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Lingo4 leucine rich repeat and Ig domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 320747, updated on 3-Apr-2024

Summary

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Official Symbol
Lingo4provided by MGI
Official Full Name
leucine rich repeat and Ig domain containing 4provided by MGI
Primary source
MGI:MGI:2444651
See related
Ensembl:ENSMUSG00000044505 AllianceGenome:MGI:2444651
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
LERN4; Lrrn6d; A530050P17Rik
Summary
Acts upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. Is expressed in several structures, including central nervous system and nasal pit. Orthologous to human LINGO4 (leucine rich repeat and Ig domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in thymus adult (RPKM 2.3), cerebellum adult (RPKM 2.1) and 13 other tissues See more
Orthologs
human all
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Genomic context

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Location:
3 F2.1; 3 40.59 cM
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (94306526..94311820)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (94399219..94404501)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr3:94170729-94171030 Neighboring gene predicted gene, 38411 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94181128-94181237 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94181285-94181542 Neighboring gene RAR-related orphan receptor gamma Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94186335-94186518 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94191975-94192234 Neighboring gene RIKEN cDNA 1700040D17 gene Neighboring gene STARR-positive B cell enhancer mm9_chr3:94216846-94217147 Neighboring gene tudor and KH domain containing protein Neighboring gene ornithine decarboxylase antizyme 3

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. Expression of the Lingo/LERN gene family during mouse embryogenesis. Haines BP, et al. Gene Expr Patterns, 2008 Jan. PMID 18297755
  2. Expression pattern of LRR and Ig domain-containing protein (LRRIG protein) in the early mouse embryo. Homma S, et al. Gene Expr Patterns, 2009 Jan. PMID 18848646
  3. Calsyntenins function as synaptogenic adhesion molecules in concert with neurexins. Um JW, et al. Cell Rep, 2014 Mar 27. PMID 24613359, Free PMC Article
  4. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. Magdaleno S, et al. PLoS Biol, 2006 Apr. PMID 16602821, Free PMC Article
  5. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article

See all (15) 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)
  • Targeted (1) 
  • Endonuclease-mediated (1) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within positive regulation of synapse assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat and immunoglobulin-like domain containing-NOGO receptor-interacting protein 4
Names
leucine rich repeat neuronal 6D
leucine-rich repeat neuronal protein 6D

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_001368653.1 → NP_001355582.1  leucine-rich repeat and immunoglobulin-like domain containing-NOGO receptor-interacting protein 4 precursor

    Status: VALIDATED

    Source sequence(s)
    AC122808, AC164562
    UniProtKB/Swiss-Prot
    A0A4X2, Q149C3
    UniProtKB/TrEMBL
    A0A0R4J0Q7
    Conserved Domains (7) summary
    smart00013
    Location:31 → 64
    LRRNT; Leucine rich repeat N-terminal domain
    smart00410
    Location:420 → 501
    IG_like; Immunoglobulin like
    COG4886
    Location:50 → 318
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:350 → 362
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:86 → 109
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:301 → 360
    LRR_8; Leucine rich repeat
    cd00096
    Location:431 → 435
    Ig; Ig strand B [structural motif]

  2. NM_177250.3 → NP_796224.2  leucine-rich repeat and immunoglobulin-like domain containing-NOGO receptor-interacting protein 4 precursor

    Status: VALIDATED

    Source sequence(s)
    AC122808, AC164562
    Consensus CDS
    CCDS17592.1
    UniProtKB/Swiss-Prot
    A0A4X2, Q149C3
    Related
    ENSMUSP00000058050.5, ENSMUST00000050975.6
    Conserved Domains (7) summary
    smart00013
    Location:31 → 64
    LRRNT; Leucine rich repeat N-terminal domain
    smart00410
    Location:420 → 501
    IG_like; Immunoglobulin like
    COG4886
    Location:50 → 318
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:350 → 362
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:86 → 109
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:301 → 360
    LRR_8; Leucine rich repeat
    cd00096
    Location:431 → 435
    Ig; Ig strand B [structural motif]

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_000069.7 Reference GRCm39 C57BL/6J

    Range
    94306526..94311820
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q149C3.2 GenPept UniProtKB/Swiss-Prot:Q149C3

Gene LinkOut

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