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

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, Nov 2024]
Expression: Biased expression in Heart (RPKM 264.9), Muscle (RPKM 252.4) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

neuronal stress differentially regulates lipoprotein receptor expression in neurons, with VLDLR upregulation as a common element as a modulator of neuronal Wnt signaling
Title: Stress-induced upregulation of VLDL receptor alters Wnt-signaling in neurons.
VLDLR requires RasGRF1/CaMKII to alter dendritic spine formation.
Title: Very low density lipoprotein receptor regulates dendritic spine formation in a RasGRF1/CaMKII dependent manner.
Data indicate that down-regulation of Mylip/Idol using shRNAs abrogated the decrease in VLDLRs induced by Reelin.
Title: Reciprocal regulation of very low density lipoprotein receptors (VLDLRs) in neurons by brain-derived neurotrophic factor (BDNF) and Reelin: involvement of the E3 ligase Mylip/Idol.
our data suggest that FE65 serves as a link between VLDLR and APP
Title: FE65 as a link between VLDLR and APP to regulate their trafficking and processing.
The present results suggest that very low density lipoprotein receptor was affected by a number of different psychotropic medications commonly used to treat schizophrenia, bipolar disorder, major depression, and autism.
Title: Chronic psychotropic drug treatment causes differential expression of Reelin signaling system in frontal cortex of rats.

Submit: New GeneRIF Correction

General gene information

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Markers

WI-18746 (e-PCR)
- UniSTS:48439

09.MMHAP31FLC3.seq (e-PCR)
- UniSTS:122971

Vldlr (e-PCR), detects polymorphism
- UniSTS:144760

Vldlr (e-PCR), detects polymorphism
- UniSTS:530810

RH94526 (e-PCR)
- UniSTS:119774

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

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Preferred Names: very low-density lipoprotein receptor

Names: VLDL receptor; VLDL-R

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)

NM_013155.2 → NP_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:71 → 103

LDLa; Low-density lipoprotein receptor domain class A

smart00135
Location:508 → 547

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:396 → 426

EGF_CA; Calcium-binding EGF-like domain

cd00112
Location:33 → 67

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:237 → 273

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:568 → 608

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:360 → 394

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

NC_086019.1 Reference GRCr8

Range

234239769..234272150

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006231197.4 → XP_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:71 → 103

LDLa; Low-density lipoprotein receptor domain class A

smart00135
Location:508 → 547

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:396 → 426

EGF_CA; Calcium-binding EGF-like domain

cd00112
Location:33 → 67

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:237 → 273

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:568 → 608

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:360 → 394

FXa_inhibition; Coagulation Factor Xa inhibitory site
XM_063282143.1 → XP_063138213.1 very low-density lipoprotein receptor isoform X2
XM_039102103.2 → XP_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:71 → 103

LDLa; Low-density lipoprotein receptor domain class A

smart00135
Location:508 → 547

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:396 → 426

EGF_CA; Calcium-binding EGF-like domain

cd00112
Location:33 → 67

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:237 → 273

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:568 → 608

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:360 → 394

FXa_inhibition; Coagulation Factor Xa inhibitory site
XM_063282122.1 → XP_063138192.1 very low-density lipoprotein receptor isoform X1

UniProtKB/TrEMBL

F1LPV2
XM_063282154.1 → XP_063138224.1 very low-density lipoprotein receptor isoform X2

Related

ENSRNOP00000105813.1, ENSRNOT00000149801.1
XM_006231198.5 → XP_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:71 → 103

LDLa; Low-density lipoprotein receptor domain class A

smart00135
Location:508 → 547

LY; Low-density lipoprotein-receptor YWTD domain

smart00179
Location:396 → 426

EGF_CA; Calcium-binding EGF-like domain

cd00112
Location:33 → 67

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:237 → 273

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00058
Location:568 → 608

Ldl_recept_b; Low-density lipoprotein receptor repeat class B

pfam14670
Location:360 → 394

FXa_inhibition; Coagulation Factor Xa inhibitory site
XM_017588829.3 → XP_017444318.1 very low-density lipoprotein receptor isoform X3

UniProtKB/Swiss-Prot

P98166

Related

ENSRNOP00000107234.1, ENSRNOT00000167761.1
XM_017588830.3 → XP_017444319.1 very low-density lipoprotein receptor isoform X4

UniProtKB/Swiss-Prot

P98166