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

    Gene ID: 320747, updated on 6-Jun-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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    See Lingo4 in Genome Data Viewer
    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)
    • Endonuclease-mediated (1) 
    • Targeted (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
      UniProtKB/TrEMBL
      A0A0R4J0Q7
      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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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