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

Summary

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, Dec 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

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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These results suggest that postsynaptic SALM5 promotes synapse development by trans-synaptically interacting with presynaptic LAR-RPTPs and is important for the regulation of excitatory synaptic strength.
Title: SALM5 trans-synaptically interacts with LAR-RPTPs in a splicing-dependent manner to regulate synapse development.
we identified herpes virus entry mediator as a functional receptor that mediates SALM5's suppressive function. Our findings reveal a molecular link between the neuronal system and the immune system, and provide potential therapeutic targets for the control of CNS diseases.
Title: Neuron-specific SALM5 limits inflammation in the CNS via its interaction with HVEM.

Submit: New GeneRIF Correction

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

PMC18818P2 (e-PCR)
- UniSTS:271737

AI604817 (e-PCR)
- UniSTS:164499

AI427653 (e-PCR)
- UniSTS:164500

D1S3693 (e-PCR)
- UniSTS:474271

RH118347 (e-PCR)
- UniSTS:160979

Lrfn5 (e-PCR), detects polymorphism
- UniSTS:525549

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)

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 ...
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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

61569356..61913554

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...
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
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