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

Gene ID: 16835, updated on 8-Feb-2024

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

Preferred Names
low-density lipoprotein receptor
Names
LDL receptor

NCBI Reference Sequences (RefSeq)

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_001252658.1NP_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:669743
    PLN00126; succinate dehydrogenase, cytochrome b subunit family; Provisional
    smart00135
    Location:553595
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:355389
    EGF_CA; Calcium-binding EGF-like domain
    pfam00057
    Location:196232
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:529569
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:319347
    FXa_inhibition; Coagulation Factor Xa inhibitory site
  2. NM_001252659.1NP_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:552594
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:354388
    EGF_CA; Calcium-binding EGF-like domain
    pfam00057
    Location:195231
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:528568
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:318346
    FXa_inhibition; Coagulation Factor Xa inhibitory site
  3. NM_010700.3NP_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:553595
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:355389
    EGF_CA; Calcium-binding EGF-like domain
    pfam00057
    Location:196232
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:529569
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:319347
    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)