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    LRFN5 leucine rich repeat and fibronectin type III domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 145581, updated on 17-Jun-2019

    Summary

    Official Symbol
    LRFN5provided by HGNC
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:20360
    See related
    Ensembl:ENSG00000165379 MIM:612811
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SALM5; FIGLER8; C14orf146
    Summary
    This gene encodes a protein that belongs to the leucine-rich repeat and fibronectin type III domain-containing family of proteins. A similar protein in mouse, a glycosylated transmembrane protein, is thought to function in presynaptic differentiation. [provided by RefSeq, Sep 2016]
    Expression
    Biased expression in brain (RPKM 2.4), adrenal (RPKM 0.8) and 13 other tissues See more
    Orthologs

    Genomic context

    See LRFN5 in Genome Data Viewer
    Location:
    14q21.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (41606856..41904549)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (42076764..42373752)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2315 Neighboring gene WD repeat domain 75 pseudogene Neighboring gene uncharacterized LOC105370469 Neighboring gene FKBP prolyl isomerase 1B pseudogene 1 Neighboring gene olfactory receptor family 10 subfamily V member 7 pseudogene Neighboring gene leucine rich pentatricopeptide repeat containing pseudogene

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval.
    NHGRI GWA Catalog
    Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project.
    NHGRI GWA Catalog

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ30803, DKFZp686G0210

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    negative regulation of inflammatory response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of macrophage activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of presynapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    synaptic membrane adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    GABA-ergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integral component of postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    leucine-rich repeat and fibronectin type-III domain-containing protein 5
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 8

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_051660.1 RefSeqGene

      Range
      5001..302694
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001330106.1NP_001317035.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.
      Source sequence(s)
      AL109662, AL121821, AL138498, AW013887
      Consensus CDS
      CCDS81800.1
      UniProtKB/TrEMBL
      G3V364
      Related
      ENSP00000451067.1, ENST00000554171.1
      Conserved Domains (6) summary
      cd05764
      Location:301374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      cd00116
      Location:41207
      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 ...
      pfam07679
      Location:287374
      I-set; Immunoglobulin I-set domain
      sd00033
      Location:5376
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:99159
      LRR_8; Leucine rich repeat
      cl15307
      Location:240272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain
    2. NM_001346173.1NP_001333102.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR comapred to variant 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AL121821, AL138498, AW013887
      Consensus CDS
      CCDS9678.1
      UniProtKB/Swiss-Prot
      Q96NI6
    3. NM_001346175.1NP_001333104.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.
      Source sequence(s)
      AL121821, AL138498, AW013887
      Consensus CDS
      CCDS81800.1
      UniProtKB/TrEMBL
      G3V364
    4. NM_152447.4NP_689660.2  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_689660.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AK096627, AL121821, AL138498, AW013887, BC043165, DA096504
      Consensus CDS
      CCDS9678.1
      UniProtKB/Swiss-Prot
      Q96NI6
      Related
      ENSP00000298119.4, ENST00000298119.8
      Conserved Domains (7) summary
      cd05764
      Location:301374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:240272
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:41207
      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 ...
      pfam07679
      Location:287374
      I-set; Immunoglobulin I-set domain
      sd00033
      Location:5376
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:421494
      fn3; Fibronectin type III domain
      pfam13855
      Location:99159
      LRR_8; Leucine rich repeat

    RNA

    1. NR_144388.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses a different splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL109662, AL121821, AL138498, AW013887
    2. NR_144389.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL109662, AL121821, AL138498, AW013887

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

      Range
      41606856..41904549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021048.1XP_016876537.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

      UniProtKB/Swiss-Prot
      Q96NI6
      Conserved Domains (7) summary
      cd05764
      Location:301374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:240272
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:41207
      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 ...
      pfam07679
      Location:287374
      I-set; Immunoglobulin I-set domain
      sd00033
      Location:5376
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:421494
      fn3; Fibronectin type III domain
      pfam13855
      Location:99159
      LRR_8; Leucine rich repeat
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