCTGAAGAAATTAGGGGACCAAACTGGGAAGAAAGCTCTAAGCACCAACTCTGAGCTTTCT
ACCTTCAGATCAGATATTCTGGATCTCCGTCAGCAACTTCAGGAGATCACAGAAAAAACCAGTA
AGAACAAAGATATGCTAGAGAAGTTGCAAGCAAATGGGGACTCATTGGTTGATAGACAAAGTCA
ACTGAAGGAAACTCTGCAGAATAATTCTTTCCTCATCACCACAGTCAACAAAACTCTCCAGGCA
TATAATGGCTATGTCACGAATCTGCAACAAGATACTAGTGTGCTCCAGGGCAATCTGCAGAGCC
AGATGTATTCTCAGAATGTGGTTATCATGAACCTCAACAACCTGAACCTGACCCAGGTTCAGCA
GAGGAACCTTATCACAAATCTGCAGCGATCTGTGGATGACACGAGCCTGGCTATCCAGCAAATT
AAGAATGACTTCCAAAATCTGCAACAGGTTTTCCTTCAAGCCAAGAAGGACACCGATTGGCTAA
AGGAGAAAGTACAGAGTTTGCAGACATTGGCTGCCAACAACTCTGCCCTGGCCAAAGCCAATAA
TGACACCCTGGAGGATATGAATAACCAGCTCAGCTCTTTCACAGGTCAGATGGACAACATTACC
ACTATCTCACAGGCTAACGAGCAGAGCATGAAAGACCTTCAGGACTTACACAAGGATACAGAAA
ATAGGACAGCTGTCAAGTTCAGCCAACTTGAGGAACGCTTCCAGGTCTTTGAGACAGATATTGT
GAACATCATTAACAACATCAGCTACACAGCCCATCACCTGAGGACGCTGACCAGCAATCTGAAT
GATGTTAGGACCACTTGCACAGACACCTTGACCAGACACACGGATGACCTGACCTCCTTGAATA
ACACACTAGTCAACATCCGCTTGGATTCTATTTCTCTCAGGATGCAGCAAGACATGATGAGGTC
AAGGTTAGACACTGAAGTAGCCAACTTATCAGTGGTTATGGAAGAGATGAAGCTGGTTGACTCC
AAGCATGGTCAGCTCATCAAGAACTTTACCATTCTACAGGGTCCTCCTGGCCCCAGAGGTCCAA
AAGGTGACAGAGGATCTCAGGGACCGCCTGGTCCAACTGGCAACAAGGGACAGAAAGGAGAGAA
GGGAGAGCCTGGTCCACCTGGCCCTGCGGGTGAGCGAGGCACAATTGGACCAGTAGGCCCTCCT
GGAGAGCGTGGCAGCAAAGGATCCAAAGGCTCACAGGGTCCCAAAGGATCACGTGGGTCCCCAG
GAAAGCCTGGCCCTCAAGGGCCTAGTGGAGACCCTGGACCACCAGGTCCACCAGGCAAGGATGG
ACTCCCTGGCCCTCAGGGCCCTCCTGGCTTCCAGGGACTACAGGGCACTGTGGGTGAACCTGGA
GTACCTGGACCTCGGGGGCTACCAGGCTTACCAGGGGTGCCAGGCATGCCTGGGCCCAAGGGAC
CACCTGGCCCCCCAGGTCCCTCAGGAGCAATGGAGCCGTTGGCTCTGCAGAATGAACCAACCCC
AGCATCAGAGGTCAACGGATGTCCGCCTCACTGGAAGAACTTCACAGATAAATGTTACTATTTT
TCGGTGGAGAAAGAAATTTTTGAAGATGCTAAGCTTTTCTGTGAAGACAAATCTTCCCATCTCG
TTTTCATAAACTCAAGAGAGGAACAGCAATGGATAAAAAAGCAGACCATGGGGAGAGAGAGCCA
CTGGATCGGCCTCACAGACTCAGAGCAAGAAAGCGAGTGGAAGTGGCTAGATGGGACACCTGTT
GATTACAAAAACTGGAAAGCTGGACAACCCGACAACTGGGGCAGTGGCCATGGGCCTGGAGAAG
ACTGTGCTGGATTGATTTATGCCGGGCAGTGGAATGACTTCCAGTGTGATGAAATCAATAACTT
CATTTGCGAAAAAGAAAGGGAGGCAGTACCATCATCCATATTATAACTGTGATATAATAGCAGG
AACGTATTTTCTGATGCCTCTCAAAGGTGAAGAATACTCGTTTCTGATGCCATCACTTCTCACC
AGATTGAATGGAAAAAGACCTGAAAAGTAGTTATTCAAAGTAAATGGATACCTACTGCACCATA
ACCGAAGGACTAGAGAGCTAAAATGCTCCCCAAGTTGATACTGATTTCCAATGTGCAAATGGAC
TGAATCACATAGATTTTTCTCAGCCATTAACCATACAATTTATGCAAATTATATCTTTCCAAAT
ATGGAATGCTCCAATCAGAAAAAGACTATCATTGGTTGTTGAGTTACAGGCTCTGTGTAAACAG
TGTGTTTCTAAAATCCCAAATATAGAAAGAATATGCAGACATACACATATATAGGCCATCTTTT
AGTAATAATATGAAATATACTTAAAGAGCTTTTAAACTTCATATTTTTGTACAAAATATTTGCC
TTTTACAATCATTTTACTTTTTTAAATTTTACCTATATAACACATAAAGCCAAAGAAAACAATA
ATTGTACTAATAAAATTTCAATGGAGTTTCTCTTCAGATTTAATCTGTCCAGCTGAAGTGAATT
TTTGTTTTATGTATCTGTGTATGTGTGATGTCTTCAGAACAGTGAATCACATGAAGCATCTGGA
AATACCCTGTGCATTTTGGTGATAGTGGAGCTCTAGCCTGAGATCATGATAGTTCATTCAAGAA
GGCTGTGCCATGAGCCCAGCACCAGCCACTTTTATAAGAGGAAGTGTTGACTTGGGATGTGCTT
TTGTTCTACTTTGTGAAATGGGAATGCTGGAGAAGCATCTGTGAGGAAGGATAGAACACCTGAA
TCTGAATGTCTGTAAGGCCCTGGTGTAAGGCTGATCCATGAACAGGCTTAGTGTCATATTCATA
CCAGAACAGACAAGAGATTATAATGTCACATCAGTTGAAGTCAGCCAAGTGATGCTTGCAAGTT
AGAAGAAACATGCTATTTGGAAAGTAGGGTTCCCAAAACATAACTCAAGACCTGGGCTAAATGA
AATGCAAAAATAAACTTTAGGTAATTTGTTGAATCAGCAAAGAATCTTCACTTGTGAGCCCAAA
ACGTCCATGCCCTCCTGTCTTTGCATCTGTTTCATAGCTGAGGCAGAGGACGAGGGTTGTCCAA
GTAGCTGCCCCATCCACCTGTAGTCTTTCTTCCCTTGTGGAGTGTAAGCTTCCACAGAATTGAT
CATATCTAAACATTTCGGATGAGCTTGAAACTCCAGGATTTAGCCAAAAGAAAAGGAAACTAAA
ATTTTAAGACCTACCTAACCTCTTCAGTTATTAATTTCTAGGCTAGACAAAGTACGTATGTCAT
CTGAAATCAAAGTCATACTTAACAACAACAGCAAACCATAATGGATAAATTGAACATGTGTGCC
ACCTCAACAGAGACTTTAAGCCTTTAGATATTACACATGAAAATGAACTGTTTCATTCACATTT
AGTTGATCTTTAATCTGAACTGGAATCAAACCTCAAACAGTTCACTGCTCTTACAGAGGATCGG
AGATCAGTTCTCAGCACCTATGTTGGAGAATTTTCAACCTCCTATAACTCCAGATCCAGGGGAC
TCAAAACCTCCCTGACATACCTGTCATATACCTATGGGTACGCAGATACACATGTATACATAAG
TAAAAAATTTTAAAGGGTTTGTTCCTAGACTTGTTTGCTCTATTCAGTGGATATTTGTGAGAGG
CCTGCTCTCTTCTGAAGTGAAACAGAGAAAGAGTGGATCTGGGGCAGTGGGGGAGGGAAGAATG
GGAGAAACAGAGGGAAGGGAAATTTCAGTCAAGATGTATTGAAAAAAAACAAATTTTAAAAAAA
CAGAAAAAGGCAAGTATATTAACTGTGATATTTGATTTCAAATGTACATTGAATATACTTATAC
CTGTCTCACAAAGTCATTGCAAATTTTAATGAGGTAATATCCAGAAATCACCTATTACAGTGTC
TGGCTCCAAA

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
	Q4V885	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001020892 ⟸ NM_001025721

- UniProtKB:

Q4V885 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

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

hide sequence

RefSeq Acc Id:

XP_017456476 ⟸ XM_017600987

- Peptide Label:

isoform X1

- Sequence:

show sequence

MPTSWPLGQGEGVILSLLTCKDRHKGIQEGTQCTKCKNNWALKFSIILLYVLCALLTITVAILG
YKVVEKMDTVTDGMETSRQTYDNKLIAVESDLKKLGDQTGKKALSTNSELSTFRSDILDLRQQL
QEITEKTSKNKDMLEKLQANGDSLVDRQSQLKETLQNNSFLITTVNKTLQAYNGYVTNLQQDTS
VLQGNLQSQMYSQNVVIMNLNNLNLTQVQQRNLITNLQRSVDDTSLAIQQIKNDFQNLQQVFLQ
AKKDTDWLKEKVQSLQTLAANNSALAKANNDTLEDMNNQLSSFTGQMDNITTISQANEQSMKDL
QDLHKDTENRTAVKFSQLEERFQVFETDIVNIINNISYTAHHLRTLTSNLNDVRTTCTDTLTRH
TDDLTSLNNTLVNIRLDSISLRMQQDMMRSRLDTEVANLSVVMEEMKLVDSKHGQLIKNFTILQ
GPPGPRGPKGDRGSQGPPGPTGNKGQKGEKGEPGPPGPAGERGTIGPVGPPGERGSKGSKGSQG
PKGSRGSPGKPGPQGPSGDPGPPGPPGKDGLPGPQGPPGFQGLQGTVGEPGVPGPRGLPGLPGV
PGMPGPKGPPGPPGPSGAMEPLALQNEPTPASEVNGCPPHWKNFTDKCYYFSVEKEIFEDAKLF
CEDKSSHLVFINSREEQQWIKKQTMGRESHWIGLTDSEQESEWKWLDGTPVDYKNWKAGQPDNW
GSGHGPGEDCAGLIYAGQWNDFQCDEINNFICEKEREAVPSSIL

hide sequence

RefSeq Acc Id:

ENSRNOP00000059663 ⟸ ENSRNOT00000065494

Protein Domains

C-type lectin Collagen-like

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:735039	AgrOrtholog
Ensembl Genes	ENSRNOG00000016366	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000059663	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000065494	ENTREZGENE, UniProtKB/Swiss-Prot
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_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
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
SMART	CLECT	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56436	UniProtKB/Swiss-Prot
UniProt	COL12_RAT	UniProtKB/Swiss-Prot, 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 - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)