Ly49s4 (Ly49 stimulatory receptor 4) - Rat Genome Database

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Gene: Ly49s4 (Ly49 stimulatory receptor 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ly49s4
Name: Ly49 stimulatory receptor 4
RGD ID: 1549723
Description: Predicted to be located in plasma membrane; INTERACTS WITH bisphenol A; vinclozolin.
Type: protein-coding
RefSeq Status: VALIDATED
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84165,807,295 - 165,830,157 (-)NCBIGRCr8
mRatBN7.24164,122,071 - 164,144,931 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4164,122,072 - 164,341,692 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4170,356,098 - 170,378,948 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04166,139,093 - 166,161,947 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04164,773,138 - 164,795,986 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04164,470,396 - 164,493,252 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4164,470,397 - 164,691,405 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04213,152,751 - 213,169,259 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44167,975,701 - 167,998,858 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4152,793,556 - 152,816,558 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
bisphenol A  (EXP)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. The genes and gene organization of the Ly49 region of the rat natural killer cell gene complex. Nylenna O, etal., Eur J Immunol 2005 Jan;35(1):261-72.
2. GOA pipeline RGD automated data pipeline
Additional References at PubMed
PMID:17028855  


Genomics

Variants

.
Variants in Ly49s4
1631 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:69
Interacting mature miRNAs:72
Transcripts:ENSRNOT00000036046
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
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
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
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


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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system renal system reproductive system respiratory system
High
Medium
Low 6 2
Below cutoff 3 6 2 8 2 1 3 3 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078219   ⟹   ENSRNOP00000072569
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4164,139,700 - 164,341,692 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090979   ⟹   ENSRNOP00000069584
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4164,122,072 - 164,341,692 (-)Ensembl
Rnor_6.0 Ensembl4164,470,397 - 164,691,405 (-)Ensembl
RefSeq Acc Id: NR_172009
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84165,807,295 - 165,830,157 (-)NCBI
mRatBN7.24164,122,071 - 164,144,931 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001009487 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAV74505 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069584.2
  ENSRNOP00000072569.2
  ENSRNOP00000072678.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000069584   ⟸   ENSRNOT00000090979
RefSeq Acc Id: ENSRNOP00000072569   ⟸   ENSRNOT00000078219
Protein Domains
C-type lectin   Ly49-like N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JVR1-F1-model_v2 AlphaFold A0A0G2JVR1 1-276 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:1549723 AgrOrtholog
BioCyc Gene G2FUF-42745 BioCyc
Ensembl Genes ENSRNOG00000051447 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000051600 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078219.2 UniProtKB/TrEMBL
  ENSRNOT00000090979.2 UniProtKB/TrEMBL
  ENSRNOT00000091932.2 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  Ly49 UniProtKB/TrEMBL
  NKR-like_CTLD UniProtKB/TrEMBL
KEGG Report rno:494195 UniProtKB/TrEMBL
NCBI Gene 494195 ENTREZGENE
PANTHER KILLER CELL LECTIN-LIKE RECEPTOR 2 UniProtKB/TrEMBL
  KILLER CELL LECTIN-LIKE RECEPTOR, SUBFAMILY A, MEMBER 17 UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/TrEMBL
  Ly49 UniProtKB/TrEMBL
PhenoGen Ly49s4 PhenoGen
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051447 RatGTEx
  ENSRNOG00000051600 RatGTEx
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A0G2JVR1_RAT UniProtKB/TrEMBL
  A0A0G2K3B3_RAT UniProtKB/TrEMBL
  A0A0G2K3K6 ENTREZGENE, UniProtKB/TrEMBL
  Q5MPX1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-09-15 Ly49s4  Ly49 stimulatory receptor 4      Symbol and Name status set to provisional 70820 PROVISIONAL