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

    Gene ID: 16835, updated on 16-Apr-2024

    Summary

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    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
    NEW
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    Genomic context

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    See Ldlr in Genome Data Viewer
    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_000075.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3818 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:21429854-21430055 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:21456989-21457190 Neighboring gene STARR-seq mESC enhancer starr_23507 Neighboring gene STARR-positive B cell enhancer ABC_E10537 Neighboring gene STARR-positive B cell enhancer ABC_E1109 Neighboring gene predicted gene, 26511 Neighboring gene STARR-positive B cell enhancer ABC_E1379 Neighboring gene STARR-seq mESC enhancer starr_23515 Neighboring gene SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae) Neighboring gene KN motif and ankyrin repeat domains 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. DNA methylation changes underlie the long-term association between periodontitis and atherosclerotic cardiovascular disease. Omar M, et al. Front Cardiovasc Med, 2023. PMID 37153468, Free PMC Article
    2. PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice. Hernandez R, et al. J Lipid Res, 2023 Apr. PMID 36871792, Free PMC Article
    3. Surface LDLR is a major receptor for lipoprotein(a) clearance in male mice lacking PCSK9. Roubtsova A, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2023 Apr. PMID 36708961
    4. Oxidative Stress and Lipid Accumulation Augments Cell Death in LDLR-Deficient RPE Cells and Ldlr(-/-) Mice. Sreekumar PG, et al. Cells, 2022 Dec 22. PMID 36611838, Free PMC Article
    5. Blockade of the BLT1-LTB(4) axis does not affect mast cell migration towards advanced atherosclerotic lesions in LDLr(-/-) mice. Depuydt MAC, et al. Sci Rep, 2022 Nov 1. PMID 36319730, Free PMC Article

    See all (1687) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Lipodystrophic gene Agpat2 deficiency aggravates hyperlipidemia and atherosclerosis in Ldlr[-/-] mice.
      Title: Lipodystrophic gene Agpat2 deficiency aggravates hyperlipidemia and atherosclerosis in Ldlr(-/-) mice.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. Adaptive activation of EFNB2/EPHB4 axis promotes post-metastatic growth of colorectal cancer liver metastases by LDLR-mediated cholesterol uptake.
      Title: Adaptive activation of EFNB2/EPHB4 axis promotes post-metastatic growth of colorectal cancer liver metastases by LDLR-mediated cholesterol uptake.
    Submit: New GeneRIF Correction See all GeneRIFs (337)

    Variation

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    Alleles

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 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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    NEW Try the new Transcript table

    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)

    1. 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

    2. 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

    3. 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

    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

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      21634872..21661215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P35951.2 GenPept UniProtKB/Swiss-Prot:P35951

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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