Aliases for LRFN1 Gene

Aliases for LRFN1 Gene

  • Leucine Rich Repeat And Fibronectin Type III Domain Containing 1 2 3 5
  • Leucine-Rich Repeat And Fibronectin Type III Domain-Containing Protein 1 3 4
  • Synaptic Adhesion-Like Molecule 2 3 4
  • SALM2 3 4
  • CTC-246B18.8 3
  • KIAA1484 4

External Ids for LRFN1 Gene

Previous GeneCards Identifiers for LRFN1 Gene

  • GC19M044489
  • GC19M039798
  • GC19M036243
  • GC19M039307
  • GC19M039364
  • GC19M040168
  • GC19M040224
  • GC19M039778
  • GC19M039421
  • GC19M039454
  • GC19M039509
  • GC19M039559
  • GC19M039606
  • GC19M039656
  • GC19M039711
  • GC19M039916

Summaries for LRFN1 Gene

GeneCards Summary for LRFN1 Gene

LRFN1 (Leucine Rich Repeat And Fibronectin Type III Domain Containing 1) 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 LRFN2.

UniProtKB/Swiss-Prot Summary for LRFN1 Gene

  • Promotes neurite outgrowth in hippocampal neurons. Involved in the regulation and maintenance of excitatory synapses. Induces the clustering of excitatory postsynaptic proteins, including DLG4, DLGAP1, GRIA1 and GRIN1 (By similarity).

Additional gene information for LRFN1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRFN1 Gene

Genomics for LRFN1 Gene

GeneHancer (GH) Regulatory Elements for LRFN1 Gene

Promoters and enhancers for LRFN1 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 LRFN1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRFN1

Top Transcription factor binding sites by QIAGEN in the LRFN1 gene promoter:
  • CREB
  • CUTL1
  • deltaCREB
  • FAC1
  • Gfi-1
  • GR
  • GR-alpha
  • GR-beta
  • NF-1
  • SEF-1 (1)

Genomic Locations for LRFN1 Gene

Genomic Locations for LRFN1 Gene
chr19:39,306,568-39,320,854
(GRCh38/hg38)
Size:
14,287 bases
Orientation:
Minus strand
chr19:39,797,208-39,805,976
(GRCh37/hg19)
Size:
8,769 bases
Orientation:
Minus strand

Genomic View for LRFN1 Gene

Genes around LRFN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRFN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRFN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRFN1 Gene

Proteins for LRFN1 Gene

  • Protein details for LRFN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P244-LRFN1_HUMAN
    Recommended name:
    Leucine-rich repeat and fibronectin type III domain-containing protein 1
    Protein Accession:
    Q9P244
    Secondary Accessions:
    • Q8TBS9

    Protein attributes for LRFN1 Gene

    Size:
    771 amino acids
    Molecular mass:
    82318 Da
    Quaternary structure:
    • Can form heteromeric complexes with LRFN2, LRFN3, LRFN4 and LRFN5 (By similarity). Forms homomeric complexes, but not across cell junctions (By similarity). Interacts with DLG1, DLG2, DLG3 and DLG4. Interacts with 2 AMPA receptor subunits GRIA1 and GRIA2 and NMDA receptor subunit GRIN1 (By similarity).

neXtProt entry for LRFN1 Gene

Post-translational modifications for LRFN1 Gene

Other Protein References for LRFN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRFN1 Gene

Domains & Families for LRFN1 Gene

Protein Domains for LRFN1 Gene

Suggested Antigen Peptide Sequences for LRFN1 Gene

GenScript: Design optimal peptide antigens:
  • Synaptic adhesion-like molecule 2 (LRFN1_HUMAN)
  • LRFN1 protein (Q96C50_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9P244

UniProtKB/Swiss-Prot:

LRFN1_HUMAN :
  • The PDZ-binding motif is required for neurite outgrowth promotion and for DLG1-, DLG3- and DLG4-binding.
  • Belongs to the LRFN family.
Domain:
  • The PDZ-binding motif is required for neurite outgrowth promotion and for DLG1-, DLG3- and DLG4-binding.
Family:
  • Belongs to the LRFN family.
genes like me logo Genes that share domains with LRFN1: view

Function for LRFN1 Gene

Molecular function for LRFN1 Gene

UniProtKB/Swiss-Prot Function:
Promotes neurite outgrowth in hippocampal neurons. Involved in the regulation and maintenance of excitatory synapses. Induces the clustering of excitatory postsynaptic proteins, including DLG4, DLGAP1, GRIA1 and GRIN1 (By similarity).

Phenotypes From GWAS Catalog for LRFN1 Gene

genes like me logo Genes that share phenotypes with LRFN1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LRFN1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRFN1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRFN1 Gene

Localization for LRFN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRFN1 Gene

Membrane; Single-pass type I membrane protein. Cell junction, synapse. Cell junction, synapse, postsynaptic density membrane. Note=Detected in excitatory, but not inhibitory, synaptic plasma membrane. {ECO:0000250}.

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 LRFN1 gene
Compartment Confidence
plasma membrane 5
nucleus 3
extracellular 1
cytoskeleton 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for LRFN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IEA,IBA 21873635
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRFN1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRFN1 Gene

Pathways & Interactions for LRFN1 Gene

genes like me logo Genes that share pathways with LRFN1: view

Pathways by source for LRFN1 Gene

Gene Ontology (GO) - Biological Process for LRFN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0099151 regulation of postsynaptic density assembly IEA --
genes like me logo Genes that share ontologies with LRFN1: view

No data available for SIGNOR curated interactions for LRFN1 Gene

Drugs & Compounds for LRFN1 Gene

No Compound Related Data Available

Transcripts for LRFN1 Gene

mRNA/cDNA for LRFN1 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 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 LRFN1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRFN1 Gene

No ASD Table

Relevant External Links for LRFN1 Gene

GeneLoc Exon Structure for
LRFN1

Expression for LRFN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRFN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRFN1 Gene

This gene is overexpressed in Whole Blood (x13.0).

Protein differential expression in normal tissues from HIPED for LRFN1 Gene

This gene is overexpressed in Colon (30.7), Heart (21.1), Fetal Brain (11.2), and Retina (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRFN1 Gene



Protein tissue co-expression partners for LRFN1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRFN1

SOURCE GeneReport for Unigene cluster for LRFN1 Gene:

Hs.97860

Evidence on tissue expression from TISSUES for LRFN1 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with LRFN1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRFN1 Gene

Orthologs for LRFN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRFN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRFN1 31 30
  • 99.65 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRFN1 31 30
  • 90.81 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRFN1 31 30
  • 89.6 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lrfn1 17 31 30
  • 87.15 (n)
rat
(Rattus norvegicus)
Mammalia Lrfn1 30
  • 86.97 (n)
oppossum
(Monodelphis domestica)
Mammalia LRFN1 31
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRFN1 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrfn1 30
  • 61.93 (n)
zebrafish
(Danio rerio)
Actinopterygii mb21d2b 31 30
  • 67.23 (n)
OneToOne
zgc63670 30
Species where no ortholog for LRFN1 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)
  • chicken (Gallus gallus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 LRFN1 Gene

ENSEMBL:
Gene Tree for LRFN1 (if available)
TreeFam:
Gene Tree for LRFN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRFN1: view image

Paralogs for LRFN1 Gene

(4) SIMAP similar genes for LRFN1 Gene using alignment to 3 proteins:

  • LRFN1_HUMAN
  • L8E910_HUMAN
  • Q96C50_HUMAN
genes like me logo Genes that share paralogs with LRFN1: view

Variants for LRFN1 Gene

Additional dbSNP identifiers (rs#s) for LRFN1 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRFN1 Gene

Variant ID Type Subtype PubMed ID
nsv833830 CNV loss 17160897

Variation tolerance for LRFN1 Gene

Residual Variation Intolerance Score: 12.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.97; 20.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRFN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRFN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRFN1 Gene

Disorders for LRFN1 Gene

Additional Disease Information for LRFN1

No disorders were found for LRFN1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRFN1 Gene

Publications for LRFN1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  4. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 54
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 54

Products for LRFN1 Gene

Sources for LRFN1 Gene