Ly6g6e (lymphocyte antigen 6 family member G6E) - Rat Genome Database

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Gene: Ly6g6e (lymphocyte antigen 6 family member G6E) Rattus norvegicus
Analyze
Symbol: Ly6g6e
Name: lymphocyte antigen 6 family member G6E
RGD ID: 1303112
Description: Predicted to enable acetylcholine receptor activator activity and acetylcholine receptor binding activity. Predicted to be involved in acetylcholine receptor signaling pathway and desensitization of G protein-coupled receptor signaling pathway. Predicted to be located in synapse. Predicted to be active in plasma membrane. Orthologous to human LY6G6E (lymphocyte antigen 6 family member G6E (pseudogene)); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: lymphocyte antigen 6 complex G6E; lymphocyte antigen 6 complex, locus G6E
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,749,352 - 3,752,578 (-)NCBIGRCr8
mRatBN7.2203,744,999 - 3,749,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,744,999 - 3,750,849 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,444,330 - 4,446,202 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,806,383 - 3,808,255 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,344,227 - 4,346,110 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,063,148 - 5,069,032 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,067,330 - 5,068,624 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,137,208 - 7,141,962 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,808,707 - 3,810,443 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,808,933 - 3,810,670 (-)NCBI
Celera204,279,251 - 4,280,984 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
plasma membrane  (IBA,ISO)
synapse  (IEA)

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. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:26276394  


Genomics

Comparative Map Data
Ly6g6e
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,749,352 - 3,752,578 (-)NCBIGRCr8
mRatBN7.2203,744,999 - 3,749,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,744,999 - 3,750,849 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,444,330 - 4,446,202 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,806,383 - 3,808,255 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,344,227 - 4,346,110 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,063,148 - 5,069,032 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,067,330 - 5,068,624 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,137,208 - 7,141,962 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,808,707 - 3,810,443 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,808,933 - 3,810,670 (-)NCBI
Celera204,279,251 - 4,280,984 (+)NCBICelera
Cytogenetic Map20p12NCBI
LY6G6E
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,711,976 - 31,714,065 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,712,341 - 31,713,812 (-)EnsemblGRCh38hg38GRCh38
GRCh37631,679,753 - 31,681,842 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,788,092 - 31,789,568 (-)NCBINCBI36Build 36hg18NCBI36
Build 34631,788,091 - 31,789,568NCBI
Celera633,277,981 - 33,280,070 (-)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,465,981 - 31,468,070 (-)NCBIHuRef
CHM1_1631,681,870 - 31,683,959 (-)NCBICHM1_1
T2T-CHM13v2.0631,565,011 - 31,567,100 (-)NCBIT2T-CHM13v2.0
Ly6g6e
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,295,843 - 35,297,781 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,295,878 - 35,297,780 (+)EnsemblGRCm39 Ensembl
GRCm381735,076,868 - 35,078,804 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,076,902 - 35,078,804 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,213,887 - 35,215,749 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,684,998 - 34,686,860 (+)NCBIMGSCv36mm8
Celera1738,173,630 - 38,175,492 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
LOC102154767
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,189,910 - 1,196,762 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,326,477 - 1,335,548 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,335,285 - 1,344,365 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1121,194,600 - 1,203,661 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,261,776 - 1,270,868 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,329,227 - 1,338,498 (-)NCBIUU_Cfam_GSD_1.0
LOC110261493
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1723,823,392 - 23,825,431 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Variants

.
Variants in Ly6g6e
109 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:57
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000037482
Prediction methods:Miranda, 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
RH135060  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,745,135 - 3,745,327 (-)MAPPERmRatBN7.2
Rnor_6.0205,068,704 - 5,068,895NCBIRnor6.0
Rnor_5.0207,141,634 - 7,141,825UniSTSRnor5.0
RGSC_v3.4203,808,844 - 3,809,035UniSTSRGSC3.4
Celera204,280,656 - 4,280,847UniSTS
RH 3.4 Map2052.3UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:498506  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,745,187 - 3,745,935 (-)MAPPERmRatBN7.2
Rnor_6.0205,068,096 - 5,068,843NCBIRnor6.0
Rnor_5.0207,141,026 - 7,141,773UniSTSRnor5.0
RGSC_v3.4203,808,896 - 3,809,643UniSTSRGSC3.4
Celera204,280,048 - 4,280,795UniSTS
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 16 14 19 2
Low 3 29 10 4 11 4 1 1 48 21 19 9 1
Below cutoff 12 29 22 5 22 6 7 10 3 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000037482   ⟹   ENSRNOP00000032019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,744,999 - 3,750,849 (-)Ensembl
Rnor_6.0 Ensembl205,067,330 - 5,068,624 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113254   ⟹   ENSRNOP00000083250
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,744,999 - 3,747,122 (-)Ensembl
RefSeq Acc Id: NM_001001972   ⟹   NP_001001972
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,749,656 - 3,751,392 (-)NCBI
mRatBN7.2203,744,999 - 3,746,736 (-)NCBI
Rnor_6.0205,067,296 - 5,069,032 (+)NCBI
Rnor_5.0207,137,208 - 7,141,962 (+)NCBI
RGSC_v3.4203,808,707 - 3,810,443 (-)RGD
Celera204,279,251 - 4,280,984 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098953   ⟹   XP_038954881
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,749,352 - 3,752,578 (-)NCBI
mRatBN7.2203,745,085 - 3,749,867 (-)NCBI
RefSeq Acc Id: XM_039098955   ⟹   XP_038954883
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,749,352 - 3,752,578 (-)NCBI
mRatBN7.2203,745,085 - 3,748,163 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001001972   ⟸   NM_001001972
- Peptide Label: precursor
- UniProtKB: Q6MG57 (UniProtKB/TrEMBL),   A6KTS9 (UniProtKB/TrEMBL),   A0A1L6ZA33 (UniProtKB/TrEMBL),   A0A1L6ZA28 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032019   ⟸   ENSRNOT00000037482
RefSeq Acc Id: XP_038954881   ⟸   XM_039098953
- Peptide Label: isoform X1
- UniProtKB: A0A1L6ZA28 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954883   ⟸   XM_039098955
- Peptide Label: isoform X2
- UniProtKB: F7FAA3 (UniProtKB/TrEMBL),   A0A1L6ZA28 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083250   ⟸   ENSRNOT00000113254
Protein Domains
Activin types I and II receptor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG57-F1-model_v2 AlphaFold Q6MG57 1-133 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:1303112 AgrOrtholog
BioCyc Gene G2FUF-4640 BioCyc
Ensembl Genes ENSRNOG00000027157 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037482.4 UniProtKB/TrEMBL
  ENSRNOT00000113254.1 UniProtKB/TrEMBL
Gene3D-CATH 2.10.60.10 UniProtKB/TrEMBL
InterPro Activin_recp UniProtKB/TrEMBL
  Ly6g6e UniProtKB/TrEMBL
  Snake_toxin-like_sf UniProtKB/TrEMBL
KEGG Report rno:406866 UniProtKB/TrEMBL
NCBI Gene 406866 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6 FAMILY MEMBER G6E UniProtKB/TrEMBL
  PTHR14569 UniProtKB/TrEMBL
Pfam Activin_recp UniProtKB/TrEMBL
PhenoGen Ly6g6e PhenoGen
RatGTEx ENSRNOG00000027157 RatGTEx
Superfamily-SCOP SSF57302 UniProtKB/TrEMBL
UniProt A0A1L6ZA28 ENTREZGENE, UniProtKB/TrEMBL
  A0A1L6ZA29_RAT UniProtKB/TrEMBL
  A0A1L6ZA33 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZWK8_RAT UniProtKB/TrEMBL
  A6KTS9 ENTREZGENE, UniProtKB/TrEMBL
  F7FAA3 ENTREZGENE, UniProtKB/TrEMBL
  Q6MG57 ENTREZGENE
UniProt Secondary Q6MG57 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Ly6g6e  lymphocyte antigen 6 family member G6E  Ly6g6e  lymphocyte antigen 6 complex, locus G6E  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-14 Ly6g6e  lymphocyte antigen 6 complex, locus G6E      Symbol and Name status set to provisional 70820 PROVISIONAL