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    LRRTM1 leucine rich repeat transmembrane neuronal 1 [ Homo sapiens (human) ]

    Gene ID: 347730, updated on 27-Nov-2024

    Summary

    Official Symbol
    LRRTM1provided by HGNC
    Official Full Name
    leucine rich repeat transmembrane neuronal 1provided by HGNC
    Primary source
    HGNC:HGNC:19408
    See related
    Ensembl:ENSG00000162951 MIM:610867; AllianceGenome:HGNC:19408
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be involved in regulation of postsynaptic density assembly and regulation of presynapse assembly. Predicted to act upstream of or within several processes, including long-term synaptic potentiation; negative regulation of receptor internalization; and positive regulation of synapse assembly. Located in endoplasmic reticulum and growth cone. Is active in GABA-ergic synapse and postsynaptic specialization membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 4.5), salivary gland (RPKM 2.3) and 7 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LRRTM1 in Genome Data Viewer
    Location:
    2p12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (80288356..80304752, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (80302025..80304899, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (80529003..80531877, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene catenin alpha 2 Neighboring gene MPRA-validated peak3752 silencer Neighboring gene uncharacterized LOC107985903 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80458363-80459016 Neighboring gene RBM7 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:80530694-80531319 Neighboring gene uncharacterized LOC107985904 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80557197-80557699 Neighboring gene uncharacterized LOC105374824

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ32082

    Gene Ontology Provided by GOA

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

    General protein information

    Preferred Names
    leucine-rich repeat transmembrane neuronal protein 1
    Names
    leucine-rich repeat transmembrane neuronal 1 protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_178839.5NP_849161.2  leucine-rich repeat transmembrane neuronal protein 1 precursor

      See identical proteins and their annotated locations for NP_849161.2

      Status: VALIDATED

      Source sequence(s)
      AA977181, AC016670, AY182024, BI756350
      Consensus CDS
      CCDS1966.1
      UniProtKB/Swiss-Prot
      A8K397, D6W5K1, Q86UE6, Q96DN1
      Related
      ENSP00000295057.3, ENST00000295057.4
      Conserved Domains (5) summary
      cd00116
      Location:85268
      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:306318
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:91114
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:257297
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:113173
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      80288356..80304752 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444146.1XP_047300102.1  leucine-rich repeat transmembrane neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K397, D6W5K1, Q86UE6, Q96DN1
      Related
      ENSP00000393562.1, ENST00000417012.5
    2. XM_017003987.3XP_016859476.1  leucine-rich repeat transmembrane neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K397, D6W5K1, Q86UE6, Q96DN1
      Conserved Domains (5) summary
      cd00116
      Location:85268
      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:306318
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:91114
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:257297
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:113173
      LRR_8; Leucine rich repeat
    3. XM_017003986.3XP_016859475.1  leucine-rich repeat transmembrane neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K397, D6W5K1, Q86UE6, Q96DN1
      Conserved Domains (5) summary
      cd00116
      Location:85268
      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:306318
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:91114
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:257297
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:113173
      LRR_8; Leucine rich repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      80302025..80304899 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341769.1XP_054197744.1  leucine-rich repeat transmembrane neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K397, D6W5K1, Q86UE6, Q96DN1
    2. XM_054341768.1XP_054197743.1  leucine-rich repeat transmembrane neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K397, D6W5K1, Q86UE6, Q96DN1