Clec7a (C-type lectin domain containing 7A) - Rat Genome Database

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Gene: Clec7a (C-type lectin domain containing 7A) Rattus norvegicus
Analyze
Symbol: Clec7a
Name: C-type lectin domain containing 7A
RGD ID: 1565140
Description: Predicted to enable several functions, including (1->3)-beta-D-glucan binding activity; (1->3)-beta-D-glucan immune receptor activity; and identical protein binding activity. Predicted to be involved in several processes, including positive regulation of cytokine production; positive regulation of nitrogen compound metabolic process; and response to fungus. Predicted to act upstream of or within several processes, including phagocytosis, engulfment; positive regulation of tumor necrosis factor production; and response to fungus. Predicted to be located in cytoplasm and external side of plasma membrane. Predicted to be active in cell surface. Human ortholog(s) of this gene implicated in aspergillosis and chronic mucocutaneous candidiasis. Orthologous to human CLEC7A (C-type lectin domain containing 7A); PARTICIPATES IN phagocytosis pathway; tuberculosis pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-type lectin domain family 7 member A; C-type lectin domain family 7, member A; Clec7b; dectin-1; LOC502902; RGD1565140; similar to Clecsf12 protein
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24162,902,731 - 162,913,931 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4162,902,732 - 162,913,897 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4169,137,545 - 169,148,615 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04164,920,504 - 164,931,574 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04163,554,549 - 163,565,619 (-)NCBIRnor_WKY
Rnor_6.04163,216,152 - 163,227,367 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4163,216,163 - 163,227,334 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04211,859,714 - 211,870,889 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44166,723,515 - 166,734,681 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4151,587,575 - 151,598,651 (-)NCBICelera
Cytogenetic Map4q42NCBI
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
1,1-dichloroethene  (ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
butyric acid  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chitosan  (ISO)
chloroprene  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
diarsenic trioxide  (ISO)
dimethylarsinic acid  (ISO)
dioxygen  (EXP)
disulfiram  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenthion  (ISO)
folic acid  (ISO)
formaldehyde  (EXP,ISO)
furan  (ISO)
GW 4064  (ISO)
L-methionine  (ISO)
leukotriene C4  (ISO)
lidocaine  (EXP)
lipopolysaccharide  (ISO)
metam  (ISO)
methylarsonic acid  (ISO)
nickel atom  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
peptidoglycan  (ISO)
phthalaldehyde  (ISO)
protein kinase inhibitor  (ISO)
resveratrol  (ISO)
silicon dioxide  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
succimer  (ISO)
tacrolimus hydrate  (ISO)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
vinclozolin  (EXP)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell recognition  (ISO)
cell surface pattern recognition receptor signaling pathway  (ISO)
cell-cell adhesion  (ISO)
cellular response to molecule of fungal origin  (IBA,ISO)
detection of fungus  (IBA,ISO)
detection of molecule of fungal origin  (IBA,ISO)
detection of yeast  (ISO)
phagocytosis, engulfment  (ISO)
phagocytosis, recognition  (IBA,ISO)
positive regulation of cell maturation  (ISO)
positive regulation of cell migration  (IBA,ISO)
positive regulation of cell population proliferation  (IBA,ISO)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
positive regulation of cytokine production involved in inflammatory response  (IBA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of interleukin-1 beta production  (ISO)
positive regulation of interleukin-10 production  (ISO)
positive regulation of interleukin-12 production  (ISO)
positive regulation of interleukin-2 production  (ISO)
positive regulation of interleukin-6 production  (ISO)
positive regulation of interleukin-8 production  (ISO)
positive regulation of killing of cells of another organism  (IBA,ISO)
positive regulation of lymphocyte activation  (IBA,ISO)
positive regulation of monocyte chemotactic protein-1 production  (ISO)
positive regulation of nitric oxide biosynthetic process  (ISO)
positive regulation of phagocytosis  (IBA,ISO)
positive regulation of protein-containing complex assembly  (ISO)
positive regulation of respiratory burst  (ISO)
positive regulation of superoxide anion generation  (ISO)
positive regulation of tumor necrosis factor production  (ISO)
positive regulation of type II interferon production  (ISO)
positive regulation of wound healing  (IBA,ISO)
response to molecule of fungal origin  (ISO)
response to yeast  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Inhibition of TREM-1 and Dectin-1 Alleviates the Severity of Fungal Keratitis by Modulating Innate Immune Responses. Zhong J, etal., PLoS One. 2016 Mar 10;11(3):e0150114. doi: 10.1371/journal.pone.0150114. eCollection 2016.
Additional References at PubMed
PMID:11567029   PMID:12477932   PMID:18667041   PMID:19358895   PMID:20544345   PMID:21691936   PMID:22267217   PMID:23285072   PMID:24721111   PMID:25246527   PMID:25251945   PMID:32790017  


Genomics

Comparative Map Data
Clec7a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24162,902,731 - 162,913,931 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4162,902,732 - 162,913,897 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4169,137,545 - 169,148,615 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04164,920,504 - 164,931,574 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04163,554,549 - 163,565,619 (-)NCBIRnor_WKY
Rnor_6.04163,216,152 - 163,227,367 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4163,216,163 - 163,227,334 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04211,859,714 - 211,870,889 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44166,723,515 - 166,734,681 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4151,587,575 - 151,598,651 (-)NCBICelera
Cytogenetic Map4q42NCBI
CLEC7A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381210,116,777 - 10,130,304 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1210,116,777 - 10,130,258 (-)EnsemblGRCh38hg38GRCh38
GRCh371210,269,376 - 10,282,798 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361210,160,643 - 10,174,135 (-)NCBINCBI36Build 36hg18NCBI36
Build 341210,171,190 - 10,174,103NCBI
Celera1215,430,059 - 15,443,548 (-)NCBICelera
Cytogenetic Map12p13.2NCBI
HuRef1210,012,523 - 10,026,010 (-)NCBIHuRef
CHM1_11210,238,652 - 10,252,134 (-)NCBICHM1_1
T2T-CHM13v2.01210,003,452 - 10,016,867 (-)NCBIT2T-CHM13v2.0
Clec7a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396129,438,554 - 129,449,748 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6129,438,554 - 129,449,742 (-)EnsemblGRCm39 Ensembl
GRCm386129,461,591 - 129,472,785 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6129,461,591 - 129,472,779 (-)EnsemblGRCm38mm10GRCm38
MGSCv376129,411,609 - 129,422,795 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366129,427,284 - 129,438,465 (-)NCBIMGSCv36mm8
Celera6131,183,577 - 131,194,776 (-)NCBICelera
Cytogenetic Map6F3NCBI
CLEC7A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11210,410,384 - 10,425,452 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1210,410,384 - 10,425,452 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01210,161,780 - 10,174,943 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CLEC7A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12735,852,685 - 35,885,673 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2735,853,099 - 36,007,157 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2710,738,120 - 10,766,549 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02736,203,142 - 36,231,601 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2736,209,883 - 36,264,356 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12736,091,248 - 36,119,494 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02736,120,431 - 36,141,974 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02710,260,084 - 10,288,263 (-)NCBIUU_Cfam_GSD_1.0
Clec7a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494597,304,630 - 97,315,165 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936902436,224 - 446,435 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLEC7A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl561,832,954 - 61,846,434 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1561,832,910 - 61,846,441 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2564,542,875 - 64,556,425 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLEC7A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1119,989,520 - 10,007,442 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl119,995,203 - 10,006,746 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660892,066,063 - 2,084,594 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clec7a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475226,871,292 - 26,891,910 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475226,871,556 - 26,885,778 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
RH130710  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24162,902,903 - 162,903,084 (+)MAPPERmRatBN7.2
Rnor_6.04163,216,335 - 163,216,515NCBIRnor6.0
Rnor_5.04211,859,887 - 211,860,067UniSTSRnor5.0
RGSC_v3.44166,723,688 - 166,723,868UniSTSRGSC3.4
Celera4151,587,748 - 151,587,928UniSTS
RH 3.4 Map41013.4UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:533
Count of miRNA genes:249
Interacting mature miRNAs:295
Transcripts:ENSRNOT00000052373, ENSRNOT00000059885
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 7 2 14 2 1 5 11
Low 3 18 42 31 5 31 5 5 7 22 11 5
Below cutoff 15 8 8 8 3 6 35 10 19 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077793   ⟹   ENSRNOP00000069723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4162,904,376 - 162,913,897 (-)Ensembl
Rnor_6.0 Ensembl4163,217,813 - 163,227,334 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091552   ⟹   ENSRNOP00000073639
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4162,902,732 - 162,913,805 (-)Ensembl
Rnor_6.0 Ensembl4163,216,163 - 163,227,242 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108367   ⟹   ENSRNOP00000087024
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4162,902,732 - 162,913,805 (-)Ensembl
RefSeq Acc Id: NM_001173386   ⟹   NP_001166857
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24162,902,731 - 162,913,805 (-)NCBI
Rnor_6.04163,216,162 - 163,227,242 (-)NCBI
Rnor_5.04211,859,714 - 211,870,889 (-)NCBI
Celera4151,587,575 - 151,598,651 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237100   ⟹   XP_006237162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24162,902,731 - 162,913,924 (-)NCBI
Rnor_6.04163,216,152 - 163,227,365 (-)NCBI
Rnor_5.04211,859,714 - 211,870,889 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108259   ⟹   XP_038964187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24162,905,942 - 162,913,930 (-)NCBI
RefSeq Acc Id: XM_039108260   ⟹   XP_038964188
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24162,907,264 - 162,913,931 (-)NCBI
RefSeq Acc Id: XR_001837491
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24162,904,367 - 162,913,929 (-)NCBI
Rnor_6.04163,217,851 - 163,227,367 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001166857   ⟸   NM_001173386
- UniProtKB: B2RYG9 (UniProtKB/TrEMBL),   B5BUZ1 (UniProtKB/TrEMBL),   E9PTB9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237162   ⟸   XM_006237100
- Peptide Label: isoform X2
- UniProtKB: B5BUZ2 (UniProtKB/TrEMBL),   E9PTT6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069723   ⟸   ENSRNOT00000077793
RefSeq Acc Id: ENSRNOP00000073639   ⟸   ENSRNOT00000091552
RefSeq Acc Id: XP_038964187   ⟸   XM_039108259
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038964188   ⟸   XM_039108260
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000087024   ⟸   ENSRNOT00000108367
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5BUZ1-F1-model_v2 AlphaFold B5BUZ1 1-235 view protein structure

Transcriptome

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

Promoters
RGD ID:13693435
Promoter ID:EPDNEW_R3960
Type:single initiation site
Name:Clec7a_1
Description:C-type lectin domain containing 7A
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_6.04163,227,268 - 163,227,328EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 163224084 163224085 C G snv GH/OmrMcwi (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 211867636 211867637 C G snv GH/OmrMcwi (MCW), Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565140 AgrOrtholog
BioCyc Gene G2FUF-42780 BioCyc
Ensembl Genes ENSRNOG00000054251 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069723.2 UniProtKB/TrEMBL
  ENSRNOP00000073639 ENTREZGENE
  ENSRNOP00000073639.1 UniProtKB/TrEMBL
  ENSRNOP00000087024 ENTREZGENE
  ENSRNOP00000087024.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077793.2 UniProtKB/TrEMBL
  ENSRNOT00000091552 ENTREZGENE
  ENSRNOT00000091552.2 UniProtKB/TrEMBL
  ENSRNOT00000108367 ENTREZGENE
  ENSRNOT00000108367.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7934181 IMAGE-MGC_LOAD
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  CLEC7A UniProtKB/TrEMBL
  NKR-like_CTLD UniProtKB/TrEMBL
KEGG Report rno:502902 UniProtKB/TrEMBL
MGC_CLONE MGC:188550 IMAGE-MGC_LOAD
NCBI Gene 502902 ENTREZGENE
PANTHER PTHR47218 UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec7a PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A0G2JW33_RAT UniProtKB/TrEMBL
  B2RYG9 ENTREZGENE, UniProtKB/TrEMBL
  B5BUZ1 ENTREZGENE, UniProtKB/TrEMBL
  B5BUZ2 ENTREZGENE, UniProtKB/TrEMBL
  E9PTB9 ENTREZGENE
  E9PTT6 ENTREZGENE
UniProt Secondary E9PTB9 UniProtKB/TrEMBL
  E9PTT6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-29 Clec7a  C-type lectin domain containing 7A  Clec7a  C-type lectin domain family 7, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-06-08 Clec7a  C-type lectin domain family 7, member A  Clec7a  C-type lectin domain family 7, member a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Clec7a  C-type lectin domain family 7, member a  RGD1565140_predicted  similar to Clecsf12 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565140_predicted  similar to Clecsf12 protein (predicted)  LOC502902  similar to Clecsf12 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC502902  similar to Clecsf12 protein      Symbol and Name status set to provisional 70820 PROVISIONAL