Clec6a-ps1 (C-type lectin domain family 6, member A, pseudogene 1) - Rat Genome Database

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Gene: Clec6a-ps1 (C-type lectin domain family 6, member A, pseudogene 1) Rattus norvegicus
Analyze
Symbol: Clec6a-ps1
Name: C-type lectin domain family 6, member A, pseudogene 1
RGD ID: 1359505
Description: Predicted to enable D-mannose binding activity; calcium ion binding activity; and pattern recognition receptor activity. Predicted to be involved in several processes, including detection of yeast; positive regulation of immune response; and positive regulation of macromolecule metabolic process. Predicted to be active in plasma membrane. Orthologous to human CLEC6A (C-type lectin domain containing 6A); INTERACTS WITH Monobutylphthalate; silicon dioxide; (-)-alpha-phellandrene (ortholog).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: PROVISIONAL
Previously known as: C-type lectin domain family 4, member n; Clec4n; DC-associated C-type lectin-2 pseudogene; Dectin-2p
RGD Orthologs
Human
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84158,225,100 - 158,244,722 (+)NCBIGRCr8
mRatBN7.24156,539,408 - 156,559,032 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)NCBImRatBN7.2 Ensembl
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4162,808,935 - 162,813,516 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04158,591,814 - 158,596,395 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04157,237,232 - 157,241,810 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04156,186,251 - 156,219,375 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4156,186,281 - 156,219,346 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.04223,202,953 - 223,236,018 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44159,822,460 - 159,841,743 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14160,067,395 - 160,086,679 (+)NCBI
Celera4145,336,271 - 145,352,372 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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.
Additional References at PubMed
PMID:23911656   PMID:28652405  


Genomics

Comparative Map Data
Clec6a-ps1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84158,225,100 - 158,244,722 (+)NCBIGRCr8
mRatBN7.24156,539,408 - 156,559,032 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)NCBImRatBN7.2 Ensembl
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4162,808,935 - 162,813,516 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04158,591,814 - 158,596,395 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04157,237,232 - 157,241,810 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04156,186,251 - 156,219,375 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4156,186,281 - 156,219,346 (+)NCBIRnor6.0rn6Rnor6.0
Rnor_5.04223,202,953 - 223,236,018 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44159,822,460 - 159,841,743 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14160,067,395 - 160,086,679 (+)NCBI
Celera4145,336,271 - 145,352,372 (+)NCBICelera
Cytogenetic Map4q42NCBI
CLEC6A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38128,455,962 - 8,478,330 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl128,455,962 - 8,478,330 (+)EnsemblGRCh38hg38GRCh38
GRCh37128,608,558 - 8,630,926 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36128,499,858 - 8,522,193 (+)NCBINCBI36Build 36hg18NCBI36
Build 34128,499,857 - 8,522,193NCBI
Celera1210,144,899 - 10,166,924 (+)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef128,391,249 - 8,413,275 (+)NCBIHuRef
CHM1_1128,577,549 - 8,599,900 (+)NCBICHM1_1
T2T-CHM13v2.0128,439,728 - 8,461,787 (+)NCBIT2T-CHM13v2.0

Variants

.
Variants in Clec6a-ps1
87 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
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
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
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)426775591168368347Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
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
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
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
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
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
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
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
731178Oia7Oil induced arthritis QTL 70.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4156050654157232313Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
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
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
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
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
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
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
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
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


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSRNOT00000013330   ⟹   ENSRNOP00000013330
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000067105   ⟹   ENSRNOP00000059978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000068661   ⟹   ENSRNOP00000063466
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114872   ⟹   ENSRNOP00000077398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4156,539,408 - 156,558,605 (+)Ensembl
RefSeq Acc Id: XR_005503857
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,225,100 - 158,244,722 (+)NCBI
mRatBN7.24156,539,408 - 156,559,032 (+)NCBI
RefSeq Acc Id: XR_005503858
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,225,100 - 158,244,722 (+)NCBI
mRatBN7.24156,539,408 - 156,559,032 (+)NCBI
RefSeq Acc Id: XR_005503859
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,225,100 - 158,244,722 (+)NCBI
mRatBN7.24156,539,408 - 156,559,032 (+)NCBI
RefSeq Acc Id: XR_010066266
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84158,225,100 - 158,244,722 (+)NCBI
Protein Sequences
Ensembl Protein ENSRNOP00000013330.8
  ENSRNOP00000059978.4
  ENSRNOP00000063466.4
  ENSRNOP00000077398.1
Ensembl Acc Id: ENSRNOP00000059978   ⟸   ENSRNOT00000067105
Ensembl Acc Id: ENSRNOP00000013330   ⟸   ENSRNOT00000013330
Ensembl Acc Id: ENSRNOP00000077398   ⟸   ENSRNOT00000114872
Ensembl Acc Id: ENSRNOP00000063466   ⟸   ENSRNOT00000068661
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZXM6-F1-model_v2 AlphaFold D3ZXM6 1-205 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:1359505 AgrOrtholog
BioCyc Gene G2FUF-43128 BioCyc
Ensembl Genes ENSRNOG00000010057 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013330.9 UniProtKB/TrEMBL
  ENSRNOT00000067105.4 UniProtKB/TrEMBL
  ENSRNOT00000068661.5 UniProtKB/TrEMBL
  ENSRNOT00000114872.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/TrEMBL
  C-type_lectin/snaclec_domain UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
NCBI Gene 474144 ENTREZGENE
PANTHER C-TYPE LECTIN DOMAIN CONTAINING 10A UniProtKB/TrEMBL
  C-TYPE LECTIN DOMAIN FAMILY 7 MEMBER A-LIKE-RELATED UniProtKB/TrEMBL
  MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
PhenoGen Clec6a-ps1 PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010057 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/TrEMBL
UniProt A0A8I5ZJG7_RAT UniProtKB/TrEMBL
  D3ZVE6_RAT UniProtKB/TrEMBL
  D3ZXM6_RAT UniProtKB/TrEMBL
  V9GZ86_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Clec6a-ps1  C-type lectin domain family 6, member A, pseudogene 1  Clec4n  C-type lectin domain family 4, member n  Data merged from RGD:15003358 737654 PROVISIONAL
2019-11-08 Clec4n  C-type lectin domain family 4, member n      Symbol and Name status set to provisional 45752 PROVISIONAL
2011-06-08 Clec6a-ps1  C-type lectin domain family 6, member A, pseudogene 1  Dectin-2p  DC-associated C-type lectin-2 pseudogene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 Dectin-2p  DC-associated C-type lectin-2 pseudogene      Symbol and Name status set to provisional 70820 PROVISIONAL