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LRRTM3 leucine rich repeat transmembrane neuronal 3 [ Homo sapiens (human) ]

Gene ID: 347731, updated on 2-Nov-2024

Summary

Official Symbol
LRRTM3provided by HGNC
Official Full Name
leucine rich repeat transmembrane neuronal 3provided by HGNC
Primary source
HGNC:HGNC:19410
See related
Ensembl:ENSG00000198739 MIM:610869; AllianceGenome:HGNC:19410
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
Involved in regulation of presynapse assembly. Acts upstream of or within positive regulation of amyloid-beta formation. Is active in glutamatergic synapse. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in brain (RPKM 4.5), adrenal (RPKM 1.0) and 2 other tissues See more
Orthologs
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Genomic context

See LRRTM3 in Genome Data Viewer
Location:
10q21.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (66926036..67101551)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (67789258..67964743)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (68685794..68861309)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene catenin alpha 3 Neighboring gene uncharacterized LOC124902441 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15324 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15354 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:68197862-68199061 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15439 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15446 Neighboring gene small nucleolar RNA U13 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15534 Neighboring gene uncharacterized LOC101928961 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:68685181-68686037 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:68990147-68990732 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:68990733-68991316 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15618 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15623 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15629 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:69087266-69087766 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15668 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15678 Neighboring gene ribosomal protein L7a pseudogene 51 Neighboring gene microRNA 7151

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC131810

Gene Ontology Provided by GOA

Component Evidence Code Pubs
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 postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
leucine-rich repeat transmembrane neuronal protein 3

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_178011.5NP_821079.3  leucine-rich repeat transmembrane neuronal protein 3 precursor

    See identical proteins and their annotated locations for NP_821079.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the protein.
    Source sequence(s)
    AC022401, AC069536, BC111492
    Consensus CDS
    CCDS7270.1
    UniProtKB/Swiss-Prot
    A8K2A3, Q2NKX7, Q6N0A3, Q86VH5
    Related
    ENSP00000355187.3, ENST00000361320.5
    Conserved Domains (4) summary
    smart00013
    Location:3361
    LRRNT; Leucine rich repeat N-terminal domain
    sd00033
    Location:6686
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:86145
    LRR_8; Leucine rich repeat
    cd21340
    Location:156342
    PPP1R42; protein phosphatase 1 regulatory subunit 42

RNA

  1. NR_111909.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two exons and contains two alternate 5' exons, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC022401, BU154601, DB029785

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    66926036..67101551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    67789258..67964743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)