Ly6g6d (lymphocyte antigen 6 family member G6D) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ly6g6d (lymphocyte antigen 6 family member G6D) Rattus norvegicus
Analyze
Symbol: Ly6g6d
Name: lymphocyte antigen 6 family member G6D
RGD ID: 1303064
Description: Predicted to enable acetylcholine receptor inhibitor activity and identical protein binding activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to be located in plasma membrane and synapse. Predicted to be part of protein-containing complex. Predicted to colocalize with external side of plasma membrane. Orthologous to human LY6G6D (lymphocyte antigen 6 family member G6D); INTERACTS WITH amphetamine; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: G6d; Ly6-D; lymphocyte antigen 6 complex G6D; lymphocyte antigen 6 complex locus protein G6d; lymphocyte antigen 6 complex, locus G6D; Ng25
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,746,630 - 3,757,036 (+)NCBIGRCr8
mRatBN7.2203,741,973 - 3,752,378 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,737,459 - 3,752,248 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,449,058 - 4,451,650 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,811,113 - 3,813,704 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,348,970 - 4,351,588 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,061,849 - 5,064,768 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,061,658 - 5,064,469 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,134,779 - 7,137,689 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,813,286 - 3,816,525 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,813,512 - 3,816,752 (+)NCBI
Celera204,273,961 - 4,276,544 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Genes encoding three new members of the leukocyte antigen 6 superfamily and a novel member of Ig superfamily, together with genes encoding the regulatory nuclear chloride ion channel protein (hRNCC) and an N omega-N omega-dimethylarginine dimethylaminohydrolase homologue, are found in a 30-kb segment of the MHC class III region. Ribas G, etal., J Immunol 1999 Jul 1;163(1):278-87.
Additional References at PubMed
PMID:17008713   PMID:26276394  


Genomics

Comparative Map Data
Ly6g6d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,746,630 - 3,757,036 (+)NCBIGRCr8
mRatBN7.2203,741,973 - 3,752,378 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,737,459 - 3,752,248 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,449,058 - 4,451,650 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,811,113 - 3,813,704 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,348,970 - 4,351,588 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,061,849 - 5,064,768 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,061,658 - 5,064,469 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,134,779 - 7,137,689 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,813,286 - 3,816,525 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,813,512 - 3,816,752 (+)NCBI
Celera204,273,961 - 4,276,544 (-)NCBICelera
Cytogenetic Map20p12NCBI
LY6G6D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,715,348 - 31,717,919 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,715,348 - 31,717,919 (+)EnsemblGRCh38hg38GRCh38
GRCh37631,683,125 - 31,685,696 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,791,112 - 31,793,560 (+)NCBINCBI36Build 36hg18NCBI36
Build 34631,791,111 - 31,793,560NCBI
Celera633,281,361 - 33,283,807 (+)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,469,361 - 31,471,809 (+)NCBIHuRef
CHM1_1631,685,250 - 31,687,698 (+)NCBICHM1_1
T2T-CHM13v2.0631,568,383 - 31,570,952 (+)NCBIT2T-CHM13v2.0
Ly6g6d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,290,318 - 35,300,215 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,290,419 - 35,297,041 (-)EnsemblGRCm39 Ensembl
GRCm381735,071,342 - 35,081,239 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,071,443 - 35,078,065 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,208,293 - 35,211,409 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,679,404 - 34,682,520 (-)NCBIMGSCv36mm8
Celera1738,168,032 - 38,171,148 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
Ly6g6d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437255,257 - 257,407 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955437254,684 - 257,284 (+)NCBIChiLan1.0ChiLan1.0
LY6G6D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,193,030 - 1,197,094 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,193,379 - 1,197,838 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,329,578 - 1,333,558 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,338,388 - 1,342,375 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,338,418 - 1,343,222 (+)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.0121,264,892 - 1,268,878 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,332,330 - 1,336,508 (+)NCBIUU_Cfam_GSD_1.0
Ly6g6d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,494,446 - 24,496,100 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,494,299 - 24,496,562 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ly6g6d
225 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:82
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000001120
Prediction methods:Microtar, Rnahybrid, Targetscan
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
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
737973Pia21Pristane induced arthritis QTL 214.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2036216564606812Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat

Markers in Region
D20Yum52  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,750,098 - 3,750,321 (-)MAPPERmRatBN7.2
Rnor_6.0205,063,709 - 5,063,931NCBIRnor6.0
Rnor_5.0207,136,639 - 7,136,861UniSTSRnor5.0
RGSC_v3.4203,813,787 - 3,814,009UniSTSRGSC3.4
Celera204,275,821 - 4,276,043UniSTS
Cytogenetic Map20p12UniSTS


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1 8 18 16 9 16 1 1 22 32 39 11 1
Below cutoff 2 31 30 18 8 18 4 4 36 3 2 4

Sequence


RefSeq Acc Id: ENSRNOT00000001120   ⟹   ENSRNOP00000001120
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,749,582 - 3,752,248 (+)Ensembl
Rnor_6.0 Ensembl205,061,658 - 5,064,469 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000037613   ⟹   ENSRNOP00000035547
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,737,489 - 3,752,222 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076253   ⟹   ENSRNOP00000068053
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,737,459 - 3,752,222 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097767   ⟹   ENSRNOP00000084821
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,741,973 - 3,752,222 (+)Ensembl
RefSeq Acc Id: NM_001001970   ⟹   NP_001001970
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,754,228 - 3,757,036 (+)NCBI
mRatBN7.2203,749,570 - 3,752,378 (+)NCBI
Rnor_6.0205,061,849 - 5,064,432 (-)NCBI
Rnor_5.0207,134,779 - 7,137,689 (-)NCBI
RGSC_v3.4203,813,286 - 3,816,525 (+)RGD
Celera204,273,961 - 4,276,544 (-)RGD
Sequence:
RefSeq Acc Id: NM_001412147   ⟹   NP_001399076
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,746,630 - 3,757,036 (+)NCBI
mRatBN7.2203,741,973 - 3,752,378 (+)NCBI
RefSeq Acc Id: NP_001001970   ⟸   NM_001001970
- Peptide Label: isoform 1 precursor
- UniProtKB: Q6MG58 (UniProtKB/Swiss-Prot),   A0A1L6ZA45 (UniProtKB/TrEMBL),   A0A1L6ZA25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001120   ⟸   ENSRNOT00000001120
RefSeq Acc Id: ENSRNOP00000068053   ⟸   ENSRNOT00000076253
RefSeq Acc Id: ENSRNOP00000035547   ⟸   ENSRNOT00000037613
RefSeq Acc Id: ENSRNOP00000084821   ⟸   ENSRNOT00000097767
RefSeq Acc Id: NP_001399076   ⟸   NM_001412147
- Peptide Label: isoform 2
- UniProtKB: A6KTS6 (UniProtKB/TrEMBL),   A0A1L6ZA25 (UniProtKB/TrEMBL)
Protein Domains
Ig-like   UPAR/Ly6

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG58-F1-model_v2 AlphaFold Q6MG58 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:1303064 AgrOrtholog
BioCyc Gene G2FUF-4639 BioCyc
Ensembl Genes ENSRNOG00000000844 Ensembl
  ENSRNOG00000027225 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055007105 UniProtKB/Swiss-Prot
  ENSRNOG00055007152 UniProtKB/Swiss-Prot
  ENSRNOG00060004205 UniProtKB/Swiss-Prot
  ENSRNOG00060005815 UniProtKB/Swiss-Prot
  ENSRNOG00065009342 UniProtKB/Swiss-Prot
  ENSRNOG00065032590 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001120 ENTREZGENE
  ENSRNOT00000001120.4 UniProtKB/Swiss-Prot
  ENSRNOT00000037613.6 UniProtKB/TrEMBL
  ENSRNOT00000097767.1 UniProtKB/TrEMBL
  ENSRNOT00055011777 UniProtKB/Swiss-Prot
  ENSRNOT00055011846 UniProtKB/Swiss-Prot
  ENSRNOT00060007018 UniProtKB/Swiss-Prot
  ENSRNOT00060009691 UniProtKB/Swiss-Prot
  ENSRNOT00065014946 UniProtKB/Swiss-Prot
  ENSRNOT00065056048 UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.60.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  LY6G6d/LY6G6f UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Snake_toxin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 415062 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6 COMPLEX LOCUS PROTEIN G6D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYMPHOCYTE ANTIGEN 6 COMPLEX LOCUS PROTEIN G6F UniProtKB/TrEMBL
  PTHR32286 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PhenoGen Ly6g6d PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000844 RatGTEx
  ENSRNOG00000027225 RatGTEx
  ENSRNOG00055007105 RatGTEx
  ENSRNOG00055007152 RatGTEx
  ENSRNOG00060004205 RatGTEx
  ENSRNOG00060005815 RatGTEx
  ENSRNOG00065009342 RatGTEx
  ENSRNOG00065032590 RatGTEx
SMART SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
  SSF57302 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140TAE8_RAT UniProtKB/TrEMBL
  A0A1L6ZA25 ENTREZGENE, UniProtKB/TrEMBL
  A0A1L6ZA26_RAT UniProtKB/TrEMBL
  A0A1L6ZA45 ENTREZGENE, UniProtKB/TrEMBL
  A6KTS6 ENTREZGENE, UniProtKB/TrEMBL
  A6KTS8_RAT UniProtKB/TrEMBL
  LY66D_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A0A1L6ZA30 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Ly6g6d  lymphocyte antigen 6 family member G6D  Ly6g6d  lymphocyte antigen 6 complex, locus G6D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-14 Ly6g6d  lymphocyte antigen 6 complex, locus G6D      Symbol and Name status set to provisional 70820 PROVISIONAL