Ly6e Gene Detail

Summary

• Symbol
  Ly6e
• Name
  lymphocyte antigen 6 complex, locus E
• Synonyms
  9804, Ly67, RIG-E, Sca-2, Tsa1, TSA-1

• Feature Type
  protein coding gene
• IDs
  MGI:106651
  NCBI Gene: 17069
• Member of
  Ly6 cluster
• Gene Overview
  MyGene.info: LY6E
• Alliance
  gene page
• Transcription Start Sites
  36 TSS

Location &
Maps

• Sequence Map
  Chr15:74826900-74831754 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 15, 34.29 cM
• Mapping Data
  7 experiments

Strain
Comparison

• SNPs within 2kb
  40 from dbSNP Build 142
• Strain Annotations
  18
• PCR
  1
• RFLP
  1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_106651	protein coding gene	Chr15:74826874-74831754 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0021945	protein coding gene	Chr15:74772380-74777234 (+)
A/J	MGP_AJ_G0021902	protein coding gene	Chr15:72090723-72096222 (+)
AKR/J	MGP_AKRJ_G0021886	protein coding gene	Chr15:73989411-73994259 (+)
BALB/cJ	MGP_BALBcJ_G0021911	protein coding gene	Chr15:72108624-72113677 (+)
C3H/HeJ	MGP_C3HHeJ_G0021684	protein coding gene	Chr15:74092192-74097250 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022351	protein coding gene	Chr15:77589280-77594134 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0019886	protein coding gene	Chr15:68460179-68465039 (+)
CAST/EiJ	MGP_CASTEiJ_G0021203	protein coding gene	Chr15:74912553-74917406 (+)
CBA/J	MGP_CBAJ_G0021650	protein coding gene	Chr15:80122421-80128837 (+)
DBA/2J	MGP_DBA2J_G0021775	protein coding gene	Chr15:71702331-71707185 (+)
FVB/NJ	MGP_FVBNJ_G0021757	protein coding gene	Chr15:70722703-70727557 (+)
LP/J	MGP_LPJ_G0021847	protein coding gene	Chr15:74856562-74861416 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0021780	protein coding gene	Chr15:85438304-85453376 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022372	protein coding gene	Chr15:74327951-74334619 (+)
PWK/PhJ	MGP_PWKPhJ_G0020944	protein coding gene	Chr15:71802822-71807662 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0020784	protein coding gene	Chr15:74180427-74185272 (+)
WSB/EiJ	MGP_WSBEiJ_G0021255	protein coding gene	Chr15:74356096-74360959 (+)

Homology

• Human Ortholog
  LY6E, lymphocyte antigen 6 family member E

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  LY6E, lymphocyte antigen 6 family member E
  
• Synonyms
  RIGE, RIG-E, SCA2, SCA-2, TSA-1
• Links
  HGNC:6727

  NCBI Gene ID: 4061

  neXtProt AC: NX_Q16553

  UniProt: Q16553

  
  
• Chr Location
  8q24.3; chr8:143018485-143022410 (+)  GRCh38.p7

---

• Alliance of Genome Resources
  Ly6e stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: LY6E
• Gene Tree
  Ly6e
  

Human Diseases

• References
  1 with disease annotations

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  30 phenotypes from 3 alleles in 3 genetic backgrounds
  31 phenotype references
  

• All Mutations and Alleles
  14
• Chemically induced (other)
  3
• Endonuclease-mediated
  1
• Gene trapped
  3
• Radiation induced
  2
• Targeted
  5
• Genomic Mutations
  5 involving Ly6e
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  16 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for disruptions in this gene die as embryos as a result of heart defects.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  15
• GO References
  6

Expression

• Assay Results
  757
• Tissues
  49
• cDNA Data
  890
• Literature Summary
  11

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Interactions

• Ly6e interacts with 171 markers (Mir1a-1, Mir1a-2, Mir1b, ...) View All

Sequences &
Gene Models

• All Sequences
  91
• RefSeq
  16
• UniProt
  8
• CCDS
  CCDS27538.1

• Ensembl
  ENSMUSG00000022587 (Evidence)
• NCBI Gene
  17069

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000022587	Ensembl Gene Model | MGI Sequence Detail	4855	C57BL/6J
transcript	ENSMUST00000188042	Ensembl | MGI Sequence Detail	714	Not Applicable
polypeptide	ENSMUSP00000141059	Ensembl | MGI Sequence Detail	136	Not Applicable

Protein
Information

• UniProt
  8 Sequences
• Protein Ontology
  PR:000009989 lymphocyte antigen 6E
  (term hierarchy)
• InterPro Domains
  IPR016054 Ly-6 antigen/uPA receptor-like

Molecular
Reagents

• All nucleic 895

  Genomic 1

  cDNA 892

  Primer pair 2

  
  

  Microarray probesets 3

Other
Accession IDs

MGD-MRK-15264, MGD-MRK-35109

References

• Summaries
  All 74

  Developmental Gene Expression 11

  Diseases 1

  Gene Ontology 6

  Phenotypes 31
• Earliest
  J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
• Latest
  J:291868 Pfaender S, et al., LY6E impairs coronavirus fusion and confers immune control of viral disease. Nat Microbiol. 2020 Jul 23;

TSS for Ly6e:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr131610	Chr15:74826038-74826046 (+)	-858 bp
Tssr131611	Chr15:74827460-74827478 (+)	569 bp
Tssr131612	Chr15:74827489-74827509 (+)	599 bp
Tssr131613	Chr15:74827755-74827770 (+)	863 bp
Tssr131614	Chr15:74828272-74828330 (+)	1,401 bp
Tssr131615	Chr15:74828967-74828993 (+)	2,080 bp
Tssr131616	Chr15:74828999-74829009 (+)	2,104 bp
Tssr131617	Chr15:74829012-74829027 (+)	2,120 bp
Tssr131618	Chr15:74829029-74829058 (+)	2,144 bp
Tssr131619	Chr15:74829065-74829076 (+)	2,171 bp
Tssr131620	Chr15:74829080-74829095 (+)	2,188 bp
Tssr131621	Chr15:74829096-74829112 (+)	2,204 bp
Tssr131622	Chr15:74829318-74829323 (+)	2,421 bp
Tssr131623	Chr15:74829338-74829356 (+)	2,447 bp
Tssr131624	Chr15:74829421-74829425 (+)	2,523 bp
Tssr131625	Chr15:74829594-74829605 (+)	2,700 bp
Tssr131626	Chr15:74829609-74829644 (+)	2,727 bp
Tssr131627	Chr15:74829646-74829671 (+)	2,759 bp
Tssr131628	Chr15:74830035-74830046 (+)	3,141 bp
Tssr131629	Chr15:74830107-74830219 (+)	3,263 bp
Tssr131630	Chr15:74830333-74830366 (+)	3,450 bp
Tssr131631	Chr15:74830370-74830383 (+)	3,477 bp
Tssr131632	Chr15:74830443-74830454 (+)	3,549 bp
Tssr131633	Chr15:74830482-74830503 (+)	3,593 bp
Tssr131634	Chr15:74830505-74830534 (+)	3,620 bp
Tssr131635	Chr15:74830568-74830596 (+)	3,682 bp
Tssr131636	Chr15:74830654-74830682 (+)	3,768 bp
Tssr131637	Chr15:74830691-74830703 (+)	3,797 bp
Tssr131638	Chr15:74830738-74830749 (+)	3,844 bp
Tssr131639	Chr15:74830756-74830768 (+)	3,862 bp
Tssr131640	Chr15:74830795-74830807 (+)	3,901 bp
Tssr131641	Chr15:74830940-74830951 (+)	4,046 bp
Tssr131642	Chr15:74830952-74830963 (+)	4,058 bp
Tssr131643	Chr15:74830970-74831015 (+)	4,093 bp
Tssr131644	Chr15:74831054-74831063 (+)	4,159 bp
Tssr131645	Chr15:74831072-74831082 (+)	4,177 bp