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

Gene ID: 145581, updated on 13-Feb-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 current GRCh38.p12 (GCF_000001405.38) 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 IEA
Inferred from Electronic Annotation
more info
 
synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
 
cell surface IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 

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.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 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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