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

Gene ID: 238205, updated on 11-Apr-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, Apr 2022]
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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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
  • 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 (26) 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 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 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 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
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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