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Lrp4 low density lipoprotein receptor-related protein 4 [ Mus musculus (house mouse) ]

Gene ID: 228357, updated on 12-May-2024

Summary

Official Symbol
Lrp4provided by MGI
Official Full Name
low density lipoprotein receptor-related protein 4provided by MGI
Primary source
MGI:MGI:2442252
See related
Ensembl:ENSMUSG00000027253 AllianceGenome:MGI:2442252
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
mdig; Megf7; D230026E03; 6430526J12Rik
Summary
Enables protein homodimerization activity and receptor tyrosine kinase binding activity. Involved in several processes, including positive regulation of presynaptic membrane organization; positive regulation of skeletal muscle acetylcholine-gated channel clustering; and synapse organization. Acts upstream of or within several processes, including animal organ development; embryonic digit morphogenesis; and regionalization. Located in neuromuscular junction and plasma membrane. Is expressed in several structures, including alimentary system; central nervous system; extraembryonic component; eye; and genitourinary system. Used to study sclerosteosis 2. Human ortholog(s) of this gene implicated in Cenani-Lenz syndactyly syndrome; congenital myasthenic syndrome 17; and sclerosteosis 2. Orthologous to human LRP4 (LDL receptor related protein 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung adult (RPKM 19.7), genital fat pad adult (RPKM 6.0) and 20 other tissues See more
Orthologs
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Genomic context

See Lrp4 in Genome Data Viewer
Location:
2 E1; 2 50.63 cM
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (91287794..91344246)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (91457456..91513901)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3385 Neighboring gene ADP-ribosylation factor GTPase activating protein 2 Neighboring gene centriolar satellite-associated tubulin polyglutamylase complex regulator 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:91148974-91149175 Neighboring gene STARR-seq mESC enhancer starr_05115 Neighboring gene predicted gene 13787 Neighboring gene STARR-positive B cell enhancer ABC_E9518 Neighboring gene STARR-positive B cell enhancer ABC_E5945 Neighboring gene predicted gene 13770 Neighboring gene cytoskeleton associated protein 5 Neighboring gene small nucleolar RNA, C/D box 67

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 apolipoprotein binding ISO
Inferred from Sequence Orthology
more info
 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables coreceptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
enables receptor tyrosine kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables receptor tyrosine kinase binding ISO
Inferred from Sequence Orthology
more info
 
enables scaffold protein binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in amyloid-beta clearance by cellular catabolic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within anatomical structure development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in dendrite morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within dorsal/ventral pattern formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic digit morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within embryonic limb morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in enzyme-linked receptor protein signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in enzyme-linked receptor protein signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in enzyme-linked receptor protein signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in generation of neurons IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within hair follicle development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney development ISO
Inferred from Sequence Orthology
more info
 
involved_in limb development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of axonogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of canonical Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of ossification ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within odontogenesis of dentin-containing tooth IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of Rac protein signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of peptidyl-tyrosine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of presynaptic membrane organization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of skeletal muscle acetylcholine-gated channel clustering IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of skeletal muscle acetylcholine-gated channel clustering IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of skeletal muscle acetylcholine-gated channel clustering IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in postsynaptic membrane assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in presynaptic membrane assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within protein localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within proximal/distal pattern formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within receptor clustering IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of postsynapse assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of postsynapse assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in skeletal muscle acetylcholine-gated channel clustering IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synapse organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in synapse organization ISO
Inferred from Sequence Orthology
more info
 
involved_in synaptic assembly at neuromuscular junction IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within synaptic assembly at neuromuscular junction IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cell surface ISO
Inferred from Sequence Orthology
more info
 
located_in dendrite ISO
Inferred from Sequence Orthology
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in neuromuscular junction IC
Inferred by Curator
more info
PubMed 
located_in neuromuscular junction IDA
Inferred from Direct Assay
more info
PubMed 
located_in neuronal cell body ISO
Inferred from Sequence Orthology
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 raft ISO
Inferred from Sequence Orthology
more info
 
located_in postsynaptic density ISO
Inferred from Sequence Orthology
more info
 
is_active_in synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in synapse IEP
Inferred from Expression Pattern
more info
PubMed 
located_in synaptic membrane ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
low-density lipoprotein receptor-related protein 4
Names
LDLR dan
LRP-4

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_001145857.1NP_001139329.1  low-density lipoprotein receptor-related protein 4 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001139329.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK032360, BC132240, BY753111
    UniProtKB/Swiss-Prot
    Q8VI56
    Related
    ENSMUST00000143874.8
    Conserved Domains (5) summary
    smart00135
    Location:460502
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:270304
    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:70105
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam14670
    Location:358393
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl00057
    Location:390432
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  2. NM_172668.3NP_766256.3  low-density lipoprotein receptor-related protein 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_766256.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF247637, AL691489, BC132240, BY753111, CN533524
    Consensus CDS
    CCDS16432.1
    UniProtKB/Swiss-Prot
    A2AGT4, Q8BPX5, Q8CBB3, Q8CCP5, Q8VI56
    Related
    ENSMUSP00000028689.4, ENSMUST00000028689.4
    Conserved Domains (9) summary
    smart00192
    Location:311343
    LDLa; Low-density lipoprotein receptor domain class A
    smart00135
    Location:505545
    LY; Low-density lipoprotein-receptor YWTD domain
    smart00179
    Location:395434
    EGF_CA; Calcium-binding EGF-like domain
    cd00112
    Location:270304
    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:10851123
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:70105
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:14831523
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:13131348
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:10851277
    NHL; NHL repeat unit of beta-propeller proteins

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    91287794..91344246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036161269.1XP_036017162.1  low-density lipoprotein receptor-related protein 4 isoform X1

    Conserved Domains (5) summary
    smart00135
    Location:59101
    LY; Low-density lipoprotein-receptor YWTD domain
    cd05819
    Location:336374
    NHL; NHL repeat [structural motif]
    cl18310
    Location:336528
    NHL; NHL repeat unit of beta-propeller proteins
    pfam00058
    Location:430470
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:564599
    FXa_inhibition; Coagulation Factor Xa inhibitory site

RNA

  1. XR_374447.5 RNA Sequence

  2. XR_003952488.2 RNA Sequence

  3. XR_004939885.1 RNA Sequence