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    LRFN4 leucine rich repeat and fibronectin type III domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 78999, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LRFN4provided by HGNC
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:28456
    See related
    Ensembl:ENSG00000173621 MIM:612810; AllianceGenome:HGNC:28456
    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
    SALM3; SALM3.; FIGLER6
    Summary
    Predicted to be involved in regulation of postsynaptic density assembly; regulation of presynapse assembly; and synaptic membrane adhesion. Predicted to be located in plasma membrane. Predicted to be active in several cellular components, including GABA-ergic synapse; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in fat (RPKM 5.8), colon (RPKM 4.2) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRFN4 in Genome Data Viewer
    Location:
    11q13.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66857064..66860475)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66853340..66856751)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66624535..66627946)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene ferritin light chain pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66580049-66580832 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:66609109-66609235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3603 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66610783-66611489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66617715-66618294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66618295-66618873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3606 Neighboring gene Ras converting CAAX endopeptidase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66644024-66644524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66644525-66645025 Neighboring gene pyruvate carboxylase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66645752-66646490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66649447-66650184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66650185-66650922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66672605-66673252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66688620-66689560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66690541-66691041 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66691815-66692466 Neighboring gene RNA, U7 small nuclear 23 pseudogene Neighboring gene microRNA 3163

    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. A neuronal transmembrane protein LRFN4 induces monocyte/macrophage migration via actin cytoskeleton reorganization. Konakahara S, et al. FEBS Lett, 2011 Jul 21. PMID 21704618
    2. [Expression and clinical significance of LRFN4 in colorectal cancer tissue]. Zheng F, et al. Zhonghua Yi Xue Za Zhi, 2020 Jun 9. PMID 32536098
    3. High SALM3 Expression in Tumor Cells and Fibroblasts Is Correlated with Poor Prognosis in Gastric Cancer Patients. Liu Y, et al. Dis Markers, 2019. PMID 31089399, Free PMC Article
    4. A neuronal transmembrane protein LRFN4 complexes with 14-3-3s and NCK1 to induce morphological change in monocytic cells via Rac1-mediated actin cytoskeleton reorganization. Konakahara S, et al. FEBS Lett, 2012 Jul 30. PMID 22677168
    5. Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion. Li Y, et al. Cell Rep, 2015 Sep 8. PMID 26321637, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [Expression and clinical significance of LRFN4 in colorectal cancer tissue].
      Title: [Expression and clinical significance of LRFN4 in colorectal cancer tissue].
    2. SALM3 is overexpressed in the tumor cells and fibroblasts of gastric cancer patients. High SALM3 expression is associated with poor prognosis.
      Title: High SALM3 Expression in Tumor Cells and Fibroblasts Is Correlated with Poor Prognosis in Gastric Cancer Patients.
    3. SALM3 regulates excitatory synapse development and locomotion behavior.
      Title: Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion.
    4. LRFN4 complexed with 14-3-3s and NCK1 to mediate elongation in monocytic cells via Rac-1-mediated actin cytoskeleton reorganization
      Title: A neuronal transmembrane protein LRFN4 complexes with 14-3-3s and NCK1 to induce morphological change in monocytic cells via Rac1-mediated actin cytoskeleton reorganization.
    5. Data indicate that LRFN4 signaling plays an important role in the migration of monocytes/macrophages.
      Title: A neuronal transmembrane protein LRFN4 induces monocyte/macrophage migration via actin cytoskeleton reorganization.
    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

    EBI GWAS Catalog

    Description
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of LRFN4 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC3103

    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 regulation of postsynaptic density assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of presynapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic membrane adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and fibronectin type-III domain-containing protein 4
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 6

    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_001363524.2 → NP_001350453.1  leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AP003176
      Consensus CDS
      CCDS8153.1
      UniProtKB/Swiss-Prot
      Q4VBZ3, Q59GV4, Q6PJG9, Q8N644, Q9BWJ0
      Conserved Domains (5) summary
      cd05764
      Location:295 → 368
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:234 → 278
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:50 → 73
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:409 → 478
      fn3; Fibronectin type III domain
      pfam13855
      Location:97 → 157
      LRR_8; Leucine rich repeat

    2. NM_024036.5 → NP_076941.2  leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor

      See identical proteins and their annotated locations for NP_076941.2

      Status: VALIDATED

      Source sequence(s)
      AP003176, BC015581, CN297399
      Consensus CDS
      CCDS8153.1
      UniProtKB/Swiss-Prot
      Q4VBZ3, Q59GV4, Q6PJG9, Q8N644, Q9BWJ0
      Related
      ENSP00000312535.4, ENST00000309602.5
      Conserved Domains (5) summary
      cd05764
      Location:295 → 368
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:234 → 278
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:50 → 73
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:409 → 478
      fn3; Fibronectin type III domain
      pfam13855
      Location:97 → 157
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      66857064..66860475
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      66853340..66856751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PJG9.1 GenPept UniProtKB/Swiss-Prot:Q6PJG9

    Gene LinkOut

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

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