Ly6c (Ly6-C antigen) - Rat Genome Database

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Gene: Ly6c (Ly6-C antigen) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ly6c
Name: Ly6-C antigen
RGD ID: 621266
Description: Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to be located in side of membrane and synapse. 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; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100911104; LOC100912078; LOC102552732; Ly6-C antigen gene; lymphocyte antigen 6B-like
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87108,840,263 - 108,844,082 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7108,840,263 - 108,878,007 (-)EnsemblGRCr8
mRatBN7.27106,959,508 - 106,963,329 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7106,959,511 - 106,963,329 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7108,692,924 - 108,696,730 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07110,916,588 - 110,920,394 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07110,862,545 - 110,866,351 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01422,868,518 - 22,872,403 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1422,868,515 - 22,890,958 (-)NCBIrn6Rnor6.0
Rnor_6.0 Ensembl1422,868,515 - 22,890,958 (-)Ensemblrn6Rnor6.0
Rnor_5.01422,767,469 - 22,771,333 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47113,179,070 - 113,182,136NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,332,905 - 103,335,971 (-)NCBICelera
RGSC_v3.17113,213,299 - 113,216,366NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Analysis of three distinct Ly6-A-related cDNA sequences isolated from rat kidney. Friedman S, etal., Immunogenetics 1990;31(2):104-11.
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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Ly6c
14 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:51
Count of miRNA genes:47
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000031916
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 (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
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
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)771621154114982716Rat
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
1331723Bw25Body weight QTL 253.348body mass (VT:0001259)body weight (CMO:0000012)796700404111672180Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
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
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)763889858108889858Rat
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
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
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
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)763889858108889858Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
10450856Livw4Liver weight QTL 43.8liver mass (VT:0003402)liver weight (CMO:0000092)772725037117725037Rat
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
23 4 44 101 109 112 59 105 59 12 374 194 11 61 97 84 53 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000031916   ⟹   ENSRNOP00000032503
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7106,959,511 - 106,963,215 (-)Ensembl
Rnor_6.0 Ensembl1422,868,515 - 22,890,958 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000081444   ⟹   ENSRNOP00000073232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7108,840,263 - 108,878,007 (-)Ensembl
mRatBN7.2 Ensembl7106,959,511 - 106,963,329 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000093784   ⟹   ENSRNOP00000095026
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7106,959,511 - 106,962,647 (-)Ensembl
RefSeq Acc Id: NM_020103   ⟹   NP_064488
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,840,263 - 108,844,082 (-)NCBI
mRatBN7.27106,959,508 - 106,963,329 (-)NCBI
Rnor_5.07116,266,851 - 116,267,012 (-)NCBI
RGSC_v3.47113,179,070 - 113,182,136 (-)RGD
Celera7103,332,905 - 103,335,971 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079794   ⟹   XP_038935722
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,840,268 - 108,843,987 (-)NCBI
mRatBN7.27106,959,508 - 106,963,234 (-)NCBI
Protein Sequences
Protein RefSeqs NP_064488 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935722 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41547 (Get FASTA)   NCBI Sequence Viewer  
  AAA41548 (Get FASTA)   NCBI Sequence Viewer  
  EDM16070 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000073232.2
RefSeq Acc Id: NP_064488   ⟸   NM_020103
- Peptide Label: precursor
- UniProtKB: Q63318 (UniProtKB/TrEMBL),   Q63319 (UniProtKB/TrEMBL),   A0A0G2K4Z4 (UniProtKB/TrEMBL),   Q78EE7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038935722   ⟸   XM_039079794
- Peptide Label: isoform X1
- UniProtKB: Q63319 (UniProtKB/TrEMBL),   Q63318 (UniProtKB/TrEMBL),   A0A0G2K4Z4 (UniProtKB/TrEMBL),   Q78EE7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000032503   ⟸   ENSRNOT00000031916
Ensembl Acc Id: ENSRNOP00000095026   ⟸   ENSRNOT00000093784
Ensembl Acc Id: ENSRNOP00000073232   ⟸   ENSRNOT00000081444
Protein Domains
UPAR/Ly6

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63318-F1-model_v2 AlphaFold Q63318 1-134 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:621266 AgrOrtholog
BioCyc Gene G2FUF-33002 BioCyc
Ensembl Genes ENSRNOG00000023397 Ensembl
  ENSRNOG00000061813 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081444.3 UniProtKB/TrEMBL
Gene3D-CATH 2.10.60.10 UniProtKB/TrEMBL
InterPro LY6_UPA_recep-like UniProtKB/TrEMBL
  LY6H/LY6L_nAChR_modulators UniProtKB/TrEMBL
  Snake_toxin-like_sf UniProtKB/TrEMBL
KEGG Report rno:56778 UniProtKB/TrEMBL
NCBI Gene 56778 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6 COMPLEX, LOCUS G2-RELATED UniProtKB/TrEMBL
  LYMPHOCYTE ANTIGEN 6H UniProtKB/TrEMBL
Pfam UPAR_LY6 UniProtKB/TrEMBL
PhenoGen Ly6c PhenoGen
RatGTEx ENSRNOG00000023397 RatGTEx
  ENSRNOG00000061813 RatGTEx
SMART SM00134 UniProtKB/TrEMBL
Superfamily-SCOP SSF57302 UniProtKB/TrEMBL
UniProt A0A0G2K4Z4 ENTREZGENE, UniProtKB/TrEMBL
  Q63318 ENTREZGENE, UniProtKB/TrEMBL
  Q63319 ENTREZGENE
  Q78EE7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q63319 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ly6c  Ly6-C antigen  LOC100911104  lymphocyte antigen 6B-like  Data merged from RGD:6495044 737654 PROVISIONAL
2015-07-29 Ly6c  Ly6-C antigen  LOC102552732  lymphocyte antigen 6B-like  Data merged from RGD:7695914 737654 PROVISIONAL
2015-07-29 Ly6c  Ly6-C antigen  LOC100912078  lymphocyte antigen 6B-like  Data merged from RGD:6489021 737654 PROVISIONAL
2013-12-18 LOC102552732  lymphocyte antigen 6B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-05 LOC100911104  lymphocyte antigen 6B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-05 LOC100912078  lymphocyte antigen 6B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 Ly6c  Ly6-C antigen    Ly6-C antigen gene  Name updated 1299863 APPROVED
2002-08-07 Ly6c  Ly6-C antigen gene      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed at highest levels in kidney 633190