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    Lrfn3 leucine rich repeat and fibronectin type III domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308495, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Lrfn3provided by RGD
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 3provided by RGD
    Primary source
    RGD:1305567
    See related
    EnsemblRapid:ENSRNOG00000020839 AllianceGenome:RGD:1305567
    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
    Salm4
    Summary
    Involved in regulation of presynapse assembly; regulation of synaptic membrane adhesion; and synaptic membrane adhesion. Is active in glutamatergic synapse; postsynaptic density membrane; and presynaptic active zone membrane. Orthologous to human LRFN3 (leucine rich repeat and fibronectin type III domain containing 3). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Adrenal (RPKM 12.9), Brain (RPKM 12.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrfn3 in Genome Data Viewer
    Location:
    1q21
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (94744315..94751001, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (85616862..85623725, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (88819439..88827002, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene spectrin repeat containing nuclear envelope family member 4 Neighboring gene succinate dehydrogenase complex assembly factor 1 Neighboring gene RNA, U2 small nuclear 57 Neighboring gene uncharacterized LOC108349559 Neighboring gene actin, gamma 1, pseudogene 6

    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 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. The SALM family of adhesion-like molecules forms heteromeric and homomeric complexes. Seabold GK, et al. J Biol Chem, 2008 Mar 28. PMID 18227064, Free PMC Article
    2. Flotillin-1 mediates neurite branching induced by synaptic adhesion-like molecule 4 in hippocampal neurons. Swanwick CC, et al. Mol Cell Neurosci, 2010 Nov. PMID 20600927
    3. Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins. Morimura N, et al. Gene, 2006 Oct 1. PMID 16828986
    4. SALM4 suppresses excitatory synapse development by cis-inhibiting trans-synaptic SALM3-LAR adhesion. Lie E, et al. Nat Commun, 2016 Aug 2. PMID 27480238, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data reveal a flotillin-1 signaling pathway for hippocampal neurite branching that is regulated by synaptic adhesion-like molecule 4.
      Title: Flotillin-1 mediates neurite branching induced by synaptic adhesion-like molecule 4 in hippocampal neurons.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    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 regulation of synaptic membrane adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synaptic membrane adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite IEA
    Inferred from Electronic Annotation
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in postsynaptic specialization membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in presynaptic active zone membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynaptic active zone membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    leucine-rich repeat and fibronectin type-III domain-containing protein 3
    Names
    synaptic adhesion-like molecule 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_001107502.1 → NP_001100972.1  leucine-rich repeat and fibronectin type-III domain-containing protein 3 precursor

      See identical proteins and their annotated locations for NP_001100972.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473979
      UniProtKB/Swiss-Prot
      B0BNK7
      Conserved Domains (7) summary
      COG4886
      Location:63 → 222
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:242 → 253
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:63 → 84
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:425 → 502
      fn3; Fibronectin type III domain
      cd00096
      Location:296 → 299
      Ig; Ig strand A [structural motif]
      cl11960
      Location:296 → 383
      Ig; Immunoglobulin domain
      cl15307
      Location:249 → 281
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    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
      94744315..94751001 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006228771.4 → XP_006228833.1  leucine-rich repeat and fibronectin type-III domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006228833.1

      UniProtKB/Swiss-Prot
      B0BNK7
      Related
      ENSRNOP00000028275.4, ENSRNOT00000028275.7
      Conserved Domains (7) summary
      COG4886
      Location:63 → 222
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:242 → 253
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:63 → 84
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:425 → 502
      fn3; Fibronectin type III domain
      cd00096
      Location:296 → 299
      Ig; Ig strand A [structural motif]
      cl11960
      Location:296 → 383
      Ig; Immunoglobulin domain
      cl15307
      Location:249 → 281
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B0BNK7.1 GenPept UniProtKB/Swiss-Prot:B0BNK7

    Gene LinkOut

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

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