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    Lrtm1 leucine-rich repeats and transmembrane domains 1 [ Mus musculus (house mouse) ]

    Gene ID: 319476, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Lrtm1provided by MGI
    Official Full Name
    leucine-rich repeats and transmembrane domains 1provided by MGI
    Primary source
    MGI:MGI:2442106
    See related
    Ensembl:ENSMUSG00000045776 AllianceGenome:MGI:2442106
    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
    A930016D02Rik
    Summary
    Predicted to enable Roundabout binding activity and heparin binding activity. Acts upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Is expressed in head. Orthologous to human LRTM1 (leucine rich repeats and transmembrane domains 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in heart adult (RPKM 33.2) and liver adult (RPKM 2.3) See more
    Orthologs
    human all
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    Genomic context

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    See Lrtm1 in Genome Data Viewer
    Location:
    14 A3; 14 16.8 cM
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (28740165..28755599)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (29018208..29033642)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L5 pseudogene Neighboring gene predicted gene, 35217 Neighboring gene calcium channel, voltage-dependent, alpha2/delta subunit 3 Neighboring gene STARR-seq mESC enhancer starr_36285 Neighboring gene STARR-seq mESC enhancer starr_36286 Neighboring gene peptidylprolyl isomerase A pseudogene 15 Neighboring gene STARR-seq mESC enhancer starr_36287 Neighboring gene STARR-seq mESC enhancer starr_36288 Neighboring gene STARR-seq mESC enhancer starr_36289 Neighboring gene STARR-seq mESC enhancer starr_36290 Neighboring gene STARR-seq mESC enhancer starr_36291 Neighboring gene predicted gene, 41118 Neighboring gene predicted gene, 57619

    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. Examination of FGFRL1 as a candidate gene for diaphragmatic defects at chromosome 4p16.3 shows that Fgfrl1 null mice have reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm. LopezJimenez N, et al. Hum Genet, 2010 Mar. PMID 20024584, Free PMC Article
    2. Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate. Nishihara H, et al. PLoS Genet, 2016 Oct. PMID 27741242, Free PMC Article
    3. Identification of potential target genes for RFX4_v3, a transcription factor critical for brain development. Zhang D, et al. J Neurochem, 2006 Aug. PMID 16893423
    4. Calsyntenins function as synaptogenic adhesion molecules in concert with neurexins. Um JW, et al. Cell Rep, 2014 Mar 27. PMID 24613359, Free PMC Article
    5. Molecular architecture of the developing mouse brain. La Manno G, et al. Nature, 2021 Aug. PMID 34321664

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm of mice with diaphragmatic defects.
      Title: Examination of FGFRL1 as a candidate gene for diaphragmatic defects at chromosome 4p16.3 shows that Fgfrl1 null mice have reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    General gene information

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    Homology

    Clone Names

    • MGC118429

    Gene Ontology Provided by MGI

    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
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and transmembrane domain-containing 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_176920.4 → NP_795894.1  leucine-rich repeat and transmembrane domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_795894.1

      Status: VALIDATED

      Source sequence(s)
      AA244770, AC115760, AK052894, BC099587
      Consensus CDS
      CCDS26889.1
      UniProtKB/Swiss-Prot
      Q8BXQ3
      UniProtKB/TrEMBL
      A0A286YE57, A6H6T2
      Related
      ENSMUSP00000061828.3, ENSMUST00000055662.4
      Conserved Domains (6) summary
      smart00013
      Location:33 → 62
      LRRNT; Leucine rich repeat N-terminal domain
      sd00031
      Location:64 → 111
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:45 → 63
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:110 → 151
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:110 → 170
      LRR_8; Leucine rich repeat
      cl15307
      Location:192 → 239
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    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_000080.7 Reference GRCm39 C57BL/6J

      Range
      28740165..28755599
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BXQ3.1 GenPept UniProtKB/Swiss-Prot:Q8BXQ3

    Gene LinkOut

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

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