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    vldlr very low density lipoprotein receptor [ Danio rerio (zebrafish) ]

    Gene ID: 393897, updated on 11-Apr-2024

    Summary

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    Official Symbol
    vldlrprovided by ZNC
    Official Full Name
    very low density lipoprotein receptorprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-803
    See related
    Ensembl:ENSDARG00000006257 AllianceGenome:ZFIN:ZDB-GENE-040426-803
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:55792
    Summary
    Predicted to enable apolipoprotein binding activity. Predicted to act upstream of or within cholesterol metabolic process; endocytosis; and lipid transport. Predicted to be located in clathrin-coated pit. Predicted to be integral component of membrane. Predicted to be part of very-low-density lipoprotein particle. Predicted to be active in plasma membrane. Is expressed in several structures, including axis; brain; pronephric duct; retinal ganglion cell layer; and spinal cord interneuron. Human ortholog(s) of this gene implicated in Alzheimer's disease; cerebellar ataxia, mental retardation and dysequlibrium syndrome; and dementia. Orthologous to human VLDLR (very low density lipoprotein receptor). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    chromosome: 10
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (15254978..15305144)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (15296859..15347022)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene secreted phosphoprotein 1 Neighboring gene SH3-domain binding protein 2 Neighboring gene potassium channel, subfamily V, member 2a Neighboring gene pumilio RNA-binding family member 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. An Attractive Reelin Gradient Establishes Synaptic Lamination in the Vertebrate Visual System. Di Donato V, et al. Neuron, 2018 Mar 7. PMID 29429939
    2. Role of Reelin in cell positioning in the cerebellum and the cerebellum-like structure in zebrafish. Nimura T, et al. Dev Biol, 2019 Nov 15. PMID 31323192
    3. Dynamic changes in the gene expression of zebrafish Reelin receptors during embryogenesis and hatching period. Imai H, et al. Dev Growth Differ, 2012 Feb. PMID 22364494
    4. Lrp13 is a novel vertebrate lipoprotein receptor that binds vitellogenins in teleost fishes. Reading BJ, et al. J Lipid Res, 2014 Nov. PMID 25217480, Free PMC Article
    5. Hypoxia-inducible factor 3 is an oxygen-dependent transcription activator and regulates a distinct transcriptional response to hypoxia. Zhang P, et al. Cell Rep, 2014 Mar 27. PMID 24613356

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC55792

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables apolipoprotein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    very low-density lipoprotein receptor
    Names
    lr8

    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)

    1. NM_200923.2 → NP_957217.2  very low-density lipoprotein receptor precursor

      Status: VALIDATED

      Source sequence(s)
      CR628386
      UniProtKB/TrEMBL
      A0A8M1PDP0, E7FF13
      Related
      ENSDARP00000020206.7, ENSDART00000023766.9
      Conserved Domains (9) summary
      smart00192
      Location:67 → 99
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:588 → 630
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:392 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:29 → 63
      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 ...
      cd05819
      Location:511 → 551
      NHL; NHL repeat [structural motif]
      pfam00057
      Location:234 → 269
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:564 → 604
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:356 → 390
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl18310
      Location:479 → 570
      NHL; NHL repeat unit of beta-propeller proteins

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007121.7 Reference GRCz11 Primary Assembly

      Range
      15254978..15305144
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005155562.4 → XP_005155619.1  very low-density lipoprotein receptor isoform X2

      UniProtKB/TrEMBL
      A0A8M2B226
      Conserved Domains (10) summary
      smart00192
      Location:67 → 99
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:588 → 630
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:392 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:29 → 63
      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 ...
      pfam01456
      Location:723 → 817
      Mucin; Mucin-like glycoprotein
      cd05819
      Location:511 → 551
      NHL; NHL repeat [structural motif]
      pfam00057
      Location:234 → 269
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:564 → 604
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:356 → 390
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl18310
      Location:479 → 570
      NHL; NHL repeat unit of beta-propeller proteins

    2. XM_005155561.4 → XP_005155618.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/TrEMBL
      A0A8M2B1M8
      Conserved Domains (10) summary
      smart00192
      Location:67 → 99
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:588 → 630
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:392 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:29 → 63
      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 ...
      pfam01456
      Location:723 → 817
      Mucin; Mucin-like glycoprotein
      cd05819
      Location:511 → 551
      NHL; NHL repeat [structural motif]
      pfam00057
      Location:234 → 269
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:564 → 604
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:356 → 390
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl18310
      Location:479 → 570
      NHL; NHL repeat unit of beta-propeller proteins

    3. XM_005155563.4 → XP_005155620.1  very low-density lipoprotein receptor isoform X3

      UniProtKB/TrEMBL
      A0A0R4IGN2, A0A8M2B2G0
      Related
      ENSDARP00000134555.2, ENSDART00000172107.2
      Conserved Domains (9) summary
      smart00192
      Location:67 → 99
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:588 → 630
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:392 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:29 → 63
      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 ...
      cd05819
      Location:511 → 551
      NHL; NHL repeat [structural motif]
      pfam00057
      Location:234 → 269
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:564 → 604
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:356 → 390
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl18310
      Location:479 → 570
      NHL; NHL repeat unit of beta-propeller proteins

    4. XM_021479122.1 → XP_021334797.1  very low-density lipoprotein receptor isoform X4

      UniProtKB/TrEMBL
      A0A8M9PTE7
      Related
      ENSDARP00000154890.1, ENSDART00000183413.1
      Conserved Domains (9) summary
      smart00192
      Location:67 → 99
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:588 → 630
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:392 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:29 → 63
      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 ...
      cd05819
      Location:511 → 551
      NHL; NHL repeat [structural motif]
      pfam00057
      Location:234 → 269
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:564 → 604
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      cl18310
      Location:479 → 570
      NHL; NHL repeat unit of beta-propeller proteins
      pfam14670
      Location:356 → 390
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    5. XM_005155564.4 → XP_005155621.1  very low-density lipoprotein receptor isoform X5

      UniProtKB/TrEMBL
      A0A8M2B2A5, E9QBA5
      Related
      ENSDARP00000121485.1, ENSDART00000139047.2
      Conserved Domains (9) summary
      smart00192
      Location:67 → 99
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:588 → 630
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:392 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:29 → 63
      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 ...
      cd05819
      Location:511 → 551
      NHL; NHL repeat [structural motif]
      pfam00057
      Location:234 → 269
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:564 → 604
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:356 → 390
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl18310
      Location:479 → 570
      NHL; NHL repeat unit of beta-propeller proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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