Ldlr low density lipoprotein receptor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ldlrprovided by MGI
Official Full Name: low density lipoprotein receptorprovided by MGI
Primary source: MGI:MGI:96765
See related: Ensembl:ENSMUSG00000032193 AllianceGenome:MGI:96765
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: Hlb301
Summary: Enables several functions, including amyloid-beta binding activity; low-density lipoprotein particle binding activity; and low-density lipoprotein particle receptor activity. Involved in several processes, including lipid transport; regulation of inflammatory response; and regulation of lipid metabolic process. Acts upstream of or within several processes, including cholesterol homeostasis; lipoprotein catabolic process; and low-density lipoprotein particle clearance. Located in several cellular components, including basolateral plasma membrane; endosome; and lysosome. Is expressed in several structures, including alimentary system; genitourinary system; musculoskeletal system; paravertebral ganglion; and sensory organ. Used to study familial hypercholesterolemia and fatty liver disease. Human ortholog(s) of this gene implicated in Alzheimer's disease; arteriosclerosis; familial hypercholesterolemia; hepatitis C; and migraine without aura. Orthologous to human LDLR (low density lipoprotein receptor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in colon adult (RPKM 56.3), adrenal adult (RPKM 52.3) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 A3; 9 7.87 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (21634872..21661215)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (21723576..21749919)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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?

Crimean-Congo haemorrhagic fever virus uses LDLR to bind and enter host cells.
Title: Crimean-Congo haemorrhagic fever virus uses LDLR to bind and enter host cells.
Deletion of Elovl5 leads to dyslipidemia and atherosclerosis in LDLR-deficient mice.
Title: Deletion of Elovl5 leads to dyslipidemia and atherosclerosis in LDLR-deficient mice.
Lipodystrophic gene Agpat2 deficiency aggravates hyperlipidemia and atherosclerosis in Ldlr[-/-] mice.
Title: Lipodystrophic gene Agpat2 deficiency aggravates hyperlipidemia and atherosclerosis in Ldlr(-/-) mice.
Proteolysis of the low-density lipoprotein receptor in hepatocytes is mediated by BMP1 but not by other astacin proteases.
Title: Proteolysis of the low-density lipoprotein receptor in hepatocytes is mediated by BMP1 but not by other astacin proteases.
The extent of damage to the blood-brain barrier in the hypercholesterolemic LDLR[-/-]/Apo E[-/-] double knockout mice depends on the animal's age, duration of pathology and brain area.
Title: The extent of damage to the blood-brain barrier in the hypercholesterolemic LDLR(-/-)/Apo E(-/-) double knockout mice depends on the animal's age, duration of pathology and brain area.
Trib1 Deficiency Promotes Hyperlipidemia, Inflammation, and Atherosclerosis in LDL Receptor Knockout Mice.
Title: Trib1 Deficiency Promotes Hyperlipidemia, Inflammation, and Atherosclerosis in LDL Receptor Knockout Mice.
PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice.
Title: PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice.
Surface LDLR is a major receptor for lipoprotein(a) clearance in male mice lacking PCSK9.
Title: Surface LDLR is a major receptor for lipoprotein(a) clearance in male mice lacking PCSK9.
Oxidative Stress and Lipid Accumulation Augments Cell Death in LDLR-Deficient RPE Cells and Ldlr[-/-] Mice.
Title: Oxidative Stress and Lipid Accumulation Augments Cell Death in LDLR-Deficient RPE Cells and Ldlr(-/-) Mice.
PCSK9 deficiency results in a specific shedding of excess LDLR in female mice only: Role of hepatic cholesterol.
Title: PCSK9 deficiency results in a specific shedding of excess LDLR in female mice only: Role of hepatic cholesterol.

Submit: New GeneRIF Correction See all GeneRIFs (338)

Variation

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Alleles

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

Chemically induced (ENU) (2)
Endonuclease-mediated (9) 1 citation
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU048745 (e-PCR)
- UniSTS:145195

NoName (e-PCR)
- UniSTS:225086

Ldlr (e-PCR), detects polymorphism
- UniSTS:532556

Ldlr (e-PCR), detects polymorphism
- UniSTS:143767

Ldlr (e-PCR), detects polymorphism
- UniSTS:508396

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables amyloid-beta binding	IPI Inferred from Physical Interaction more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables lipoprotein particle binding	IBA Inferred from Biological aspect of Ancestor more info
enables low-density lipoprotein particle binding	IDA Inferred from Direct Assay more info	PubMed
enables low-density lipoprotein particle binding	ISO Inferred from Sequence Orthology more info
enables low-density lipoprotein particle receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables low-density lipoprotein particle receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables low-density lipoprotein particle receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables low-density lipoprotein particle receptor activity	ISO Inferred from Sequence Orthology more info
enables low-density lipoprotein particle receptor activity	TAS Traceable Author Statement more info
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info
enables protease binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables very-low-density lipoprotein particle receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables very-low-density lipoprotein particle receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in amyloid-beta clearance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in amyloid-beta clearance by cellular catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in artery morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to fatty acid	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to low-density lipoprotein particle stimulus	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cholesterol homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cholesterol homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cholesterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol import	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol import	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in endocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of localization in cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in high-density lipoprotein particle clearance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in intestinal cholesterol absorption	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipid metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lipid transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipoprotein catabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within lipoprotein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lipoprotein metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in long-term memory	IGI Inferred from Genetic Interaction more info	PubMed
involved_in long-term memory	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within low-density lipoprotein particle clearance	IDA Inferred from Direct Assay more info	PubMed
involved_in low-density lipoprotein particle clearance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in low-density lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of amyloid fibril formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of astrocyte activation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of low-density lipoprotein particle clearance	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of microglial cell activation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of protein metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of receptor recycling	ISO Inferred from Sequence Orthology more info
involved_in phagocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in plasma lipoprotein particle clearance	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of inflammatory response	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of lysosomal protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of triglyceride biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of triglyceride catabolic process	ISO Inferred from Sequence Orthology more info
involved_in receptor-mediated endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor-mediated endocytosis involved in cholesterol transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in receptor-mediated endocytosis involved in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of cholesterol metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of phosphatidylcholine catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of protein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in response to caloric restriction	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to caloric restriction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within steroid metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of PCSK9-LDLR complex	ISO Inferred from Sequence Orthology more info
located_in apical part of cell	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in caveola	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated pit	ISO Inferred from Sequence Orthology more info
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
located_in extracellular space	HDA more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	ISO Inferred from Sequence Orthology more info
part_of low-density lipoprotein particle	IEA Inferred from Electronic Annotation more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info	PubMed
located_in recycling endosome membrane	ISO Inferred from Sequence Orthology more info
located_in somatodendritic compartment	IDA Inferred from Direct Assay more info	PubMed
located_in sorting endosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: low-density lipoprotein receptor

Names: LDL receptor

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_001252658.1 → NP_001239587.1 low-density lipoprotein receptor isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.

Source sequence(s)

AC161371, BC053041

Consensus CDS

CCDS90516.1

UniProtKB/TrEMBL

A0A1L1SRE8, Q3TDD1

Related

ENSMUSP00000149431.2, ENSMUST00000213114.2

Conserved Domains (6) summary

PLN00126
Location:669 → 743

PLN00126; succinate dehydrogenase, cytochrome b subunit family; Provisional

smart00135
Location:553 → 595

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:355 → 389

EGF_CA; Calcium-binding EGF-like domain

pfam00057
Location:196 → 232

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:529 → 569

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:319 → 347

FXa_inhibition; Coagulation Factor Xa inhibitory site
NM_001252659.1 → NP_001239588.1 low-density lipoprotein receptor isoform 3 presursor precursor

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.

Source sequence(s)

AC161371, BC053041

UniProtKB/TrEMBL

Q3TVR4, Q3U8R7, Q8VCT0

Conserved Domains (5) summary

smart00135
Location:552 → 594

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:354 → 388

EGF_CA; Calcium-binding EGF-like domain

pfam00057
Location:195 → 231

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:528 → 568

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:318 → 346

FXa_inhibition; Coagulation Factor Xa inhibitory site
NM_010700.3 → NP_034830.2 low-density lipoprotein receptor isoform 1 precursor

See identical proteins and their annotated locations for NP_034830.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC161371, BC053041

Consensus CDS

CCDS22910.1

UniProtKB/Swiss-Prot

P35951, Q6GTJ9

UniProtKB/TrEMBL

Q3TVR4, Q3U8R7, Q8VCT0

Related

ENSMUSP00000034713.8, ENSMUST00000034713.9

Conserved Domains (5) summary

smart00135
Location:553 → 595

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:355 → 389

EGF_CA; Calcium-binding EGF-like domain

pfam00057
Location:196 → 232

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:529 → 569

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:319 → 347

FXa_inhibition; Coagulation Factor Xa inhibitory site