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    Lrrtm4 leucine rich repeat transmembrane neuronal 4 [ Mus musculus (house mouse) ]

    Gene ID: 243499, updated on 9-May-2024

    Summary

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    Official Symbol
    Lrrtm4provided by MGI
    Official Full Name
    leucine rich repeat transmembrane neuronal 4provided by MGI
    Primary source
    MGI:MGI:2389180
    See related
    Ensembl:ENSMUSG00000052581 AllianceGenome:MGI:2389180
    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
    A230052N11; 7530419J18Rik
    Summary
    Enables heparan sulfate proteoglycan binding activity. Involved in regulation of synapse assembly. Acts upstream of or within AMPA glutamate receptor clustering; positive regulation of synapse assembly; and regulation of presynaptic membrane organization. Located in glutamatergic synapse and postsynaptic membrane. Part of AMPA glutamate receptor complex. Is expressed in several structures, including central nervous system; embryo mesenchyme; and future midbrain. Orthologous to human LRRTM4 (leucine rich repeat transmembrane neuronal 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in cortex adult (RPKM 3.0), frontal lobe adult (RPKM 2.8) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    6 C3; 6 35.05 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (79995828..80787143)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (80018858..80810162)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L47 pseudogene Neighboring gene mt-Rnr2 like 7 Neighboring gene STARR-seq mESC enhancer starr_16405 Neighboring gene predicted gene, 44240 Neighboring gene STARR-seq mESC enhancer starr_16406 Neighboring gene STARR-seq mESC enhancer starr_16407 Neighboring gene predicted gene, 32091 Neighboring gene STARR-seq mESC enhancer starr_16408 Neighboring gene STARR-seq mESC enhancer starr_16409 Neighboring gene STARR-seq mESC enhancer starr_16410 Neighboring gene STARR-seq mESC enhancer starr_16411 Neighboring gene STARR-seq mESC enhancer starr_16412 Neighboring gene STARR-seq mESC enhancer starr_16414 Neighboring gene STARR-seq mESC enhancer starr_16415 Neighboring gene STARR-seq mESC enhancer starr_16416 Neighboring gene STARR-seq mESC enhancer starr_16417 Neighboring gene STARR-seq mESC enhancer starr_16418 Neighboring gene predicted gene, 38838 Neighboring gene predicted gene, 26264

    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. LRRTM4 is a member of the transsynaptic complex between rod photoreceptors and bipolar cells. Agosto MA, et al. J Comp Neurol, 2021 Jan. PMID 32390181, Free PMC Article
    2. An LRRTM4-HSPG complex mediates excitatory synapse development on dentate gyrus granule cells. Siddiqui TJ, et al. Neuron, 2013 Aug 21. PMID 23911104
    3. LRRTMs Organize Synapses through Differential Engagement of Neurexin and PTPσ. Roppongi RT, et al. Neuron, 2020 Apr 8. PMID 31995730
    4. LRRTM4: A Novel Regulator of Presynaptic Inhibition and Ribbon Synapse Arrangements of Retinal Bipolar Cells. Sinha R, et al. Neuron, 2020 Mar 18. PMID 31974009, Free PMC Article
    5. LRRTM3 Regulates Excitatory Synapse Development through Alternative Splicing and Neurexin Binding. Um JW, et al. Cell Rep, 2016 Feb 2. PMID 26776509

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LRRTM4 is a member of the transsynaptic complex between rod photoreceptors and bipolar cells.
      Title: LRRTM4 is a member of the transsynaptic complex between rod photoreceptors and bipolar cells.
    2. LRRTMs engage the protein domains of Nrx but require its heparan sulfate (HS) modification to induce presynaptic differentiation. Binding to HS of Nrx is sufficient for LRRTM3 and LRRTM4 to induce synaptogenesis. Nrx1gamma is a potent synapse organizer and LRRTM4 is its postsynaptic ligand. Mice expressing a mutant form of LRRTM4 that can't bind HS show structural and functional deficits at dentate gyrus excitatory syn...
      Title: LRRTMs Organize Synapses through Differential Engagement of Neurexin and PTPσ.
    3. LRRTM4 is a key synapse organizing molecule at rod bipolar cell (RBC) terminals, where it regulates function of GABAergic synapse and assembly of RBC synaptic dyads.
      Title: LRRTM4: A Novel Regulator of Presynaptic Inhibition and Ribbon Synapse Arrangements of Retinal Bipolar Cells.
    4. This study demonistrated that LRRTM4-HSPG complex mediates excitatory synapse development on dentate gyrus granule cells.
      Title: An LRRTM4-HSPG complex mediates excitatory synapse development on dentate gyrus granule cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables heparan sulfate proteoglycan binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within AMPA glutamate receptor clustering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neurotransmitter-gated ion channel clustering IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of synapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of presynaptic membrane organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within synapse organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of AMPA glutamate receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in GABA-ergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    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 glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    is_active_in photoreceptor ribbon synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in postsynaptic density membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in postsynaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    leucine-rich repeat transmembrane neuronal protein 4

    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_001134743.1 → NP_001128215.1  leucine-rich repeat transmembrane neuronal protein 4 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001128215.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in both UTR's and has multiple differences in the coding region, compared to variant 1. The encoded isoform (3) has distinct N- and C-termini and is longer than isoform 1.
      Source sequence(s)
      BC037216, BY130176
      Consensus CDS
      CCDS71778.1
      UniProtKB/TrEMBL
      A0A0R4J1T4
      Related
      ENSMUSP00000117263.2, ENSMUST00000147663.8
      Conserved Domains (3) summary
      sd00031
      Location:304 → 316
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:65 → 87
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:134 → 194
      LRR_8; Leucine rich repeat

    2. NM_001282102.1 → NP_001269031.1  leucine-rich repeat transmembrane neuronal protein 4 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001269031.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' terminal exon, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences result in translation initiation at an alternate AUG and result in an isoform (2) with a longer and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK038656, BY130176
      Consensus CDS
      CCDS71779.1
      UniProtKB/TrEMBL
      E9Q8Y9
      Related
      ENSMUSP00000121621.2, ENSMUST00000136421.2
      Conserved Domains (4) summary
      COG4886
      Location:55 → 315
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:304 → 316
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:65 → 87
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:135 → 194
      LRR_8; Leucine rich repeat

    3. NM_001347261.1 → NP_001334190.1  leucine-rich repeat transmembrane neuronal protein 4 isoform 4 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR and has multiple differences in the coding region, compared to variant 1. The encoded isoform (4) has distinct N- and C-termini and is longer than isoform 1.
      Source sequence(s)
      AC153827, AC156282
      Consensus CDS
      CCDS90065.1
      UniProtKB/Swiss-Prot
      Q80XG9, Q8C030, Q8JZS8
      Conserved Domains (4) summary
      COG4886
      Location:54 → 314
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:303 → 315
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:64 → 86
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:134 → 193
      LRR_8; Leucine rich repeat

    4. NM_178731.5 → NP_848846.3  leucine-rich repeat transmembrane neuronal protein 4 isoform 1 precursor

      See identical proteins and their annotated locations for NP_848846.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the shortest isoform (1).
      Source sequence(s)
      AK038656, CJ059997
      Consensus CDS
      CCDS20259.2
      UniProtKB/Swiss-Prot
      Q80XG9
      UniProtKB/TrEMBL
      Q8BYQ8
      Related
      ENSMUSP00000074232.5, ENSMUST00000074662.5
      Conserved Domains (4) summary
      cd00116
      Location:84 → 295
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:303 → 315
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:64 → 86
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:133 → 193
      LRR_8; Leucine rich repeat

    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_000072.7 Reference GRCm39 C57BL/6J

      Range
      79995828..80787143
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006506089.4 → XP_006506152.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X4

      See identical proteins and their annotated locations for XP_006506152.1

      UniProtKB/TrEMBL
      E9Q8Y9
      Conserved Domains (4) summary
      COG4886
      Location:55 → 315
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:304 → 316
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:65 → 87
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:135 → 194
      LRR_8; Leucine rich repeat

    2. XM_006506088.4 → XP_006506151.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X3

      Conserved Domains (4) summary
      COG4886
      Location:55 → 315
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:304 → 316
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:65 → 87
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:135 → 194
      LRR_8; Leucine rich repeat

    3. XM_011241336.4 → XP_011239638.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X5

      Conserved Domains (4) summary
      COG4886
      Location:55 → 315
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:304 → 316
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:65 → 87
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:135 → 194
      LRR_8; Leucine rich repeat

    4. XM_036166111.1 → XP_036022004.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X2

      Conserved Domains (3) summary
      sd00031
      Location:304 → 316
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:65 → 87
      LRR_RI; leucine-rich repeat [structural motif]
      cd21340
      Location:91 → 312
      PPP1R42; protein phosphatase 1 regulatory subunit 42

    5. XM_006506087.2 → XP_006506150.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006506150.1

      UniProtKB/Swiss-Prot
      Q80XG9, Q8C030, Q8JZS8
      Conserved Domains (4) summary
      COG4886
      Location:54 → 314
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:303 → 315
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:64 → 86
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:134 → 193
      LRR_8; Leucine rich repeat

    6. XM_006506085.3 → XP_006506148.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006506148.1

      UniProtKB/Swiss-Prot
      Q80XG9, Q8C030, Q8JZS8
      Related
      ENSMUSP00000121124.2, ENSMUST00000126399.2
      Conserved Domains (4) summary
      COG4886
      Location:54 → 314
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:303 → 315
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:64 → 86
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:134 → 193
      LRR_8; Leucine rich repeat

    7. XM_006506086.3 → XP_006506149.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006506149.1

      UniProtKB/Swiss-Prot
      Q80XG9, Q8C030, Q8JZS8
      Related
      ENSMUSP00000115016.2, ENSMUST00000133918.8
      Conserved Domains (4) summary
      COG4886
      Location:54 → 314
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:303 → 315
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:64 → 86
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:134 → 193
      LRR_8; Leucine rich repeat
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80XG9.2 GenPept UniProtKB/Swiss-Prot:Q80XG9

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