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

Gene ID: 314164, updated on 2-Nov-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, Nov 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 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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