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    Vldlr very low density lipoprotein receptor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25696, updated on 9-Dec-2024

    Summary

    Official Symbol
    Vldlrprovided by RGD
    Official Full Name
    very low density lipoprotein receptorprovided by RGD
    Primary source
    RGD:3963
    See related
    EnsemblRapid:ENSRNOG00000027491 AllianceGenome:RGD:3963
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable several functions, including reelin receptor activity; very-low-density lipoprotein particle binding activity; and very-low-density lipoprotein particle receptor activity. Involved in several processes, including cellular response to glucose starvation; cellular response to insulin stimulus; and cellular response to lipopolysaccharide. Located in apical part of cell; cell surface; and perinuclear region of cytoplasm. Biomarker of focal segmental glomerulosclerosis and nephrotic syndrome. Human ortholog(s) of this gene implicated in Alzheimer's disease; cerebellar ataxia, impaired intellectual development, and dysequilibrium syndrome 1; and dementia. Orthologous to human VLDLR (very low density lipoprotein receptor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 264.9), Muscle (RPKM 252.4) and 8 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Vldlr in Genome Data Viewer
    Location:
    1q52
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (234239769..234272150)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (224813539..224850400)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (245236819..245273688)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102557104 Neighboring gene uncharacterized LOC120100010 Neighboring gene uncharacterized LOC134485215 Neighboring gene potassium voltage-gated channel modifier subfamily V member 2 Neighboring gene uncharacterized LOC102555808 Neighboring gene pumilio RNA-binding family member 3

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables apolipoprotein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables apolipoprotein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables apolipoprotein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables calcium-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables calcium-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables cargo receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein tyrosine kinase activator activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables reelin receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables reelin receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables very-low-density lipoprotein particle binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables very-low-density lipoprotein particle binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables very-low-density lipoprotein particle receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables very-low-density lipoprotein particle receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables very-low-density lipoprotein particle receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to glucose starvation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to hypoxia IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to insulin stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to interleukin-1 IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cerebral cortex development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glycoprotein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glycoprotein transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in heart development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of dendrite development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of dendrite development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of protein kinase activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in receptor-mediated endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in receptor-mediated endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in reelin-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in reelin-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to hormone IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to nutrient IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to xenobiotic stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in ventral spinal cord development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventral spinal cord development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in very-low-density lipoprotein particle clearance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in very-low-density lipoprotein particle clearance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in very-low-density lipoprotein particle clearance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in clathrin-coated pit IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of receptor complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of receptor complex ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in synapse ISO
    Inferred from Sequence Orthology
    more info
     
    part_of very-low-density lipoprotein particle IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    very low-density lipoprotein receptor
    Names
    VLDL receptor
    VLDL-R

    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_013155.2NP_037287.2  very low-density lipoprotein receptor precursor

      See identical proteins and their annotated locations for NP_037287.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      P98166
      UniProtKB/TrEMBL
      F1LPV2
      Conserved Domains (7) summary
      smart00192
      Location:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:508547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
      pfam00057
      Location:237273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360394
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      234239769..234272150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006231197.4XP_006231259.1  very low-density lipoprotein receptor isoform X1

      See identical proteins and their annotated locations for XP_006231259.1

      UniProtKB/Swiss-Prot
      P98166
      UniProtKB/TrEMBL
      F1LPV2
      Conserved Domains (7) summary
      smart00192
      Location:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:508547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
      pfam00057
      Location:237273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360394
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    2. XM_063282143.1XP_063138213.1  very low-density lipoprotein receptor isoform X2

      UniProtKB/Swiss-Prot
      P98166
    3. XM_039102103.2XP_038958031.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/Swiss-Prot
      P98166
      UniProtKB/TrEMBL
      F1LPV2
      Related
      ENSRNOP00000036229.2, ENSRNOT00000035814.5
      Conserved Domains (7) summary
      smart00192
      Location:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:508547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
      pfam00057
      Location:237273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360394
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    4. XM_063282122.1XP_063138192.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/Swiss-Prot
      P98166
      UniProtKB/TrEMBL
      F1LPV2
    5. XM_063282154.1XP_063138224.1  very low-density lipoprotein receptor isoform X2

      UniProtKB/Swiss-Prot
      P98166
      Related
      ENSRNOP00000105813.1, ENSRNOT00000149801.1
    6. XM_006231198.5XP_006231260.1  very low-density lipoprotein receptor isoform X1

      See identical proteins and their annotated locations for XP_006231260.1

      UniProtKB/Swiss-Prot
      P98166
      UniProtKB/TrEMBL
      F1LPV2
      Conserved Domains (7) summary
      smart00192
      Location:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:508547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
      pfam00057
      Location:237273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360394
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    7. XM_017588829.3XP_017444318.1  very low-density lipoprotein receptor isoform X3

      UniProtKB/Swiss-Prot
      P98166
      Related
      ENSRNOP00000107234.1, ENSRNOT00000167761.1
    8. XM_017588830.3XP_017444319.1  very low-density lipoprotein receptor isoform X4

      UniProtKB/Swiss-Prot
      P98166