Colec12 (collectin sub-family member 12) - Rat Genome Database
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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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.218732,950 - 920,620 (+)NCBI
Rnor_6.0 Ensembl18867,048 - 1,052,606 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.018867,048 - 1,054,047 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.018910,945 - 1,096,505 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.418996,297 - 1,188,288 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1181,162,605 - 1,163,261 (+)NCBI
Celera18629,852 - 811,837 (+)NCBICelera
Cytogenetic Map18p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11564734   PMID:12477932   PMID:23376485   PMID:25204797   PMID:31344978  


Genomics

Comparative Map Data
Colec12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.218732,950 - 920,620 (+)NCBI
Rnor_6.0 Ensembl18867,048 - 1,052,606 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.018867,048 - 1,054,047 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.018910,945 - 1,096,505 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.418996,297 - 1,188,288 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1181,162,605 - 1,163,261 (+)NCBI
Celera18629,852 - 811,837 (+)NCBICelera
Cytogenetic Map18p13NCBI
COLEC12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl18316,737 - 500,722 (-)EnsemblGRCh38hg38GRCh38
GRCh3818316,737 - 500,701 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3718316,737 - 500,701 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3618309,356 - 490,685 (-)NCBINCBI36hg18NCBI36
Build 3418309,355 - 490,685NCBI
Celera18194,506 - 375,871 (-)NCBI
Cytogenetic Map18p11.32NCBI
HuRef18279,136 - 440,551 (-)NCBIHuRef
CHM1_118318,475 - 499,849 (-)NCBICHM1_1
Colec12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39189,707,648 - 9,877,995 (+)NCBIGRCm39mm39
GRCm39 Ensembl189,707,595 - 9,882,644 (+)Ensembl
GRCm38189,707,648 - 9,877,995 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl189,707,595 - 9,882,644 (+)EnsemblGRCm38mm10GRCm38
MGSCv37189,707,646 - 9,877,993 (+)NCBIGRCm37mm9NCBIm37
MGSCv36189,707,675 - 9,877,990 (+)NCBImm8
Celera189,737,717 - 9,907,507 (+)NCBICelera
Cytogenetic Map18A1NCBI
Colec12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554029,468,421 - 9,614,286 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554029,445,419 - 9,614,956 (+)NCBIChiLan1.0ChiLan1.0
COLEC12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11817,461,650 - 17,641,404 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1817,461,678 - 17,640,721 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01813,819,575 - 14,001,383 (+)NCBIMhudiblu_PPA_v0panPan3
COLEC12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl767,193,626 - 67,372,755 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1767,192,191 - 67,373,524 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Colec12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936550169,084 - 350,209 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COLEC12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6105,808,212 - 106,007,730 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16105,808,157 - 106,000,197 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COLEC12
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11859,701,131 - 59,884,445 (-)NCBI
ChlSab1.1 Ensembl1859,699,348 - 59,884,461 (-)Ensembl
Colec12
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477010,860,097 - 11,136,478 (-)NCBI

Position Markers
D18Mit12  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018938,503 - 938,738NCBIRnor6.0
Rnor_5.018982,400 - 982,635UniSTSRnor5.0
RGSC_v3.4181,069,988 - 1,070,224RGDRGSC3.4
RGSC_v3.4181,069,989 - 1,070,224UniSTSRGSC3.4
RGSC_v3.1181,069,989 - 1,070,224RGD
Celera18695,687 - 695,922UniSTS
RH 3.4 Map1827.7UniSTS
RH 3.4 Map1827.7RGD
RH 2.0 Map18834.3RGD
Cytogenetic Map18p13UniSTS
D18Rat114  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018971,826 - 971,979NCBIRnor6.0
Rnor_5.0181,015,723 - 1,015,876UniSTSRnor5.0
RGSC_v3.4181,104,768 - 1,104,921UniSTSRGSC3.4
RGSC_v3.4181,104,767 - 1,104,921RGDRGSC3.4
RGSC_v3.1181,104,768 - 1,104,921RGD
Celera18729,300 - 729,459UniSTS
RH 3.4 Map1831.5RGD
RH 3.4 Map1831.5UniSTS
RH 2.0 Map18840.8RGD
SHRSP x BN Map180.23RGD
Cytogenetic Map18p13UniSTS
D2Rat367  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02264,265,266 - 264,265,491NCBIRnor6.0
Rnor_6.0181,026,832 - 1,027,045NCBIRnor6.0
Rnor_5.0181,070,729 - 1,070,942UniSTSRnor5.0
Rnor_5.02282,393,650 - 282,393,875UniSTSRnor5.0
RGSC_v3.4181,161,596 - 1,161,809UniSTSRGSC3.4
RGSC_v3.42256,054,885 - 256,055,110UniSTSRGSC3.4
RGSC_v3.1181,161,167 - 1,161,810RGD
Celera18785,146 - 785,359UniSTS
Celera2238,774,849 - 238,775,080UniSTS
SHRSP x BN Map2112.4598RGD
SHRSP x BN Map2112.4598UniSTS
Cytogenetic Map18p13UniSTS
D18Chm30  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.018971,885 - 972,267NCBIRnor6.0
Rnor_6.018972,083 - 972,267NCBIRnor6.0
Rnor_5.0181,015,980 - 1,016,164UniSTSRnor5.0
Rnor_5.0181,015,782 - 1,016,164UniSTSRnor5.0
RGSC_v3.4181,105,025 - 1,105,209UniSTSRGSC3.4
RGSC_v3.4181,104,827 - 1,105,209UniSTSRGSC3.4
Celera18729,563 - 729,747UniSTS
Celera18729,359 - 729,747UniSTS
Cytogenetic Map18p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125999214Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125999214Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065494   ⟹   ENSRNOP00000059663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl18867,048 - 1,052,606 (+)Ensembl
RefSeq Acc Id: NM_001025721   ⟹   NP_001020892
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.218732,950 - 920,620 (+)NCBI
Rnor_6.018867,048 - 1,052,608 (+)NCBI
Rnor_5.018910,945 - 1,096,505 (+)NCBI
RGSC_v3.418996,297 - 1,188,288 (+)RGD
Celera18629,852 - 811,837 (+)RGD
Sequence:
RefSeq Acc Id: XM_017600987   ⟹   XP_017456476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0181,005,061 - 1,054,047 (+)NCBI
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:
RefSeq Acc Id: XP_017456476   ⟸   XM_017600987
- Peptide Label: isoform X1
- 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 AssemblyChrPosition (strand)Source
Rnor_6.018867,000 - 867,060EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

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