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    Lrfn4 leucine rich repeat and fibronectin type III domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 225875, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Lrfn4provided by MGI
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 4provided by MGI
    Primary source
    MGI:MGI:2385612
    See related
    Ensembl:ENSMUSG00000045045 AllianceGenome:MGI:2385612
    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
    Salm3
    Summary
    Involved in regulation of postsynaptic density assembly; regulation of presynapse assembly; and synaptic membrane adhesion. Located in cell surface. Is active in GABA-ergic synapse and glutamatergic synapse. Is expressed in several structures, including central nervous system; liver; primary head vein; reproductive system; and sensory organ. Orthologous to human LRFN4 (leucine rich repeat and fibronectin type III domain containing 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in ovary adult (RPKM 41.2), colon adult (RPKM 28.0) and 22 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lrfn4 in Genome Data Viewer
    Location:
    19 A; 19 4.07 cM
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (4661817..4665720, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (4611784..4615667, complement)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA A930001C03 gene Neighboring gene synaptotagmin XII Neighboring gene RIKEN cDNA 2010003K11 gene Neighboring gene STARR-positive B cell enhancer ABC_E778 Neighboring gene pyruvate carboxylase Neighboring gene STARR-seq mESC enhancer starr_45350 Neighboring gene microRNA 6986 Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene Ras converting CAAX endopeptidase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data 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

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    Related articles in PubMed

    1. Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ. Karki S, et al. Sci Rep, 2020 Jul 14. PMID 32665594, Free PMC Article
    2. Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion. Li Y, et al. Cell Rep, 2015 Sep 8. PMID 26321637, Free PMC Article
    3. Synaptic adhesion-like molecules (SALMs) promote neurite outgrowth. Wang PY, et al. Mol Cell Neurosci, 2008 Sep. PMID 18585462, Free PMC Article
    4. miR-15b/16-2 deletion promotes B-cell malignancies. Lovat F, et al. Proc Natl Acad Sci U S A, 2015 Sep 15. PMID 26324892, Free PMC Article
    5. Selected SALM (synaptic adhesion-like molecule) family proteins regulate synapse formation. Mah W, et al. J Neurosci, 2010 Apr 21. PMID 20410109, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPsigma.
      Title: Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ.
    2. SALM4 cis-interacts with SALM3, inhibits trans-synaptic SALM3 interaction with presynaptic LAR family receptor tyrosine phosphatases and suppresses SALM3-dependent presynaptic differentiation.
      Title: SALM4 suppresses excitatory synapse development by cis-inhibiting trans-synaptic SALM3-LAR adhesion.
    3. Data show that the C-terminal PDZ binding domains of synaptic adhesion-like molecules (SALMs)1-3 are required for neurite outgrowth, and that the N-termini of SALMs 2 and 4 are alsoinvolved in neurite outgrowth.
      Title: Synaptic adhesion-like molecules (SALMs) promote neurite outgrowth.
    4. Expression of SALM family proteins SALM3 and SALM5 in nonneural and neural cells induces both excitatory and inhibitory presynaptic differentiation in contacting axons.
      Title: Selected SALM (synaptic adhesion-like molecule) family proteins regulate synapse formation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (1) 

    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

    Clone Names

    • MGC36464, MGC36545

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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
    is_active_in GABA-ergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in GABA-ergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in postsynaptic density membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and fibronectin type-III domain-containing protein 4
    Names
    synaptic adhesion-like molecule 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_001426059.1 → NP_001412988.1  leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AC128739
      UniProtKB/Swiss-Prot
      Q3TQG8, Q460G5, Q80XU8, Q8K3C4
      Related
      ENSMUSP00000050039.3, ENSMUST00000053597.3

    2. NM_153388.5 → NP_700437.2  leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor

      See identical proteins and their annotated locations for NP_700437.2

      Status: VALIDATED

      Source sequence(s)
      AC128739
      Consensus CDS
      CCDS29431.1
      UniProtKB/Swiss-Prot
      Q3TQG8, Q460G5, Q80XU8, Q8K3C4
      Related
      ENSMUSP00000109453.3, ENSMUST00000113822.3
      Conserved Domains (5) summary
      smart00082
      Location:234 → 278
      LRRCT; Leucine rich repeat C-terminal domain
      COG4886
      Location:39 → 205
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:50 → 73
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:409 → 478
      fn3; Fibronectin type III domain
      cl11960
      Location:295 → 368
      Ig; Immunoglobulin domain

    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_000085.7 Reference GRCm39 C57BL/6J

      Range
      4661817..4665720 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80XU8.1 GenPept UniProtKB/Swiss-Prot:Q80XU8

    Gene LinkOut

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

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