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Aliases for LRFN1 Gene

Aliases for LRFN1 Gene

  • Leucine Rich Repeat And Fibronectin Type III Domain Containing 1 2 3 5
  • 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

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 Transmission across Chemical Synapses and SALM protein interactions at the synapse. An important paralog of this gene is LINGO1.

UniProtKB/Swiss-Prot 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).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRFN1 Gene

Genomics for LRFN1 Gene

Regulatory Elements for LRFN1 Gene

Enhancers for LRFN1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LRFN1 on UCSC Golden Path with GeneCards custom track

Promoters for LRFN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LRFN1 on UCSC Golden Path with GeneCards custom track

Genomic Location for LRFN1 Gene

Chromosome:
19
Start:
39,306,568 bp from pter
End:
39,320,854 bp from pter
Size:
14,287 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

Proteomics data for LRFN1 Gene at MOPED

Post-translational modifications for LRFN1 Gene

Other Protein References for LRFN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for LRFN1 Gene

Domains & Families for LRFN1 Gene

Suggested Antigen Peptide Sequences for LRFN1 Gene

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.
  • Contains 7 LRR (leucine-rich) repeats.
Domain:
  • The PDZ-binding motif is required for neurite outgrowth promotion and for DLG1-, DLG3- and DLG4-binding.
  • Contains 1 fibronectin type-III domain.
  • Contains 1 Ig-like (immunoglobulin-like) domain.
  • Contains 1 LRRCT domain.
  • Contains 1 LRRNT domain.
Family:
  • Belongs to the LRFN family.
Similarity:
  • Contains 7 LRR (leucine-rich) repeats.
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 for LRFN1 Gene

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

Animal Model Products

  • Taconic Biosciences Mouse Models for LRFN1

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 cell membrane, postsynaptic density. Note=Detected in excitatory, but not inhibitory, synaptic plasma membrane. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LRFN1 Gene COMPARTMENTS Subcellular localization image for LRFN1 gene
Compartment Confidence
plasma membrane 5
nucleus 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for LRFN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0014069 postsynaptic density IEA --
GO:0016021 integral component of membrane IEA --
GO:0045211 postsynaptic membrane IEA --
genes like me logo Genes that share ontologies with LRFN1: view

Pathways & Interactions for LRFN1 Gene

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

Pathways by source for LRFN1 Gene

2 Reactome pathways for LRFN1 Gene

Gene Ontology (GO) - Biological Process for LRFN1 Gene

None

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

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(21) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LRFN1 Gene

Leucine rich repeat and fibronectin type III domain containing 1:
Representative Sequences:

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

No ASD Table

Relevant External Links for LRFN1 Gene

GeneLoc Exon Structure for
LRFN1
ECgene alternative splicing isoforms for
LRFN1

Expression for LRFN1 Gene

mRNA expression in normal human tissues 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, PaxDb, MOPED, and MaxQB for LRFN1 Gene



SOURCE GeneReport for Unigene cluster for LRFN1 Gene Hs.97860

genes like me logo Genes that share expression patterns with LRFN1: view

Protein tissue co-expression partners for LRFN1 Gene

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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
cow
(Bos Taurus)
Mammalia LRFN1 35
  • 89.6 (n)
  • 95.71 (a)
LRFN1 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LRFN1 35
  • 90.81 (n)
  • 96.36 (a)
LRFN1 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lrfn1 35
  • 87.15 (n)
  • 96.34 (a)
Lrfn1 16
Lrfn1 36
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LRFN1 35
  • 99.65 (n)
  • 99.74 (a)
LRFN1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lrfn1 35
  • 86.97 (n)
  • 96.34 (a)
oppossum
(Monodelphis domestica)
Mammalia LRFN1 36
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRFN1 36
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrfn1 35
  • 61.93 (n)
  • 66.91 (a)
zebrafish
(Danio rerio)
Actinopterygii mb21d2b 35
  • 67.23 (n)
  • 64.22 (a)
zgc63670 35
mb21d2b 36
  • 56 (a)
OneToOne
Species with no ortholog for LRFN1:
  • 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)

Paralogs for LRFN1 Gene

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

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

Variants for LRFN1 Gene

Sequence variations from dbSNP and Humsavar for LRFN1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs12978870 -- 39,322,392(+) gtgtg(C/T)gccac upstream-variant-2KB
rs12979175 -- 39,313,914(+) GGACT(A/G)CAGCA intron-variant
rs13343914 -- 39,322,599(+) atgcc(C/T)ggcta upstream-variant-2KB
rs62643365 -- 39,307,724(+) CGGCC(A/G)CGCCC reference, missense
rs71169583 -- 39,309,507(+) AAAAA(-/A)CCATC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv833830 CNV Loss 17160897
nsv911679 CNV Loss 21882294
nsv911680 CNV Loss 21882294
nsv911681 CNV Loss 21882294

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)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for LRFN1 Gene

Disorders for LRFN1 Gene

Relevant External Links for LRFN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 Res. 2000) 2 3 4 67
  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
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. A directed protein interaction network for investigating intracellular signal transduction. (PMID: 21900206) Vinayagam A. … Wanker E.E. (Sci Signal 2011) 3
  5. A human protein-protein interaction network: a resource for annotating the proteome. (PMID: 16169070) Stelzl U. … Wanker E.E. (Cell 2005) 3

Products for LRFN1 Gene

Sources for LRFN1 Gene

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