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LRRTM1 leucine rich repeat transmembrane neuronal 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 679668, updated on 4-Jan-2025

Summary

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Official Symbol
LRRTM1provided by RGD
Official Full Name
leucine rich repeat transmembrane neuronal 1provided by RGD
Primary source
RGD:1585921
See related
EnsemblRapid:ENSRNOG00000006093 AllianceGenome:RGD:1585921
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Involved in regulation of postsynaptic density assembly and regulation of presynapse assembly. Acts upstream of or within synapse organization. Located in excitatory synapse. Is active in glutamatergic synapse and postsynaptic membrane. Orthologous to human LRRTM1 (leucine rich repeat transmembrane neuronal 1). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Biased expression in Brain (RPKM 76.1), Testes (RPKM 10.4) and 1 other tissue See more
Orthologs
human mouse all
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Genomic context

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See LRRTM1 in Genome Data Viewer
Location:
4q33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (111246213..111295638)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (109701815..109718924)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (108300927..108316373)

Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein L6, pseudogene 15 Neighboring gene U6 spliceosomal RNA Neighboring gene catenin alpha 2 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene U11 spliceosomal RNA

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. LRRTM1-deficient mice show a rare phenotype of avoiding small enclosures--a tentative mouse model for claustrophobia-like behaviour. Voikar V, et al. Behav Brain Res, 2013 Feb 1. PMID 23089646, Free PMC Article
  2. Impaired cognitive function and altered hippocampal synapse morphology in mice lacking Lrrtm1, a gene associated with schizophrenia. Takashima N, et al. PLoS One, 2011. PMID 21818371, Free PMC Article
  3. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Francks C, et al. Mol Psychiatry, 2007 Dec. PMID 17667961, Free PMC Article
  4. Circular RNA Hecw1 Regulates the Inflammatory Imbalance in Spinal Cord Injury via miR-3551-3p/LRRTM1 Axis. Ban D, et al. Appl Biochem Biotechnol, 2022 Nov. PMID 35699802
  5. Leucine-rich repeat transmembrane proteins are essential for maintenance of long-term potentiation. Soler-Llavina GJ, et al. Neuron, 2013 Aug 7. PMID 23931994, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circular RNA Hecw1 Regulates the Inflammatory Imbalance in Spinal Cord Injury via miR-3551-3p/LRRTM1 Axis.
    Title: Circular RNA Hecw1 Regulates the Inflammatory Imbalance in Spinal Cord Injury via miR-3551-3p/LRRTM1 Axis.
Submit: New GeneRIF Correction

General gene information

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Homology

Gene Ontology Provided by RGD

Process Evidence Code Pubs
acts_upstream_of establishment of localization in cell ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within exploration behavior ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within locomotory behavior ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within long-term synaptic potentiation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of receptor internalization 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 protein localization to synapse ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of receptor internalization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of postsynaptic density assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of postsynaptic density assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 
acts_upstream_of_or_within synapse organization IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within synapse organization ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in GABA-ergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in axon ISO
Inferred from Sequence Orthology
more info
  
NOT located_in cell surface ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
located_in excitatory 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 
located_in growth cone ISO
Inferred from Sequence Orthology
more info
  
is_active_in postsynaptic membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in postsynaptic specialization membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
leucine-rich repeat transmembrane neuronal protein 1

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_001395622.1 → NP_001382551.1  leucine-rich repeat transmembrane neuronal protein 1 precursor

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000004
    UniProtKB/Swiss-Prot
    D4A6D8
    Related
    ENSRNOP00000107518.1, ENSRNOT00000124442.1
    Conserved Domains (3) summary
    COG4886
    Location:75 → 315
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:306 → 318
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:91 → 114
    LRR_RI; leucine-rich repeat [structural motif]

RNA

  1. NR_172650.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000004

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
    111246213..111295638
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006236700.5 → XP_006236762.1  leucine-rich repeat transmembrane neuronal protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006236762.1

    UniProtKB/Swiss-Prot
    D4A6D8
    Conserved Domains (3) summary
    COG4886
    Location:75 → 315
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:306 → 318
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:91 → 114
    LRR_RI; leucine-rich repeat [structural motif]

RNA

  1. XR_005503313.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
D4A6D8.1 GenPept UniProtKB/Swiss-Prot:D4A6D8

Gene LinkOut

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