Ly96 (lymphocyte antigen 96) - Rat Genome Database

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Gene: Ly96 (lymphocyte antigen 96) Rattus norvegicus
Analyze
Symbol: Ly96
Name: lymphocyte antigen 96
RGD ID: 1302993
Description: Predicted to enable lipopolysaccharide immune receptor activity. Predicted to be involved in pattern recognition receptor signaling pathway; positive regulation of tumor necrosis factor production; and response to lipopolysaccharide. Predicted to act upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway and response to lipopolysaccharide. Predicted to be located in plasma membrane. Predicted to be part of lipopolysaccharide receptor complex. Orthologous to human LY96 (lymphocyte antigen 96); PARTICIPATES IN Toll-like receptor signaling pathway; toxoplasmosis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 4,4'-diaminodiphenylmethane; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LPS co-receptor MD-2; MD-2; MD2
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.252,582,233 - 2,612,357 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl52,582,254 - 2,612,386 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx54,700,247 - 4,729,411 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.056,339,109 - 6,368,273 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.056,037,630 - 6,066,747 (-)NCBIRnor_WKY
Rnor_6.051,972,212 - 1,989,448 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.051,967,544 - 1,984,775 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.451,701,969 - 1,705,247 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera52,204,184 - 2,228,082 (-)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
acetamide  (EXP)
adenosine  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldehydo-D-glucose  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
epoxiconazole  (ISO)
ethanol  (EXP)
ethyl methanesulfonate  (ISO)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fucoxanthin  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indole-3-methanol  (EXP)
indometacin  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
melatonin  (EXP)
mercury dichloride  (EXP)
methamphetamine  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
Morroniside  (ISO)
N-methylformamide  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (ISO)
nickel dichloride  (ISO)
O-methyleugenol  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
platycodin D  (EXP)
prednisolone  (ISO)
propanal  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
succimer  (ISO)
tartrazine  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Toll-like receptors. Moresco EM, etal., Curr Biol. 2011 Jul 12;21(13):R488-93. doi: 10.1016/j.cub.2011.05.039.
2. Myeloid differentiation 2 as a therapeutic target of inflammatory disorders. Park SH, etal., Pharmacol Ther. 2012 Mar;133(3):291-8. doi: 10.1016/j.pharmthera.2011.11.001. Epub 2011 Nov 19.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Innate immune regulation of Serratia marcescens-induced corneal inflammation and infection. Zhou R, etal., Invest Ophthalmol Vis Sci. 2012 Oct 25;53(11):7382-8. doi: 10.1167/iovs.12-10238.
Additional References at PubMed
PMID:10880523   PMID:11274165   PMID:12594207   PMID:16386178   PMID:19252480   PMID:19584052   PMID:20023008   PMID:20646617   PMID:21849156   PMID:23568774   PMID:24380872   PMID:25342286  
PMID:28965884   PMID:33181267   PMID:34112866  


Genomics

Comparative Map Data
Ly96
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.252,582,233 - 2,612,357 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl52,582,254 - 2,612,386 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx54,700,247 - 4,729,411 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.056,339,109 - 6,368,273 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.056,037,630 - 6,066,747 (-)NCBIRnor_WKY
Rnor_6.051,972,212 - 1,989,448 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.051,967,544 - 1,984,775 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.451,701,969 - 1,705,247 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera52,204,184 - 2,228,082 (-)NCBICelera
Cytogenetic Map5q11NCBI
LY96
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38873,991,392 - 74,099,857 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl873,991,392 - 74,029,079 (+)EnsemblGRCh38hg38GRCh38
GRCh37874,903,627 - 74,941,314 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36875,066,144 - 75,103,859 (+)NCBINCBI36Build 36hg18NCBI36
Build 34875,066,143 - 75,103,859NCBI
Celera870,901,437 - 70,939,164 (+)NCBICelera
Cytogenetic Map8q21.11NCBI
HuRef870,394,473 - 70,432,211 (+)NCBIHuRef
CHM1_1874,955,493 - 74,993,242 (+)NCBICHM1_1
T2T-CHM13v2.0874,420,655 - 74,458,331 (+)NCBIT2T-CHM13v2.0
Ly96
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,758,680 - 16,779,829 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,758,275 - 16,779,835 (+)EnsemblGRCm39 Ensembl
GRCm38116,688,456 - 16,709,605 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,688,051 - 16,709,611 (+)EnsemblGRCm38mm10GRCm38
MGSCv37116,678,537 - 16,699,686 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,673,670 - 16,694,819 (+)NCBIMGSCv36mm8
Celera116,621,307 - 16,642,544 (+)NCBICelera
Cytogenetic Map1A3NCBI
Ly96
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554446,356,154 - 6,387,529 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554446,356,121 - 6,387,350 (-)NCBIChiLan1.0ChiLan1.0
LY96
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1872,169,986 - 72,207,380 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl872,169,986 - 72,207,372 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0870,525,058 - 70,567,839 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LY96
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12922,493,757 - 22,515,147 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2922,493,896 - 22,515,117 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2922,758,770 - 22,780,161 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02922,604,586 - 22,625,987 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2922,604,724 - 22,625,957 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12922,663,372 - 22,684,762 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02922,698,527 - 22,719,904 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02922,981,883 - 23,003,258 (+)NCBIUU_Cfam_GSD_1.0
Ly96
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530356,777,115 - 56,795,405 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366482,653,252 - 2,671,453 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LY96
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl461,926,064 - 61,950,697 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1461,919,806 - 61,950,712 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2467,631,664 - 67,656,017 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LY96
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1869,591,885 - 69,629,939 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl869,591,941 - 69,630,274 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603971,667,502 - 71,779,874 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ly96
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474417,208,990 - 17,241,347 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474417,209,285 - 17,241,347 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ly96
78 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:7
Count of miRNA genes:7
Interacting mature miRNAs:7
Transcripts:ENSRNOT00000062050
Prediction methods: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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)522822265904428Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat

Markers in Region
RH134630  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.252,637,816 - 2,638,009 (+)MAPPERmRatBN7.2
Rnor_6.052,020,567 - 2,020,759NCBIRnor6.0
Rnor_5.052,020,235 - 2,020,427UniSTSRnor5.0
RGSC_v3.452,007,241 - 2,007,433UniSTSRGSC3.4
Celera52,259,617 - 2,259,809UniSTS
Cytogenetic Map5q11UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000106635   ⟹   ENSRNOP00000088425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl52,582,254 - 2,612,386 (-)Ensembl
RefSeq Acc Id: NM_001024279   ⟹   NP_001019450
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.252,582,721 - 2,612,357 (-)NCBI
RefSeq Acc Id: XM_039110517   ⟹   XP_038966445
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.252,582,233 - 2,612,102 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_038966445   ⟸   XM_039110517
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001019450   ⟸   NM_001024279
- Peptide Label: precursor
- UniProtKB: Q56DL5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000088425   ⟸   ENSRNOT00000106635
Protein Domains
ML

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:1302993 AgrOrtholog
BioCyc Gene G2FUF-42315 BioCyc
Ensembl Genes ENSRNOG00000067966 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000088425 ENTREZGENE
  ENSRNOP00000088425.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000106635 ENTREZGENE
  ENSRNOT00000106635.1 UniProtKB/TrEMBL
InterPro Ig_E-set UniProtKB/TrEMBL
  LY96 UniProtKB/TrEMBL
  MD-2_lipid-recog UniProtKB/TrEMBL
KEGG Report rno:448830 UniProtKB/TrEMBL
NCBI Gene 448830 ENTREZGENE
PANTHER PTHR15218 UniProtKB/TrEMBL
Pfam E1_DerP2_DerF2 UniProtKB/TrEMBL
PhenoGen Ly96 PhenoGen
SMART SM00737 UniProtKB/TrEMBL
Superfamily-SCOP Ig_E-set UniProtKB/TrEMBL
UniProt Q56DL5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-28 Ly96        Symbol and Name status set to provisional 70820 PROVISIONAL