Ly6a (lymphocyte antigen 6 family member A) - Rat Genome Database

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Gene: Ly6a (lymphocyte antigen 6 family member A) Rattus norvegicus
Analyze
Symbol: Ly6a
Name: lymphocyte antigen 6 family member A
RGD ID: 1307571
Description: Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to act upstream of or within response to bacterium. Predicted to be located in external side of plasma membrane. Predicted to be active in plasma membrane. Orthologous to human LY6H (lymphocyte antigen 6 family member H); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; amitrole.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC362935; Ly6al; lymphocyte antigen 6 complex, locus A; lymphocyte antigen 6 complex, locus A-like
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87109,064,222 - 109,067,757 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.27107,177,191 - 107,189,436 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,183,469 - 107,189,981 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7108,924,268 - 108,927,790 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07111,147,936 - 111,151,458 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07111,093,877 - 111,097,399 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07116,557,519 - 116,561,058 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7116,557,519 - 116,561,208 (-)Ensemblrn6Rnor6.0
Rnor_5.07116,439,542 - 116,453,810 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47113,434,499 - 113,438,036 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,550,953 - 103,554,488 (-)NCBICelera
RGSC_v3.17113,468,728 - 113,523,356 (-)NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
osteoporosis  (ISS)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-diaminotoluene  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid A  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (ISO)
bisphenol A  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
cholesterol  (ISO)
choline  (ISO)
chrysene  (ISO)
ciguatoxin CTX1B  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclophosphamide  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzofurans  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (ISO)
diiodine  (ISO)
dioxygen  (ISO)
diuron  (EXP)
ferric oxide  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
glucose  (ISO)
inulin  (ISO)
isoprenaline  (ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
melatonin  (ISO)
methimazole  (EXP)
methoxychlor  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (ISO)
naphthalene  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propiconazole  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
trichloroethene  (ISO)
triptonide  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ly6a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87109,064,222 - 109,067,757 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.27107,177,191 - 107,189,436 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,183,469 - 107,189,981 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7108,924,268 - 108,927,790 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07111,147,936 - 111,151,458 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07111,093,877 - 111,097,399 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07116,557,519 - 116,561,058 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7116,557,519 - 116,561,208 (-)Ensemblrn6Rnor6.0
Rnor_5.07116,439,542 - 116,453,810 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47113,434,499 - 113,438,036 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,550,953 - 103,554,488 (-)NCBICelera
RGSC_v3.17113,468,728 - 113,523,356 (-)NCBI
Cytogenetic Map7q34NCBI
Ly6a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391574,866,726 - 74,869,880 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1574,866,726 - 74,869,880 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381574,994,877 - 74,998,031 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1574,994,877 - 74,998,031 (-)Ensemblmm10GRCm38
MGSCv371574,825,307 - 74,828,318 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361574,822,132 - 74,825,143 (-)NCBIMGSCv36mm8
Celera1576,500,422 - 76,503,177 (-)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1534.29NCBI

Variants

.
Variants in Ly6a
11 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:61
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000056556
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)731770293110435881Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)771621154114982716Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)773618702118618702Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
1331723Bw25Body weight QTL 253.348body mass (VT:0001259)body weight (CMO:0000012)796700404111672180Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)773557047118557047Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)749682832115766396Rat
10450862Kidm55Kidney mass QTL 554.9kidney mass (VT:0002707)kidney weight (CMO:0000081)772725037117725037Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
10450856Livw4Liver weight QTL 43.8liver mass (VT:0003402)liver weight (CMO:0000092)772725037117725037Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)749682832115766396Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)749682832115766396Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 9 22 63 85 86 57 53 57 3 260 101 11 38 78 65 29 4 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001128099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000056556
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7116,557,520 - 116,561,208 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076594
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7107,183,469 - 107,189,981 (-)Ensembl
Rnor_6.0 Ensembl7116,557,519 - 116,559,993 (-)Ensembl
RefSeq Acc Id: NM_001128099   ⟹   NP_001121571
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87109,064,222 - 109,067,757 (-)NCBI
mRatBN7.27107,183,469 - 107,187,004 (-)NCBI
Rnor_6.07116,557,519 - 116,561,058 (-)NCBI
Rnor_5.07116,439,542 - 116,453,810 (-)NCBI
RGSC_v3.47113,434,499 - 113,438,036 (-)RGD
Celera7103,550,953 - 103,554,488 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001121571 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001121571   ⟸   NM_001128099
- Peptide Label: precursor
- UniProtKB: A0A8I6AQU6 (UniProtKB/TrEMBL)
- Sequence:

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:1307571 AgrOrtholog
BioCyc Gene G2FUF-32995 BioCyc
Ensembl Genes ENSRNOG00000037374 Ensembl
NCBI Gene 362935 ENTREZGENE
PhenoGen Ly6a PhenoGen
RatGTEx ENSRNOG00000037374 RatGTEx
UniProt A0A8I6AQU6 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-06-19 Ly6a  lymphocyte antigen 6 family member A  Ly6a  lymphocyte antigen 6 complex, locus A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2023-04-11 Ly6a  lymphocyte antigen 6 complex, locus A  Ly6al  lymphocyte antigen 6 complex, locus A-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-05 Ly6al  lymphocyte antigen 6 complex, locus A-like  Ly6a_predicted  lymphocyte antigen 6 complex, locus A (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Ly6a_predicted  lymphocyte antigen 6 complex, locus A (predicted)      Symbol and Name status set to approved 70820 APPROVED