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    Lrfn5 leucine rich repeat and fibronectin type III domain containing 5 [ Mus musculus (house mouse) ]

    Gene ID: 238205, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Lrfn5provided by MGI
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 5provided by MGI
    Primary source
    MGI:MGI:2144814
    See related
    Ensembl:ENSMUSG00000035653 AllianceGenome:MGI:2144814
    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
    Salm5; mKIAA4208; C130061B21
    Summary
    Involved in negative regulation of macrophage activation and regulation of presynapse assembly. Located in cell surface. Is active in GABA-ergic synapse and glutamatergic synapse. Is expressed in several structures, including central nervous system; dorsal root ganglion; and retina. Orthologous to human LRFN5 (leucine rich repeat and fibronectin type III domain containing 5). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in CNS E18 (RPKM 10.2), cortex adult (RPKM 6.3) and 5 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lrfn5 in Genome Data Viewer
    Location:
    12 C1; 12 26.43 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (61569356..61913554)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (61522851..61857928)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_32262 Neighboring gene STARR-seq mESC enhancer starr_32263 Neighboring gene Nanog pseudogene 2 Neighboring gene predicted gene, 20063 Neighboring gene eukaryotic translation initiation factor 4E-like Neighboring gene STARR-seq mESC enhancer starr_32264 Neighboring gene STARR-seq mESC enhancer starr_32265 Neighboring gene STARR-seq mESC enhancer starr_32266 Neighboring gene STARR-seq mESC enhancer starr_32267 Neighboring gene pyrophosphatase (inorganic) 2 pseudogene Neighboring gene predicted gene, 24750

    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. 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. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler. Noack F, et al. Nat Neurosci, 2022 Feb. PMID 35132236, Free PMC Article
    4. The SALM/Lrfn family of leucine-rich repeat-containing cell adhesion molecules. Nam J, et al. Semin Cell Dev Biol, 2011 Jul. PMID 21736948
    5. 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

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA4208

    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 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 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic membrane adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 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 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_001310586.1 → NP_001297515.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001297515.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' structure, resulting in a novel 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus, and is shorter than isoform 1.
      Source sequence(s)
      AK162923, BC052038
      Consensus CDS
      CCDS79117.1
      UniProtKB/Swiss-Prot
      Q5DTH4, Q8BJH4, Q8BXA0, Q8BZL0
      Related
      ENSMUSP00000113123.2, ENSMUST00000119481.2
      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. NM_178714.5 → NP_848829.2  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_848829.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC133079, CT030140
      Consensus CDS
      CCDS25936.1
      UniProtKB/Swiss-Prot
      Q8BXA0
      Related
      ENSMUSP00000051546.8, ENSMUST00000055815.14
      Conserved Domains (5) summary
      cd05764
      Location:301 → 374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:100 → 159
      LRR_8; Leucine rich repeat
      pfam00041
      Location:421 → 493
      fn3; Fibronectin type III domain
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like 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_000078.7 Reference GRCm39 C57BL/6J

      Range
      61569356..61913554
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017315056.3 → XP_017170545.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q5DTH4, Q8BJH4, Q8BXA0, Q8BZL0
      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_036157395.1 → XP_036013288.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q5DTH4, Q8BJH4, Q8BXA0, Q8BZL0
      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 ...

    3. XM_006515830.4 → XP_006515893.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_006515893.1

      UniProtKB/Swiss-Prot
      Q8BXA0
      Conserved Domains (5) summary
      cd05764
      Location:301 → 374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:100 → 159
      LRR_8; Leucine rich repeat
      pfam00041
      Location:421 → 493
      fn3; Fibronectin type III domain
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    4. XM_006515831.5 → XP_006515894.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_006515894.1

      UniProtKB/Swiss-Prot
      Q8BXA0
      Conserved Domains (5) summary
      cd05764
      Location:301 → 374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:100 → 159
      LRR_8; Leucine rich repeat
      pfam00041
      Location:421 → 493
      fn3; Fibronectin type III domain
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    RNA

    1. XR_001780450.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BXA0.1 GenPept UniProtKB/Swiss-Prot:Q8BXA0

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