Aliases for LRFN3 Gene

Aliases for LRFN3 Gene

  • Leucine Rich Repeat And Fibronectin Type III Domain Containing 3 2 3 5
  • Leucine-Rich Repeat And Fibronectin Type-III Domain-Containing Protein 3 3 4
  • Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 1 2 3
  • Synaptic Adhesion-Like Molecule 4 3 4
  • SALM4 3 4
  • FIGLER1 3

External Ids for LRFN3 Gene

Previous GeneCards Identifiers for LRFN3 Gene

  • GC19P041119
  • GC19P036427
  • GC19P032933
  • GC19P035982
  • GC19P037065
  • GC19P037235
  • GC19P037303
  • GC19P036003
  • GC19P036030
  • GC19P036032
  • GC19P036268
  • GC19P036429
  • GC19P036591
  • GC19P036756
  • GC19P036903

Summaries for LRFN3 Gene

GeneCards Summary for LRFN3 Gene

LRFN3 (Leucine Rich Repeat And Fibronectin Type III Domain Containing 3) is a Protein Coding gene. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. An important paralog of this gene is LRFN1.

UniProtKB/Swiss-Prot Summary for LRFN3 Gene

  • Cell adhesion molecule that mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons (By similarity).

Additional gene information for LRFN3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRFN3 Gene

Genomics for LRFN3 Gene

GeneHancer (GH) Regulatory Elements for LRFN3 Gene

Promoters and enhancers for LRFN3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRFN3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRFN3

Top Transcription factor binding sites by QIAGEN in the LRFN3 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • NF-kappaB
  • NF-kappaB1

Genomic Locations for LRFN3 Gene

Genomic Locations for LRFN3 Gene
chr19:35,935,358-35,945,767
(GRCh38/hg38)
Size:
10,410 bases
Orientation:
Plus strand
chr19:36,426,260-36,436,669
(GRCh37/hg19)
Size:
10,410 bases
Orientation:
Plus strand

Genomic View for LRFN3 Gene

Genes around LRFN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRFN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRFN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRFN3 Gene

Proteins for LRFN3 Gene

  • Protein details for LRFN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BTN0-LRFN3_HUMAN
    Recommended name:
    Leucine-rich repeat and fibronectin type-III domain-containing protein 3
    Protein Accession:
    Q9BTN0
    Secondary Accessions:
    • Q6UY10

    Protein attributes for LRFN3 Gene

    Size:
    628 amino acids
    Molecular mass:
    66260 Da
    Quaternary structure:
    • Can form heteromeric complexes with LRFN1, LRFN2, LRFN4 and LRFN5. Able to form homomeric complexes across cell junctions, between adjacent cells. Does not interact with DLG4 (By similarity).

neXtProt entry for LRFN3 Gene

Post-translational modifications for LRFN3 Gene

Other Protein References for LRFN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRFN3 Gene

Domains & Families for LRFN3 Gene

Protein Domains for LRFN3 Gene

Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin I-set
  • Cysteine-rich flanking region, C-terminal
  • Cysteine-rich flanking region, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LRFN3 Gene

GenScript: Design optimal peptide antigens:
  • Synaptic adhesion-like molecule 4 (LRFN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BTN0

UniProtKB/Swiss-Prot:

LRFN3_HUMAN :
  • Lacks a cytoplasmic PDZ-binding domain, which has been implicated in function of related Lrfn proteins.
  • Belongs to the LRFN family.
Domain:
  • Lacks a cytoplasmic PDZ-binding domain, which has been implicated in function of related Lrfn proteins.
Family:
  • Belongs to the LRFN family.
genes like me logo Genes that share domains with LRFN3: view

Function for LRFN3 Gene

Molecular function for LRFN3 Gene

UniProtKB/Swiss-Prot Function:
Cell adhesion molecule that mediates homophilic cell-cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons (By similarity).

Phenotypes From GWAS Catalog for LRFN3 Gene

genes like me logo Genes that share phenotypes with LRFN3: view

Animal Models for LRFN3 Gene

MGI Knock Outs for LRFN3:
  • Lrfn3 Lrfn3<tm1(KOMP)Vlcg>

Animal Model Products

  • Taconic Biosciences Mouse Models for LRFN3

CRISPR Products

miRNA for LRFN3 Gene

miRTarBase miRNAs that target LRFN3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRFN3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRFN3 Gene

Localization for LRFN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRFN3 Gene

Cell membrane; Single-pass type I membrane protein. Cell projection, axon. Cell projection, dendrite. Cell junction, synapse. Cell junction, synapse, presynaptic cell membrane. Cell junction, synapse, postsynaptic cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRFN3 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
endoplasmic reticulum 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for LRFN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with LRFN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRFN3 Gene

Pathways & Interactions for LRFN3 Gene

genes like me logo Genes that share pathways with LRFN3: view

Pathways by source for LRFN3 Gene

Gene Ontology (GO) - Biological Process for LRFN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0099179 regulation of synaptic membrane adhesion IBA 21873635
GO:0099560 synaptic membrane adhesion IBA 21873635
GO:1905606 regulation of presynapse assembly IBA 21873635
genes like me logo Genes that share ontologies with LRFN3: view

No data available for SIGNOR curated interactions for LRFN3 Gene

Drugs & Compounds for LRFN3 Gene

No Compound Related Data Available

Transcripts for LRFN3 Gene

mRNA/cDNA for LRFN3 Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRFN3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRFN3 Gene

No ASD Table

Relevant External Links for LRFN3 Gene

GeneLoc Exon Structure for
LRFN3

Expression for LRFN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRFN3 Gene

Protein differential expression in normal tissues from HIPED for LRFN3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRFN3 Gene



Protein tissue co-expression partners for LRFN3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRFN3

SOURCE GeneReport for Unigene cluster for LRFN3 Gene:

Hs.143792

Evidence on tissue expression from TISSUES for LRFN3 Gene

  • Lung(4.1)
  • Muscle(4.1)
genes like me logo Genes that share expression patterns with LRFN3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRFN3 Gene

Orthologs for LRFN3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRFN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRFN3 31 30
  • 99.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRFN3 31 30
  • 90.28 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRFN3 31 30
  • 87.66 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lrfn3 17 31 30
  • 86.34 (n)
rat
(Rattus norvegicus)
Mammalia Lrfn3 30
  • 85.9 (n)
oppossum
(Monodelphis domestica)
Mammalia LRFN3 31
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRFN3 31
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRFN3 31
  • 55 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRFN3 31
  • 54 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486910 30
  • 58.89 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:172282 30
  • 58.59 (n)
LRFN3 31
  • 53 (a)
OneToOne
Species where no ortholog for LRFN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRFN3 Gene

ENSEMBL:
Gene Tree for LRFN3 (if available)
TreeFam:
Gene Tree for LRFN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRFN3: view image

Paralogs for LRFN3 Gene

(4) SIMAP similar genes for LRFN3 Gene using alignment to 1 proteins:

  • LRFN3_HUMAN
genes like me logo Genes that share paralogs with LRFN3: view

Variants for LRFN3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRFN3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs34933126 - p.Ala14Val

Additional dbSNP identifiers (rs#s) for LRFN3 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRFN3 Gene

Variant ID Type Subtype PubMed ID
dgv51n68 CNV loss 17160897
nsv953287 CNV deletion 24416366

Variation tolerance for LRFN3 Gene

Residual Variation Intolerance Score: 17.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.81; 66.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRFN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRFN3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRFN3 Gene

Disorders for LRFN3 Gene

Additional Disease Information for LRFN3

No disorders were found for LRFN3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRFN3 Gene

Publications for LRFN3 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 54
  2. Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins. (PMID: 16828986) Morimura N … Aruga J (Gene 2006) 2 3 54
  3. A novel family of adhesion-like molecules that interacts with the NMDA receptor. (PMID: 16495444) Wang CY … Wenthold RJ (The Journal of neuroscience : the official journal of the Society for Neuroscience 2006) 2 3 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for LRFN3 Gene

Sources for LRFN3 Gene