Clec4a (C-type lectin domain family 4, member A) - Rat Genome Database

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Gene: Clec4a (C-type lectin domain family 4, member A) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Clec4a
Name: C-type lectin domain family 4, member A
RGD ID: 1359662
Description: Predicted to enable calcium ion binding activity; mannose binding activity; and pattern recognition receptor activity. Predicted to be involved in several processes, including positive regulation of immune response; regulation of cytokine production; and response to fungus. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC4A (C-type lectin domain family 4 member A); INTERACTS WITH (1->4)-beta-D-glucan (ortholog); 1,1-dichloroethene (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 6; C-type lectin domain family 4 member A; C-type lectin superfamily member 6; Clecsf6; Dcir1; dendritic cell inhibitory receptor 1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84158,026,138 - 158,119,904 (+)NCBIGRCr8
mRatBN7.24156,340,439 - 156,434,212 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4156,414,688 - 156,432,402 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4162,678,777 - 162,695,191 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04158,461,653 - 158,478,065 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04157,107,078 - 157,123,494 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04156,049,800 - 156,069,260 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4156,050,054 - 156,069,313 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04223,068,344 - 223,087,733 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44159,692,487 - 159,709,965 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14159,937,404 - 159,954,884 (+)NCBI
Celera4145,221,913 - 145,239,583 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Identification of lectin-like receptors expressed by antigen presenting cells and neutrophils and their mapping to a novel gene complex. Flornes LM, etal., Immunogenetics 2004 Oct;56(7):506-17. Epub 2004 Sep 11.
2. 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.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Clec4a
923 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:23
Count of miRNA genes:22
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000039855
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (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
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
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
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
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)compact 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
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4153031106158841762Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
731178Oia7Oil induced arthritis QTL 70.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4156050654157232313Rat


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 10 3 1
Low 3 29 50 34 9 34 8 10 45 31 26 10 8
Below cutoff 4 3 3 3 1 15 4 8

Sequence


RefSeq Acc Id: ENSRNOT00000039855   ⟹   ENSRNOP00000037071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4156,414,688 - 156,432,402 (+)Ensembl
Rnor_6.0 Ensembl4156,050,054 - 156,067,424 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077840   ⟹   ENSRNOP00000072877
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4156,414,688 - 156,432,402 (+)Ensembl
Rnor_6.0 Ensembl4156,052,009 - 156,067,518 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087933   ⟹   ENSRNOP00000068540
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4156,051,915 - 156,069,313 (+)Ensembl
RefSeq Acc Id: NM_001005899   ⟹   NP_001005899
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,100,615 - 158,118,094 (+)NCBI
mRatBN7.24156,414,923 - 156,432,402 (+)NCBI
Rnor_6.04156,050,040 - 156,067,518 (+)NCBI
Rnor_5.04223,068,344 - 223,087,733 (+)NCBI
RGSC_v3.44159,692,487 - 159,709,965 (+)RGD
Celera4145,221,913 - 145,239,583 (+)RGD
Sequence:
RefSeq Acc Id: XM_017592740   ⟹   XP_017448229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,100,354 - 158,119,904 (+)NCBI
mRatBN7.24156,414,662 - 156,434,212 (+)NCBI
Rnor_6.04156,049,800 - 156,069,260 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592741   ⟹   XP_017448230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,100,354 - 158,118,392 (+)NCBI
mRatBN7.24156,414,662 - 156,432,700 (+)NCBI
Rnor_6.04156,049,800 - 156,067,816 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039108012   ⟹   XP_038963940
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,026,138 - 158,118,392 (+)NCBI
mRatBN7.24156,340,439 - 156,432,700 (+)NCBI
RefSeq Acc Id: XM_063286437   ⟹   XP_063142507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,100,354 - 158,119,904 (+)NCBI
RefSeq Acc Id: XR_005503276
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,100,354 - 158,117,882 (+)NCBI
mRatBN7.24156,414,662 - 156,432,190 (+)NCBI
RefSeq Acc Id: XR_005503277
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,100,354 - 158,117,882 (+)NCBI
mRatBN7.24156,414,662 - 156,432,319 (+)NCBI
RefSeq Acc Id: NP_001005899   ⟸   NM_001005899
- UniProtKB: Q67EQ0 (UniProtKB/Swiss-Prot),   Q56TZ2 (UniProtKB/TrEMBL),   Q2TUM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448229   ⟸   XM_017592740
- Peptide Label: isoform X1
- UniProtKB: Q67EQ0 (UniProtKB/Swiss-Prot),   A0A0G2K425 (UniProtKB/TrEMBL),   Q2TUM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448230   ⟸   XM_017592741
- Peptide Label: isoform X2
- UniProtKB: Q67EQ0 (UniProtKB/Swiss-Prot),   Q2TUM1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068540   ⟸   ENSRNOT00000087933
RefSeq Acc Id: ENSRNOP00000072877   ⟸   ENSRNOT00000077840
RefSeq Acc Id: ENSRNOP00000037071   ⟸   ENSRNOT00000039855
RefSeq Acc Id: XP_038963940   ⟸   XM_039108012
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063142507   ⟸   XM_063286437
- Peptide Label: isoform X2
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q67EQ0-F1-model_v2 AlphaFold Q67EQ0 1-240 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359662 AgrOrtholog
BioCyc Gene G2FUF-43133 BioCyc
Ensembl Genes ENSRNOG00000010045 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039855.4 UniProtKB/TrEMBL
  ENSRNOT00000077840 ENTREZGENE
  ENSRNOT00000077840.2 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:474143 UniProtKB/TrEMBL
NCBI Gene 474143 ENTREZGENE
PANTHER C-TYPE LECTIN DOMAIN FAMILY 19 MEMBER A-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clec4a PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010045 RatGTEx
SMART CLECT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K425 ENTREZGENE, UniProtKB/TrEMBL
  CLC4A_RAT UniProtKB/Swiss-Prot
  F1LRI3_RAT UniProtKB/TrEMBL
  Q2TUM1 ENTREZGENE, UniProtKB/TrEMBL
  Q56TZ2 ENTREZGENE, UniProtKB/TrEMBL
  Q67EQ0 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-06-26 Clec4a  C-type lectin domain family 4, member A  Clecsf6  C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 Clecsf6  C-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 6      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains member of inhibitory C-type lectin superfamily (CLSF) receptors 1359744