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    LRRN3 leucine rich repeat neuronal 3 [ Homo sapiens (human) ]

    Gene ID: 54674, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LRRN3provided by HGNC
    Official Full Name
    leucine rich repeat neuronal 3provided by HGNC
    Primary source
    HGNC:HGNC:17200
    See related
    Ensembl:ENSG00000173114 MIM:619748; AllianceGenome:HGNC:17200
    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
    Also known as
    NLRR3; NLRR-3; FIGLER5
    Summary
    Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in adrenal (RPKM 13.7), brain (RPKM 11.9) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRN3 in Genome Data Viewer
    Location:
    7q31.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (111091127..111125454)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (112409397..112443727)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (110731183..110765510)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901723 Neighboring gene Sharpr-MPRA regulatory region 11752 Neighboring gene NANOG hESC enhancer GRCh37_chr7:110230392-110230942 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:110358473-110359258 Neighboring gene uncharacterized LOC124901724 Neighboring gene inner mitochondrial membrane peptidase subunit 2 Neighboring gene NANOG hESC enhancer GRCh37_chr7:110444579-110445080 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110490168-110490726 Neighboring gene Sharpr-MPRA regulatory region 15683 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110691790-110692442 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110736847-110737774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26505 Neighboring gene uncharacterized LOC124901853 Neighboring gene MPRA-validated peak6687 silencer Neighboring gene uncharacterized LOC124901725 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110832884-110833522 Neighboring gene MPRA-validated peak6688 silencer Neighboring gene uncharacterized LOC124900232

    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
    • 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. Intracellular fragment of NLRR3 (NLRR3-ICD) stimulates ATRA-dependent neuroblastoma differentiation. Akter J, et al. Biochem Biophys Res Commun, 2014 Oct 10. PMID 25256744
    2. Expression of NLRR3 orphan receptor gene is negatively regulated by MYCN and Miz-1, and its downregulation is associated with unfavorable outcome in neuroblastoma. Akter J, et al. Clin Cancer Res, 2011 Nov 1. PMID 21908575
    3. Rat neuronal leucine-rich repeat protein-3: cloning and regulation of the gene expression. Fukamachi K, et al. Biochem Biophys Res Commun, 2001 Sep 14. PMID 11549284
    4. Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry. Sousa I, et al. Mol Autism, 2010 Mar 25. PMID 20678249, Free PMC Article
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NLRR3 is proteolytically processed by secretases and its intracellular domain is then released to translocate into the cell nucleus during ATRA-mediated neuroblastoma differentiation.
      Title: Intracellular fragment of NLRR3 (NLRR3-ICD) stimulates ATRA-dependent neuroblastoma differentiation.
    2. NLRR3 is a direct target of MYCN, which associates with Miz-1 and negatively regulates NLRR3 expression. NLRR3 may play a role in NBL differentiation and the survival of NBL patients by inversely correlating with MYCN amplification.
      Title: Expression of NLRR3 orphan receptor gene is negatively regulated by MYCN and Miz-1, and its downregulation is associated with unfavorable outcome in neuroblastoma.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11129

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat neuronal protein 3
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 5
    leucine-rich repeat protein, neuronal 3
    neuronal leucine-rich repeat 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_001099658.2 → NP_001093128.1  leucine-rich repeat neuronal protein 3 precursor

      See identical proteins and their annotated locations for NP_001093128.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AL442092, AY358280, BC035133, DA494543
      Consensus CDS
      CCDS5754.1
      UniProtKB/Swiss-Prot
      O43377, Q6I9V8, Q8IYQ6, Q9H3W5
      UniProtKB/TrEMBL
      A4D0T1, A8K941
      Related
      ENSP00000312001.5, ENST00000308478.10
      Conserved Domains (6) summary
      TIGR00864
      Location:341 → 442
      PCC; polycystin cation channel protein
      smart00013
      Location:28 → 72
      LRRNT; Leucine rich repeat N-terminal domain
      COG4886
      Location:75 → 355
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:94 → 117
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:526 → 593
      fn3; Fibronectin type III domain
      cl11960
      Location:437 → 513
      Ig; Immunoglobulin domain

    2. NM_001099660.2 → NP_001093130.1  leucine-rich repeat neuronal protein 3 precursor

      See identical proteins and their annotated locations for NP_001093130.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AK001991, AL442092, AY358280, BC035133, DA494543
      Consensus CDS
      CCDS5754.1
      UniProtKB/Swiss-Prot
      O43377, Q6I9V8, Q8IYQ6, Q9H3W5
      UniProtKB/TrEMBL
      A4D0T1, A8K941
      Related
      ENSP00000397312.1, ENST00000451085.5
      Conserved Domains (6) summary
      TIGR00864
      Location:341 → 442
      PCC; polycystin cation channel protein
      smart00013
      Location:28 → 72
      LRRNT; Leucine rich repeat N-terminal domain
      COG4886
      Location:75 → 355
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:94 → 117
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:526 → 593
      fn3; Fibronectin type III domain
      cl11960
      Location:437 → 513
      Ig; Immunoglobulin domain

    3. NM_018334.5 → NP_060804.3  leucine-rich repeat neuronal protein 3 precursor

      See identical proteins and their annotated locations for NP_060804.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AF134481, AL442092, DA494543, DB095402
      Consensus CDS
      CCDS5754.1
      UniProtKB/Swiss-Prot
      O43377, Q6I9V8, Q8IYQ6, Q9H3W5
      UniProtKB/TrEMBL
      A4D0T1, A8K941
      Related
      ENSP00000412417.2, ENST00000422987.3
      Conserved Domains (6) summary
      TIGR00864
      Location:341 → 442
      PCC; polycystin cation channel protein
      smart00013
      Location:28 → 72
      LRRNT; Leucine rich repeat N-terminal domain
      COG4886
      Location:75 → 355
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:94 → 117
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:526 → 593
      fn3; Fibronectin type III domain
      cl11960
      Location:437 → 513
      Ig; Immunoglobulin domain

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      111091127..111125454
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      112409397..112443727
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H3W5.1 GenPept UniProtKB/Swiss-Prot:Q9H3W5

    Gene LinkOut

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

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