LY6S (lymphocyte antigen 6 family member S) - Rat Genome Database

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Gene: LY6S (lymphocyte antigen 6 family member S) Homo sapiens
Analyze
Symbol: LY6S
Name: lymphocyte antigen 6 family member S
RGD ID: 38648935
HGNC Page HGNC:54397
Description: Predicted to act upstream of or within response to bacterium. Predicted to be located in external side of plasma membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC105375795; LOC124906792; LY6A; Lymphocyte antigen 6S; uncharacterized LOC105375795; uncharacterized LOC124906792
RGD Orthologs
Mouse
Rat
Bonobo
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388143,040,839 - 143,076,471 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8143,040,839 - 143,048,319 (-)EnsemblGRCh38hg38GRCh38
GRCh378144,122,256 - 144,127,127 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
T2T-CHM13v2.08144,184,770 - 144,189,740 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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  (ISO)
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)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (ISO)
bilirubin IXalpha  (EXP)
bisphenol A  (ISO)
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)
ferric oxide  (ISO)
folic acid  (ISO)
genistein  (ISO)
glucose  (ISO)
inulin  (ISO)
isoprenaline  (ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (ISO)
naphthalene  (ISO)
nickel atom  (EXP)
ozone  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
trichostatin A  (EXP)
triptonide  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:35440514   PMID:36928550  


Genomics

Comparative Map Data
LY6S
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388143,040,839 - 143,076,471 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8143,040,839 - 143,048,319 (-)EnsemblGRCh38hg38GRCh38
GRCh378144,122,256 - 144,127,127 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
T2T-CHM13v2.08144,184,770 - 144,189,740 (-)NCBIT2T-CHM13v2.0
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 Ensembl
GRCm381574,994,877 - 74,998,031 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1574,994,877 - 74,998,031 (-)EnsemblGRCm38mm10GRCm38
MGSCv371574,825,307 - 74,828,318 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361574,822,132 - 74,825,143 (-)NCBIMGSCv36mm8
Celera1576,500,422 - 76,503,177 (-)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1534.29NCBI
Ly6al1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87108,892,342 - 108,898,892 (-)NCBIGRCr8
mRatBN7.27107,011,585 - 107,018,125 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,011,623 - 107,015,179 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.07116,373,318 - 116,377,259 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07116,268,691 - 116,272,614 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47113,242,197 - 113,245,765 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7103,383,921 - 103,387,578 (-)NCBICelera
Cytogenetic Map7q34NCBI
LOC129398654
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27160,501,883 - 160,504,468 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan18136,014,402 - 136,018,734 (-)NCBINHGRI_mPanPan1

Variants

.
Variants in LY6S
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000053678] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3		 pathogenic
GRCh38/hg38 8q24.3(chr8:139004218-145049449)x3 copy number gain See cases [RCV000137340] Chr8:139004218..145049449 [GRCh38]
Chr8:140016461..146274835 [GRCh37]
Chr8:140085643..146245639 [NCBI36]
Chr8:8q24.3		 likely pathogenic
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3		 pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3		 pathogenic
GRCh38/hg38 8q24.3(chr8:141738068-144140607)x1 copy number loss See cases [RCV000140913] Chr8:141738068..144140607 [GRCh38]
Chr8:142764538..145195510 [GRCh37]
Chr8:142823655..145267498 [NCBI36]
Chr8:8q24.3		 pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124498498-145068712)x3 copy number gain See cases [RCV000137346] Chr8:124498498..145068712 [GRCh38]
Chr8:125510739..146294098 [GRCh37]
Chr8:125579920..146264902 [NCBI36]
Chr8:8q24.13-24.3		 pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3		 pathogenic
GRCh38/hg38 8q24.3(chr8:142201468-144002730)x1 copy number loss See cases [RCV000135981] Chr8:142201468..144002730 [GRCh38]
Chr8:143282829..145076898 [GRCh37]
Chr8:143280736..145148886 [NCBI36]
Chr8:8q24.3		 pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3		 pathogenic
GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 copy number gain See cases [RCV000050638] Chr8:113580402..145054634 [GRCh38]
Chr8:114592631..146280020 [GRCh37]
Chr8:114661807..146250824 [NCBI36]
Chr8:8q23.3-24.3		 pathogenic
GRCh38/hg38 8q24.21-24.3(chr8:128220912-145049449)x3 copy number gain See cases [RCV000050830] Chr8:128220912..145049449 [GRCh38]
Chr8:129233158..146274835 [GRCh37]
Chr8:129302340..146245639 [NCBI36]
Chr8:8q24.21-24.3		 pathogenic
GRCh38/hg38 8q24.3(chr8:139236824-145068712)x3 copy number gain See cases [RCV000137466] Chr8:139236824..145068712 [GRCh38]
Chr8:140249067..146294098 [GRCh37]
Chr8:140318249..146264902 [NCBI36]
Chr8:8q24.3		 likely pathogenic
GRCh38/hg38 8q24.22-24.3(chr8:130639182-145068712)x3 copy number gain See cases [RCV000137644] Chr8:130639182..145068712 [GRCh38]
Chr8:131651428..146294098 [GRCh37]
Chr8:131720610..146264902 [NCBI36]
Chr8:8q24.22-24.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3		 pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3		 pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3		 pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3		 pathogenic|likely pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
406960637GWAS609613_Hacute myeloid leukemia QTL GWAS609613 (human)0.000003acute myeloid leukemia8143051052143051053Human


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENST00000706920   ⟹   ENSP00000516627
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl8143,040,839 - 143,045,710 (-)Ensembl
Ensembl Acc Id: ENST00000715543   ⟹   ENSP00000520463
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl8143,040,853 - 143,048,319 (-)Ensembl
Ensembl Acc Id: ENST00000715551   ⟹   ENSP00000520471
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl8143,040,839 - 143,045,706 (-)Ensembl
Ensembl Acc Id: ENST00000715552   ⟹   ENSP00000520472
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl8143,043,025 - 143,045,674 (-)Ensembl
RefSeq Acc Id: NM_001406477   ⟹   NP_001393406
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,040,839 - 143,045,710 (-)NCBI
T2T-CHM13v2.08144,184,770 - 144,189,740 (-)NCBI
RefSeq Acc Id: NM_001406478   ⟹   NP_001393407
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,040,839 - 143,045,710 (-)NCBI
T2T-CHM13v2.08144,184,770 - 144,189,740 (-)NCBI
RefSeq Acc Id: XM_054328424   ⟹   XP_054184399
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,071,063 - 143,076,471 (-)NCBI
RefSeq Acc Id: XM_054328425   ⟹   XP_054184400
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,061,895 - 143,076,471 (-)NCBI
RefSeq Acc Id: XR_008485573
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,040,839 - 143,076,471 (-)NCBI
RefSeq Acc Id: XR_008485574
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,061,895 - 143,063,452 (-)NCBI
Ensembl Acc Id: ENSP00000516627   ⟸   ENST00000706920
RefSeq Acc Id: NP_001393407   ⟸   NM_001406478
- Peptide Label: precursor
- UniProtKB: P0DTL4 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001393406   ⟸   NM_001406477
- Peptide Label: precursor
- UniProtKB: P0DTL4 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054184400   ⟸   XM_054328425
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054184399   ⟸   XM_054328424
- Peptide Label: isoform X1
Ensembl Acc Id: ENSP00000520472   ⟸   ENST00000715552
Ensembl Acc Id: ENSP00000520471   ⟸   ENST00000715551
Ensembl Acc Id: ENSP00000520463   ⟸   ENST00000715543
Protein Domains
UPAR/Ly6


Additional Information

Database Acc Id Source(s)
COSMIC LY6S COSMIC
Ensembl Genes ENSG00000291309 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000706920 ENTREZGENE
  ENST00000706920.2 UniProtKB/Swiss-Prot
  ENST00000715543.1 UniProtKB/TrEMBL
  ENST00000715551 ENTREZGENE
  ENST00000715551.1 UniProtKB/Swiss-Prot
  ENST00000715552.1 UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.60.10 UniProtKB/Swiss-Prot
GTEx ENSG00000291309 GTEx
HGNC ID HGNC:54397 ENTREZGENE
Human Proteome Map LY6S Human Proteome Map
InterPro CD59_antigen_CS UniProtKB/Swiss-Prot
  LY6_UPA_recep-like UniProtKB/Swiss-Prot
  LY6H/LY6L_nAChR_modulators UniProtKB/Swiss-Prot
  Snake_toxin-like_sf UniProtKB/Swiss-Prot
NCBI Gene LOC105375795 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6 COMPLEX, LOCUS G2-RELATED UniProtKB/Swiss-Prot
  LYMPHOCYTE ANTIGEN 6H UniProtKB/Swiss-Prot
Pfam UPAR_LY6 UniProtKB/Swiss-Prot
PharmGKB PA166351944 PharmGKB
PROSITE LY6_UPAR UniProtKB/Swiss-Prot
SMART SM00134 UniProtKB/Swiss-Prot
Superfamily-SCOP Snake toxin-like UniProtKB/Swiss-Prot
UniProt A0AAQ5BIF1_HUMAN UniProtKB/TrEMBL
  LY6S_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-03-23 LY6S  lymphocyte antigen 6 family member S  LOC124906792  uncharacterized LOC124906792  Data merged from RGD:151672182 737654 PROVISIONAL
2022-05-20 LY6S  lymphocyte antigen 6 family member S  LOC105375795  uncharacterized LOC105375795  Symbol and/or name change 5135510 APPROVED