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    Lrfn5 leucine rich repeat and fibronectin type III domain containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314164, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lrfn5provided by RGD
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 5provided by RGD
    Primary source
    RGD:1309357
    See related
    EnsemblRapid:ENSRNOG00000005550 AllianceGenome:RGD:1309357
    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
    Summary
    Involved in synaptic membrane adhesion. Is active in postsynaptic density membrane. Orthologous to human LRFN5 (leucine rich repeat and fibronectin type III domain containing 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Restricted expression toward (RPKM 95.6) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrfn5 in Genome Data Viewer
    Location:
    6q23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (85201465..85557872)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (79466403..79822821)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (83082593..83438601)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene poly(rC) binding protein 2, pseudogene 9 Neighboring gene endosome associated trafficking regulator 1 like 1 Neighboring gene translocase of inner mitochondrial membrane 17a-like 1 Neighboring gene small nucleolar RNA U3 like 1 Neighboring gene U6 spliceosomal RNA Neighboring gene inorganic pyrophosphatase 2, pseudogene

    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. SALM5 trans-synaptically interacts with LAR-RPTPs in a splicing-dependent manner to regulate synapse development. Choi Y, et al. Sci Rep, 2016 May 26. PMID 27225731, Free PMC Article
    2. 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
    3. Neuron-specific SALM5 limits inflammation in the CNS via its interaction with HVEM. Zhu Y, et al. Sci Adv, 2016 Apr. PMID 27152329, Free PMC Article
    4. 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
    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

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in negative regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of macrophage activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of macrophage activation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of presynapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of presynapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in synaptic membrane adhesion EXP
    Inferred from Experiment
    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 IEP
    Inferred from Expression Pattern
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in GABA-ergic synapse ISO
    Inferred from Sequence Orthology
    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
    		  
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    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 

    General protein information

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    Preferred Names
    leucine-rich repeat and fibronectin type-III domain-containing protein 5

    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_001108024.1 → NP_001101494.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 precursor

      See identical proteins and their annotated locations for NP_001101494.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473947
      UniProtKB/Swiss-Prot
      D4A1J9
      Related
      ENSRNOP00000007600.6, ENSRNOT00000007600.9
      Conserved Domains (5) summary
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      cd05764
      Location:287 → 374
      IgI_SALM5_like; Immunoglobulin domain of human Synaptic Adhesion-Like Molecule 5 (SALM5) and similar proteins; member of the I-set of IgSF domains
      cd21340
      Location:56 → 211
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
      cl21522
      Location:421 → 494
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    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_086024.1 Reference GRCr8

      Range
      85201465..85557872
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039112241.2 → XP_038968169.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X2

      Related
      ENSRNOP00000103257.1, ENSRNOT00000148545.1
      Conserved Domains (5) summary
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      cd05764
      Location:287 → 374
      IgI_SALM5_like; Immunoglobulin domain of human Synaptic Adhesion-Like Molecule 5 (SALM5) and similar proteins; member of the I-set of IgSF domains
      cd21340
      Location:56 → 211
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
      cl21522
      Location:421 → 494
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    2. XM_039112240.2 → XP_038968168.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

      UniProtKB/Swiss-Prot
      D4A1J9
      Conserved Domains (5) summary
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      cd05764
      Location:287 → 374
      IgI_SALM5_like; Immunoglobulin domain of human Synaptic Adhesion-Like Molecule 5 (SALM5) and similar proteins; member of the I-set of IgSF domains
      cd21340
      Location:56 → 211
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
      cl21522
      Location:421 → 494
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

    RNA

    1. XR_593049.4 RNA Sequence

    2. XR_001838166.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D4A1J9.1 GenPept UniProtKB/Swiss-Prot:D4A1J9

    Gene LinkOut

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

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