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

Gene ID: 500219, updated on 11-Apr-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
Ensembl: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. Is integral component of postsynaptic density membrane. Orthologous to human LRRTM4 (leucine rich repeat transmembrane neuronal 4). [provided by Alliance of Genome Resources, Apr 2022]
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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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

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

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

    UniProtKB/Swiss-Prot
    B4F7C5
    UniProtKB/TrEMBL
    A0A8L2RB96, A6IAG5
    Related
    ENSRNOP00000075874.2

  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
    F1LNW2
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
B4F7C5.1 GenPept UniProtKB/Swiss-Prot:B4F7C5

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