Ly6a lymphocyte antigen 6 family member A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ly6aprovided by MGI
Official Full Name: lymphocyte antigen 6 family member Aprovided by MGI
Primary source: MGI:MGI:107527
See related: Ensembl:ENSMUSG00000075602 AllianceGenome:MGI:107527
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: TAP; Sca1; Sca-1; Ly-6A.2; Ly-6A/E; Ly-6E.1
Summary: Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Acts upstream of or within response to bacterium. Located in external side of plasma membrane. Is expressed in several structures, including alimentary system; bone marrow; extraembryonic component; metanephros; and uterus. Used to study osteoporosis. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in kidney adult (RPKM 243.9), mammary gland adult (RPKM 162.3) and 15 other tissues See more
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Genomic context

Location:: 15 D3; 15 34.29 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (74866726..74869880, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (74994877..74998031, complement)

Chromosome 15 - NC_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protein LY6E as a candidate for mediating transport of adeno-associated virus across the human blood-brain barrier.
Title: Protein LY6E as a candidate for mediating transport of adeno-associated virus across the human blood-brain barrier.
Sox2 is necessary for androgen ablation-induced neuroendocrine differentiation from Pten null Sca-1(+) prostate luminal cells.
Title: Sox2 is necessary for androgen ablation-induced neuroendocrine differentiation from Pten null Sca-1(+) prostate luminal cells.
Novel Sca-1(+) macrophages modulate the pathogenic progress of endotoxemia.
Title: Novel Sca-1(+) macrophages modulate the pathogenic progress of endotoxemia.
Murine sca1/flk1-positive cells are not endothelial progenitor cells, but B2 lymphocytes.
Title: Murine sca1/flk1-positive cells are not endothelial progenitor cells, but B2 lymphocytes.
Reconstitution of aged BM with young Sca-1(+) cells resulted in effective homing of functional stem cells in the aged heart.
Title: Long-term repopulation of aged bone marrow stem cells using young Sca-1 cells promotes aged heart rejuvenation.
Our findings therefore support the hypothesis that Ly6a protects the bladder from fibrotic remodeling after obstruction, in part by influencing the proliferation of cells responding to the injury
Title: Stem cell antigen/Ly6a protects against bladder fibrosis in mice.
Based on our recent observation that this phenotype is mouse strain dependent, we used whole-exome sequencing-based genetics to map this phenotype to a specific haplotype of lymphocyte antigen 6 complex, locus A (Ly6a) (stem cell antigen-1 [Sca-1]), which encodes a glycosylphosphatidylinositol (GPI)-anchored protein whose function had been thought to be limited to the biology of hematopoiesis
Title: The GPI-Linked Protein LY6A Drives AAV-PHP.B Transport across the Blood-Brain Barrier.
This study observed enrichment in subpopulations of mammary carcinoma cells expressing elevated surface levels of Sca-1 after cytotoxic treatment. Irradiation induces Sca-1-expressing cells with enhanced migratory and metastatic ability.
Title: Genotoxic stress induces Sca-1-expressing metastatic mammary cancer cells.
Colony-forming unit assays revealed that CFU-granulocyte-macrophage formation of bone marrow cells from Fpr2(-/-) mice was significantly reduced. After heat-inactivated bacterial stimulation in the airway, the expansion of c-kit(+) Sca-1(+) cells in bone marrow and recruitment of Ly6G(+) cells to the lungs and CD11b(+)Ly6C(+)TNFalpha(+) cells to the spleen of Fpr2(-/-) mice was significantly reduced.
Title: Deficiency in Fpr2 results in reduced numbers of Lin(-)cKit(+)Sca1(+) myeloid progenitor cells.
Sca-1 mRNA was found to be highly expressed in mouse trophoblasts stem (TS) cells in culture, and in a subset of trophoblast within the chorion and labyrinth layer of the mouse placenta. Further results identified a subpopulation of TS cell-like cells that persist in the mid- to late- gestation mouse placenta as well as a cell surface protein that can be used to identify and isolate these cells.
Title: Sca-1 identifies a trophoblast population with multipotent potential in the mid-gestation mouse placenta.

Submit: New GeneRIF Correction See all GeneRIFs (90)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (8)
Targeted (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Ly6a (e-PCR), detects polymorphism
- UniSTS:463365

NoName (e-PCR)
- UniSTS:495521

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables acetylcholine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables acetylcholine receptor inhibitor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in acetylcholine receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to bacterium	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular anatomical structure	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: lymphocyte antigen 6A-2/6E-1

Names: T-cell-activating protein; lymphocyte antigen 6 complex, locus A; stem cell antigen 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001271416.1 → NP_001258345.1 lymphocyte antigen 6A-2/6E-1 precursor

See identical proteins and their annotated locations for NP_001258345.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.

Source sequence(s)

AC124637

Consensus CDS

CCDS27540.1

UniProtKB/Swiss-Prot

P05533, Q8BPD0

Related

ENSMUSP00000140638.2, ENSMUST00000189068.7

Conserved Domains (1) summary

smart00134
Location:27 → 111

LU; Ly-6 antigen / uPA receptor -like domain
NM_001271417.1 → NP_001258346.1 lymphocyte antigen 6A-2/6E-1 precursor

See identical proteins and their annotated locations for NP_001258346.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.

Source sequence(s)

AC124637, BG085582

Consensus CDS

CCDS27540.1

UniProtKB/Swiss-Prot

P05533, Q8BPD0

Related

ENSMUSP00000140998.2, ENSMUST00000186526.7

Conserved Domains (1) summary

smart00134
Location:27 → 111

LU; Ly-6 antigen / uPA receptor -like domain
NM_001271418.1 → NP_001258347.1 lymphocyte antigen 6A-2/6E-1 precursor

See identical proteins and their annotated locations for NP_001258347.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses two alternate splice sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.

Source sequence(s)

AC124637

Consensus CDS

CCDS27540.1

UniProtKB/Swiss-Prot

P05533, Q8BPD0

Conserved Domains (1) summary

smart00134
Location:27 → 111

LU; Ly-6 antigen / uPA receptor -like domain
NM_001271419.1 → NP_001258348.1 lymphocyte antigen 6A-2/6E-1 precursor

See identical proteins and their annotated locations for NP_001258348.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses two alternate splice sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.

Source sequence(s)

AC124637, J03636

Consensus CDS

CCDS27540.1

UniProtKB/Swiss-Prot

P05533, Q8BPD0

Related

ENSMUSP00000140287.2, ENSMUST00000187994.7

Conserved Domains (1) summary

smart00134
Location:27 → 111

LU; Ly-6 antigen / uPA receptor -like domain
NM_001271446.1 → NP_001258375.1 lymphocyte antigen 6A-2/6E-1 precursor

See identical proteins and their annotated locations for NP_001258375.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses two alternate splice sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.

Source sequence(s)

AC124637

Consensus CDS

CCDS27540.1

UniProtKB/Swiss-Prot

P05533, Q8BPD0

Conserved Domains (1) summary

smart00134
Location:27 → 111

LU; Ly-6 antigen / uPA receptor -like domain
NM_010738.3 → NP_034868.1 lymphocyte antigen 6A-2/6E-1 precursor

See identical proteins and their annotated locations for NP_034868.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.

Source sequence(s)

AC124637, BY228083

Consensus CDS

CCDS27540.1

UniProtKB/Swiss-Prot

P05533, Q8BPD0

Related

ENSMUSP00000140099.2, ENSMUST00000187171.2

Conserved Domains (1) summary

smart00134
Location:27 → 111

LU; Ly-6 antigen / uPA receptor -like domain