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

Gene ID: 308571, updated on 27-Nov-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
EnsemblRapid: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 and postsynaptic density membrane. Orthologous to human LRRC4B (leucine rich repeat containing 4B). [provided by Alliance of Genome Resources, Nov 2024]
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, ENSRNOT00000026259.9
    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

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