Lyst lysosomal trafficking regulator [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lystprovided by MGI
Official Full Name: lysosomal trafficking regulatorprovided by MGI
Primary source: MGI:MGI:107448
See related: Ensembl:ENSMUSG00000019726 AllianceGenome:MGI:107448
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: bg; beige; D13Sfk13
Summary: Predicted to enable protein kinase binding activity. Acts upstream of or within several processes, including defense response to other organism; phospholipid homeostasis; and vesicle organization. Located in cytosol. Is expressed in axial skeleton. Used to study Chediak-Higashi syndrome; exfoliation syndrome; and platelet storage pool deficiency. Human ortholog(s) of this gene implicated in Chediak-Higashi syndrome. Orthologous to human LYST (lysosomal trafficking regulator). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 5.4), spleen adult (RPKM 3.5) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 A1; 13 5.28 cM

Exon count:: 55

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (13764896..13953388)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (13590311..13778803)

Chromosome 13 - NC_000079.7 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?

Lyst as a specific regulator of TLR3- and TLR4-mediated TRIF signaling pathways reveals how the regulation of the intracellular membrane trafficking network is functionally linked to specific TLR signaling pathways.
Title: Lysosomal trafficking regulator Lyst links membrane trafficking to toll-like receptor-mediated inflammatory responses.
results identify an association between oxidative damage to lipid membranes and the severity of Lyst-mutant phenotypes, revealing a new mechanism that contributes to pathophysiology involving LYST
Title: Elevated oxidative membrane damage associated with genetic modifiers of Lyst-mutant phenotypes.
These results demonstrated that mutation of the Lyst gene can produce ocular features of human XFS (exfoliation syndrome) and suggested that LYST or LYST-interacting genes may contribute to XFS.
Title: Lyst mutation in mice recapitulates iris defects of human exfoliation syndrome.
The upregulation of LYST/Beige in infected cells functions as a host innate response to limit parasite growth.
Title: Control of parasitophorous vacuole expansion by LYST/Beige restricts the intracellular growth of Leishmania amazonensis.
Apolipoprotein E (ApoE)-deficient beige mice have markedly reduced development of atherosclerotic lesions when fed a chow diet; expression of the beige mutation in all cell types involved in lesion development contributes to atheroprotection.
Title: Expression of the Lyst(beige) mutation is atheroprotective in chow-fed apolipoprotein E-deficient mice.
the Lyst(Ing3618 )allele could represent a new model for adult Chediak-Higashi syndrome with neurological impairment
Title: A missense mutation in the WD40 domain of murine Lyst is linked to severe progressive Purkinje cell degeneration.

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Variation

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Alleles

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

Spontaneous (10) 1 citation
Targeted (3)
Chemically induced (ENU) (14) 1 citation
Radiation induced (1)
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

U52461 (e-PCR)
- UniSTS:125767

U70015 (e-PCR)
- UniSTS:185962

D13Sfk15 (e-PCR), detects polymorphism
- UniSTS:141949

D13Sfk16 (e-PCR), detects polymorphism
- UniSTS:141950

Lyst (e-PCR), detects polymorphism
- UniSTS:226197

Lyst (e-PCR), detects polymorphism
- UniSTS:226198

Lyst (e-PCR), detects polymorphism
- UniSTS:143807

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein kinase binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell mediated immunity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood coagulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within defense response to protozoan	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosome to lysosome transport via multivesicular body sorting pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within granulocyte chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lysosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mast cell secretory granule organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within melanosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within microtubule-based process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in natural killer cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neutrophil mediated immunity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within phagocytosis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within phospholipid homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within phospholipid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pigment granule organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pigmentation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of natural killer cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to xenobiotic stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within secretion of lysosomal enzymes	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in microtubule cytoskeleton	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysosomal-trafficking regulator

Names: CHS1 homolog

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_010748.2 → NP_034878.2 lysosomal-trafficking regulator

See identical proteins and their annotated locations for NP_034878.2

Status: VALIDATED

Source sequence(s)

CT010431, U70015

Consensus CDS

CCDS36597.1

UniProtKB/Swiss-Prot

P97412, Q62403, Q8VBS6

UniProtKB/TrEMBL

G5E8Q0

Related

ENSMUSP00000106188.2, ENSMUST00000110559.3

Conserved Domains (5) summary

smart01026
Location:3118 → 3408

Beach; Beige/BEACH domain

COG2319
Location:3526 → 3764

WD40; WD40 repeat [General function prediction only]

pfam14844
Location:3006 → 3101

PH_BEACH; PH domain associated with Beige/BEACH

sd00039
Location:3555 → 3600

7WD40; WD40 repeat [structural motif]

cl02567
Location:3463 → 3764

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000079.7 Reference GRCm39 C57BL/6J

Range

13764896..13953388

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006516561.2 → XP_006516624.1 lysosomal-trafficking regulator isoform X1

UniProtKB/Swiss-Prot

P97412, Q62403, Q8VBS6

Conserved Domains (4) summary

smart01026
Location:3170 → 3460

Beach; Beige/BEACH domain

sd00039
Location:3607 → 3652

7WD40; WD40 repeat [structural motif]

pfam14844
Location:3058 → 3153

PH_BEACH; PH domain associated with Beige/BEACH

cl29593
Location:3515 → 3816

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_006516562.2 → XP_006516625.1 lysosomal-trafficking regulator isoform X2

UniProtKB/Swiss-Prot

P97412, Q62403, Q8VBS6

Conserved Domains (4) summary

smart01026
Location:3169 → 3459

Beach; Beige/BEACH domain

sd00039
Location:3606 → 3651

7WD40; WD40 repeat [structural motif]

pfam14844
Location:3057 → 3152

PH_BEACH; PH domain associated with Beige/BEACH

cl29593
Location:3514 → 3815

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_006516563.4 → XP_006516626.1 lysosomal-trafficking regulator isoform X3