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    LRRTM2 leucine rich repeat transmembrane neuronal 2 [ Homo sapiens (human) ]

    Gene ID: 26045, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LRRTM2provided by HGNC
    Official Full Name
    leucine rich repeat transmembrane neuronal 2provided by HGNC
    Primary source
    HGNC:HGNC:19409
    See related
    Ensembl:ENSG00000146006 MIM:610868; AllianceGenome:HGNC:19409
    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 enable neurexin family protein binding activity. Predicted to be involved in regulation of postsynaptic density 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. Is active in GABA-ergic synapse and postsynaptic specialization membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 12.7), placenta (RPKM 1.4) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRTM2 in Genome Data Viewer
    Location:
    5q31.2
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (138868921..138875335, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (139395050..139401453, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138204610..138211024, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137976937-137977490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137977491-137978044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:137986181-137986979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138001425-138001925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16402 Neighboring gene Sharpr-MPRA regulatory region 9755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:138089147-138089714 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:138089715-138090281 Neighboring gene CTNNA1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23216 Neighboring gene catenin alpha 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138164188-138164688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138188550-138189082 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:138279886-138280098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138284538-138285402 Neighboring gene uncharacterized LOC124901079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138289067-138290004 Neighboring gene SIL1 nucleotide exchange factor Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138346233-138346880 Neighboring gene uncharacterized LOC124901080 Neighboring gene RNA, 5S ribosomal pseudogene 194

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction. Yamagata A, et al. Nat Commun, 2018 Sep 27. PMID 30262834, Free PMC Article
    2. Bidirectional transcription from human LRRTM2/CTNNA1 and LRRTM1/CTNNA2 gene loci leads to expression of N-terminally truncated CTNNA1 and CTNNA2 isoforms. Kask M, et al. Biochem Biophys Res Commun, 2011 Jul 22. PMID 21708131
    3. A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. Laurén J, et al. Genomics, 2003 Apr. PMID 12676565
    4. Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. Loh KH, et al. Cell, 2016 Aug 25. PMID 27565350, Free PMC Article
    5. Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis. Graubert TA, et al. PLoS One, 2009. PMID 19240791, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Nrxn1beta-LRRTM2 interface involves Ca(2+)-mediated interactions and overlaps with the Nrxn-neuroligin interface.
      Title: Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction.
    2. CTNNA1 and CTNNA2 contain alternative 5' exons linked to bidirectional promoters that are shared with the antisense oriented LRRTM2 and LRRTM1 genes, respectively.
      Title: Bidirectional transcription from human LRRTM2/CTNNA1 and LRRTM1/CTNNA2 gene loci leads to expression of N-terminally truncated CTNNA1 and CTNNA2 isoforms.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ52416, FLJ76283, FLJ99831

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables neurexin family protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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 regulation of postsynaptic density 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 Schaffer collateral - CA1 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in excitatory synapse IEA
    Inferred from Electronic Annotation
    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 hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    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

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    Preferred Names
    leucine-rich repeat transmembrane neuronal protein 2
    Names
    leucine-rich repeat neuronal 2 protein
    leucine-rich repeat transmembrane neuronal 2 protein

    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_015564.3 → NP_056379.1  leucine-rich repeat transmembrane neuronal protein 2 precursor

      See identical proteins and their annotated locations for NP_056379.1

      Status: VALIDATED

      Source sequence(s)
      AB007876, AC011405, DA400927
      Consensus CDS
      CCDS47272.1
      UniProtKB/Swiss-Prot
      A0AVL3, A8K4U9, B7ZLN8, O43300, Q7L770
      Related
      ENSP00000274711.5, ENST00000274711.7
      Conserved Domains (3) summary
      TIGR00864
      Location:284 → 351
      PCC; polycystin cation channel protein
      COG4886
      Location:65 → 312
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:66 → 86
      LRR_RI; leucine-rich repeat [structural motif]

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      138868921..138875335 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      139395050..139401453 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43300.3 GenPept UniProtKB/Swiss-Prot:O43300

    Gene LinkOut

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

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