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ldlra low density lipoprotein receptor a [ Danio rerio (zebrafish) ]

Gene ID: 387529, updated on 11-Apr-2024

Summary

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Official Symbol
ldlraprovided by ZNC
Official Full Name
low density lipoprotein receptor aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-031217-1
See related
Ensembl:ENSDARG00000029476 AllianceGenome:ZFIN:ZDB-GENE-031217-1
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
ldlr
Summary
Enables low-density lipoprotein particle receptor activity. Acts upstream of or within cellular response to lipopolysaccharide; cholesterol homeostasis; and receptor-mediated endocytosis involved in cholesterol transport. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in early endosome and plasma membrane. Is expressed in intestine and liver. 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]
Orthologs
human mouse all
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Genomic context

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See ldlra in Genome Data Viewer
Location:
chromosome: 3
Exon count:
19
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (19299136..19323698)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (19149400..19173958)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene interleukin 12 receptor, beta 2a, like Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4a Neighboring gene KRI1 homolog Neighboring gene SPC24 component of NDC80 kinetochore complex

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. Analysis of mycobacterial infection-induced changes to host lipid metabolism in a zebrafish infection model reveals a conserved role for LDLR in infection susceptibility. Johansen MD, et al. Fish Shellfish Immunol, 2018 Dec. PMID 30219383
  2. Positional cloning of the young mutation identifies an essential role for the Brahma chromatin remodeling complex in mediating retinal cell differentiation. Gregg RG, et al. Proc Natl Acad Sci U S A, 2003 May 27. PMID 12748389, Free PMC Article
  3. A PCR based protocol for detecting indel mutations induced by TALENs and CRISPR/Cas9 in zebrafish. Yu C, et al. PLoS One, 2014. PMID 24901507, Free PMC Article
  4. Anti-hypercholesterolemic Effect of Berbamine Isolated from Rhizoma Coptidis in Hypercholesterolemic Zebrafish Induced by High-Cholesterol Diet. Han B, et al. Iran J Pharm Res, 2018 Winter. PMID 29755560, Free PMC Article
  5. Disruption of ldlr causes increased LDL-c and vascular lipid accumulation in a zebrafish model of hypercholesterolemia. O'Hare EA, et al. J Lipid Res, 2014 Nov. PMID 25201834, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables lipoprotein particle binding IBA
Inferred from Biological aspect of Ancestor
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cellular response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cholesterol homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within endocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in receptor-mediated endocytosis involved in cholesterol transport IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within receptor-mediated endocytosis involved in cholesterol transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of lipid metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
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
  

General protein information

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Preferred Names
low density lipoprotein receptor a; low-density lipoprotein 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)

  1. NM_001030283.1 → NP_001025454.1  low density lipoprotein receptor a precursor

    See identical proteins and their annotated locations for NP_001025454.1

    Status: PROVISIONAL

    Source sequence(s)
    AY218841
    UniProtKB/TrEMBL
    A0A8M1N7V5, F6P6T4, Q7ZZT0
    Related
    ENSDARP00000046296.7, ENSDART00000046297.7
    Conserved Domains (8) summary
    smart00192
    Location:144 → 176
    LDLa; Low-density lipoprotein receptor domain class A
    smart00135
    Location:510 → 551
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:350 → 380
    EGF_CA; Calcium-binding EGF-like domain
    PHA03247
    Location:666 → 808
    PHA03247; large tegument protein UL36; Provisional
    cd00112
    Location:106 → 140
    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 ...
    pfam00058
    Location:485 → 525
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam00057
    Location:231 → 266
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam14670
    Location:314 → 348
    FXa_inhibition; Coagulation Factor Xa inhibitory site

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_007114.7 Reference GRCz11 Primary Assembly

    Range
    19299136..19323698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005163870.4 → XP_005163927.1  low-density lipoprotein receptor isoform X1

    UniProtKB/TrEMBL
    A0A8M2BB14, E9QGD4
    Related
    ENSDARP00000115492.1, ENSDART00000146955.3
    Conserved Domains (7) summary
    smart00192
    Location:144 → 176
    LDLa; Low-density lipoprotein receptor domain class A
    smart00135
    Location:550 → 591
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:350 → 380
    EGF_CA; Calcium-binding EGF-like domain
    cd00112
    Location:106 → 140
    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:192 → 227
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:525 → 565
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:314 → 348
    FXa_inhibition; Coagulation Factor Xa inhibitory site
Nucleotide Protein Strain
Heading Accession and Version

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