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    Lrrc4b leucine rich repeat containing 4B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308571, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Lrrc4bprovided by RGD
    Official Full Name
    leucine rich repeat containing 4Bprovided by RGD
    Primary source
    RGD:1307121
    See related
    Ensembl:ENSRNOG00000019418 AllianceGenome:RGD:1307121
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Lrig4; NGL-3
    Summary
    Predicted to enable signaling receptor binding activity. Involved in regulation of postsynaptic density assembly; regulation of presynapse assembly; and synaptic membrane adhesion. Is active in glutamatergic synapse. Is integral component of postsynaptic density membrane. Orthologous to human LRRC4B (leucine rich repeat containing 4B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Heart (RPKM 318.0), Brain (RPKM 281.0) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrrc4b in Genome Data Viewer
    Location:
    1q22
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (104058558..104092831)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (94922034..94956309)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (100434418..100468914)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene SH3 and multiple ankyrin repeat domains 1 Neighboring gene simlar to human chromosome 19 open reading frame 81 Neighboring gene synaptotagmin 3 Neighboring gene uncharacterized LOC108349570 Neighboring gene aspartate dehydrogenase domain containing Neighboring gene Josephin domain containing 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Trans-synaptic adhesion between NGL-3 and LAR regulates the formation of excitatory synapses. Woo J, et al. Nat Neurosci, 2009 Apr. PMID 19252495
    2. IL-1 receptor accessory protein-like 1 associated with mental retardation and autism mediates synapse formation by trans-synaptic interaction with protein tyrosine phosphatase δ. Yoshida T, et al. J Neurosci, 2011 Sep 21. PMID 21940441, Free PMC Article
    3. NGL family PSD-95-interacting adhesion molecules regulate excitatory synapse formation. Kim S, et al. Nat Neurosci, 2006 Oct. PMID 16980967
    4. mSYD1A, a mammalian synapse-defective-1 protein, regulates synaptogenic signaling and vesicle docking. Wentzel C, et al. Neuron, 2013 Jun 19. PMID 23791195, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables signaling receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of postsynaptic density assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of postsynaptic density assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of postsynaptic density assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of presynapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of presynapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of presynapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synaptic membrane adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic membrane adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic membrane adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cerebellar mossy fiber ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic density membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in presynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 4B
    Names
    netrin-G3 ligand
    protein NGL-3

    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_001271081.1 → NP_001258010.1  leucine-rich repeat-containing protein 4B precursor

      See identical proteins and their annotated locations for NP_001258010.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      P0CC10
      Related
      ENSRNOP00000026259.5, ENSRNOT00000026259.8
      Conserved Domains (6) summary
      smart00013
      Location:59 → 92
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:313 → 363
      LRRCT; Leucine rich repeat C-terminal domain
      COG4886
      Location:89 → 299
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:90 → 113
      LRR_RI; leucine-rich repeat [structural motif]
      pfam07679
      Location:366 → 455
      I-set; Immunoglobulin I-set domain
      cd00096
      Location:366 → 369
      Ig; Ig strand A [structural motif]

    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
      104058558..104092831
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006229055.4 → XP_006229117.1  leucine-rich repeat-containing protein 4B isoform X1

      See identical proteins and their annotated locations for XP_006229117.1

      UniProtKB/Swiss-Prot
      P0CC10
      Conserved Domains (6) summary
      smart00013
      Location:59 → 92
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:313 → 363
      LRRCT; Leucine rich repeat C-terminal domain
      COG4886
      Location:89 → 299
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:90 → 113
      LRR_RI; leucine-rich repeat [structural motif]
      pfam07679
      Location:366 → 455
      I-set; Immunoglobulin I-set domain
      cd00096
      Location:366 → 369
      Ig; Ig strand A [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0CC10.1 GenPept UniProtKB/Swiss-Prot:P0CC10

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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