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    Lrrtm4 leucine rich repeat transmembrane neuronal 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500219, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lrrtm4provided by RGD
    Official Full Name
    leucine rich repeat transmembrane neuronal 4provided by RGD
    Primary source
    RGD:1560707
    See related
    EnsemblRapid:ENSRNOG00000021938 AllianceGenome:RGD:1560707
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1560707
    Summary
    Predicted to enable heparan sulfate proteoglycan binding activity. Acts upstream of or within synapse organization. Is active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human LRRTM4 (leucine rich repeat transmembrane neuronal 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 96.9) and Heart (RPKM 4.0) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrrtm4 in Genome Data Viewer
    Location:
    4q34
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (114103783..114894696)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (112545874..113338713)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (110699577..111497643)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA51 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene uncharacterized LOC134486803 Neighboring gene ribosomal protein S9, pseudogene 10 Neighboring gene lactate dehydrogenase A, pseudogene 9

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. An LRRTM4-HSPG complex mediates excitatory synapse development on dentate gyrus granule cells. Siddiqui TJ, et al. Neuron, 2013 Aug 21. PMID 23911104
    2. An unbiased expression screen for synaptogenic proteins identifies the LRRTM protein family as synaptic organizers. Linhoff MW, et al. Neuron, 2009 Mar 12. PMID 19285470, Free PMC Article
    3. Unbiased discovery of glypican as a receptor for LRRTM4 in regulating excitatory synapse development. de Wit J, et al. Neuron, 2013 Aug 21. PMID 23911103, Free PMC Article
    4. PTPσ functions as a presynaptic receptor for the glypican-4/LRRTM4 complex and is essential for excitatory synaptic transmission. Ko JS, et al. Proc Natl Acad Sci U S A, 2015 Feb 10. PMID 25624497, Free PMC Article
    5. High-resolution proteomics unravel architecture and molecular diversity of native AMPA receptor complexes. Schwenk J, et al. Neuron, 2012 May 24. PMID 22632720

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC188202

    Gene Ontology Provided by RGD

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

    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_001134746.1 → NP_001128218.1  leucine-rich repeat transmembrane neuronal protein 4 precursor

      See identical proteins and their annotated locations for NP_001128218.1

      Status: PROVISIONAL

      Source sequence(s)
      BC168219
      UniProtKB/Swiss-Prot
      B4F7C5
      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5
      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_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      114103783..114894696
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017592811.3 → XP_017448300.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5

    2. XM_063286521.1 → XP_063142591.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5
      Related
      ENSRNOP00000075874.3, ENSRNOT00000092261.3

    3. XM_063286520.1 → XP_063142590.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X3

      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5

    4. XM_008763025.4 → XP_008761247.2  leucine-rich repeat transmembrane neuronal protein 4 isoform X2

      UniProtKB/Swiss-Prot
      B4F7C5
      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5

    5. XM_008763026.4 → XP_008761248.2  leucine-rich repeat transmembrane neuronal protein 4 isoform X2

      UniProtKB/Swiss-Prot
      B4F7C5
      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5

    6. XM_063286522.1 → XP_063142592.1  leucine-rich repeat transmembrane neuronal protein 4 isoform X5

      UniProtKB/TrEMBL
      A0A8L2RB96, A6IAG5, F1LNW2
      Related
      ENSRNOP00000034217.5, ENSRNOT00000030588.7
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B4F7C5.1 GenPept UniProtKB/Swiss-Prot:B4F7C5

    Gene LinkOut

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

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