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Aliases for LRFN4 Gene

Aliases for LRFN4 Gene

  • Leucine Rich Repeat And Fibronectin Type III Domain Containing 4 2 3 5
  • Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 6 2 3
  • SALM3 3 4
  • Leucine-Rich Repeat And Fibronectin Type-III Domain-Containing Protein 4 3
  • FIGLER6 3
  • SALM3. 3

External Ids for LRFN4 Gene

Previous GeneCards Identifiers for LRFN4 Gene

  • GC11P066400
  • GC11P066381
  • GC11P066625
  • GC11P062952

Summaries for LRFN4 Gene

GeneCards Summary for LRFN4 Gene

LRFN4 (Leucine Rich Repeat And Fibronectin Type III Domain Containing 4) is a Protein Coding gene. Among its related pathways are Transmission across Chemical Synapses and Protein-protein interactions at synapses. An important paralog of this gene is LRFN2.

UniProtKB/Swiss-Prot for LRFN4 Gene

  • Promotes neurite outgrowth in hippocampal neurons. May play a role in redistributing DLG4 to the cell periphery (By similarity).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRFN4 Gene

Genomics for LRFN4 Gene

Regulatory Elements for LRFN4 Gene

Enhancers for LRFN4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F066854 0.8 ENCODE 17.1 +0.3 271 3.5 HDGF ARID4B SIN3A YBX1 DMAP1 GLIS2 ELK1 ZNF207 KLF7 KLF13 LRFN4 SPTBN2 ACTN3 LOC101928069 GC11M066908 GC11M066909
GH11F066865 0.5 ENCODE 12.3 +9.8 9846 3.0 CTCF ZIC2 RAD21 ZNF316 ZFHX2 POLR2A SCRT2 ZNF600 ZNF24 ZBTB33 LRFN4 PC RHOD GC11M066908 GC11M066909
GH11F066879 0.6 Ensembl ENCODE 12.2 +25.5 25511 4.8 TBP PKNOX1 SREBF2 ZNF76 ARID4B SIN3A ZNF2 RAD21 RFX5 ZNF143 C11orf80 ACTN3 CTSF RAD9A RCE1 LRFN4 PC RNU7-23P RHOD LOC100505504
GH11F066886 0.8 Ensembl ENCODE 12.2 +30.6 30593 1.8 SCRT1 NRF1 SIN3A ZEB2 NR3C1 ARID1B OSR2 ZFP69B FOSL1 JUND LRFN4 PC RCE1 RNU7-23P LOC100505504 RHOD ACTN3 GC11M066908 GC11M066909
GH11F066891 1.3 FANTOM5 Ensembl ENCODE 12.2 +36.1 36112 1.8 PKNOX1 CREB3L1 MLX ARID4B SIN3A FEZF1 SLC30A9 FOS JUNB REST LOC105369353 RAD9A LRFN4 RBM4B RNU7-23P SYT12 ACTN3 CDK2AP2 CLCF1 RBM4
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LRFN4 on UCSC Golden Path with GeneCards custom track

Promoters for LRFN4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000685631 420 2201 HDGF ARID4B SIN3A YBX1 DMAP1 GLIS2 ZNF207 KLF7 KLF13 DEK

Genomic Location for LRFN4 Gene

Chromosome:
11
Start:
66,856,480 bp from pter
End:
66,860,475 bp from pter
Size:
3,996 bases
Orientation:
Plus strand

Genomic View for LRFN4 Gene

Genes around LRFN4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRFN4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRFN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRFN4 Gene

Proteins for LRFN4 Gene

  • Protein details for LRFN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6PJG9-LRFN4_HUMAN
    Recommended name:
    Leucine-rich repeat and fibronectin type-III domain-containing protein 4
    Protein Accession:
    Q6PJG9
    Secondary Accessions:
    • Q4VBZ3
    • Q59GV4
    • Q8N644
    • Q9BWJ0

    Protein attributes for LRFN4 Gene

    Size:
    635 amino acids
    Molecular mass:
    66860 Da
    Quaternary structure:
    • Can form heteromeric complexes with LRFN1, LRFN2, LRFN3 and LRFN5. Unable to form homophilic interactions across cell junctions (By similarity). Interacts with DLG1, DLG2, DLG3 and DLG4.

neXtProt entry for LRFN4 Gene

Post-translational modifications for LRFN4 Gene

Other Protein References for LRFN4 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for LRFN4
  • Santa Cruz Biotechnology (SCBT) Antibodies for LRFN4

No data available for DME Specific Peptides for LRFN4 Gene

Domains & Families for LRFN4 Gene

Graphical View of Domain Structure for InterPro Entry

Q6PJG9

UniProtKB/Swiss-Prot:

LRFN4_HUMAN :
  • The PDZ-binding motif is required for neurite outgrowth promotion (By similarity). This motif is also involved in 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 (By similarity). This motif is also involved in 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 LRFN4: view

Function for LRFN4 Gene

Molecular function for LRFN4 Gene

UniProtKB/Swiss-Prot Function:
Promotes neurite outgrowth in hippocampal neurons. May play a role in redistributing DLG4 to the cell periphery (By similarity).

Gene Ontology (GO) - Molecular Function for LRFN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LRFN4: view
genes like me logo Genes that share phenotypes with LRFN4: view

Animal Models for LRFN4 Gene

MGI Knock Outs for LRFN4:

Animal Model Products

  • Taconic Biosciences Mouse Models for LRFN4

miRNA for LRFN4 Gene

miRTarBase miRNAs that target LRFN4

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRFN4 Gene

Localization for LRFN4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRFN4 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LRFN4 Gene COMPARTMENTS Subcellular localization image for LRFN4 gene
Compartment Confidence
plasma membrane 3
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
lysosome 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for LRFN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRFN4: view

Pathways & Interactions for LRFN4 Gene

genes like me logo Genes that share pathways with LRFN4: view

Pathways by source for LRFN4 Gene

Gene Ontology (GO) - Biological Process for LRFN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007268 chemical synaptic transmission TAS --
GO:0007409 axonogenesis IBA --
genes like me logo Genes that share ontologies with LRFN4: view

No data available for SIGNOR curated interactions for LRFN4 Gene

Transcripts for LRFN4 Gene

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRFN4 Gene

No ASD Table

Relevant External Links for LRFN4 Gene

GeneLoc Exon Structure for
LRFN4
ECgene alternative splicing isoforms for
LRFN4

Expression for LRFN4 Gene

mRNA expression in normal human tissues for LRFN4 Gene

Protein differential expression in normal tissues from HIPED for LRFN4 Gene

This gene is overexpressed in Fetal Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRFN4 Gene



Protein tissue co-expression partners for LRFN4 Gene

NURSA nuclear receptor signaling pathways regulating expression of LRFN4 Gene:

LRFN4

SOURCE GeneReport for Unigene cluster for LRFN4 Gene:

Hs.209979
genes like me logo Genes that share expression patterns with LRFN4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for LRFN4 Gene

Orthologs for LRFN4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRFN4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRFN4 35
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LRFN4 35
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LRFN4 34 35
  • 90.68 (n)
cow
(Bos Taurus)
Mammalia LRFN4 34 35
  • 90.41 (n)
mouse
(Mus musculus)
Mammalia Lrfn4 34 16 35
  • 87.83 (n)
rat
(Rattus norvegicus)
Mammalia Lrfn4 34
  • 87.51 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 42 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia lrfn2 34
  • 58.29 (n)
zebrafish
(Danio rerio)
Actinopterygii lrfn4b 34 35
  • 60.87 (n)
lrfn4a 35
  • 41 (a)
OneToMany
Species where no ortholog for LRFN4 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 LRFN4 Gene

ENSEMBL:
Gene Tree for LRFN4 (if available)
TreeFam:
Gene Tree for LRFN4 (if available)

Paralogs for LRFN4 Gene

(6) SIMAP similar genes for LRFN4 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LRFN4: view

Variants for LRFN4 Gene

Sequence variations from dbSNP and Humsavar for LRFN4 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs111498329 -- 66,859,790(+) CTGCC(A/G)GCCTC intron-variant, reference, synonymous-codon
rs112380440 -- 66,860,784(+) AGCAC(A/G)TGTGA intron-variant, downstream-variant-500B
rs112634850 -- 66,857,753(+) GCCCC(A/G)CCGCT intron-variant, upstream-variant-2KB, reference, synonymous-codon
rs113659922 -- 66,860,294(+) TTATT(C/G)TCAGT intron-variant, utr-variant-3-prime
rs114035451 -- 66,860,701(+) GGCCT(A/C/G)CCCTC intron-variant, downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for LRFN4 Gene

Variant ID Type Subtype PubMed ID
nsv1070968 CNV deletion 25765185
nsv468602 CNV loss 19166990
nsv508638 CNV deletion 20534489
nsv555225 CNV loss 21841781
nsv555226 CNV gain 21841781
nsv951020 CNV deletion 24416366

Variation tolerance for LRFN4 Gene

Residual Variation Intolerance Score: 28.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.30; 76.57% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRFN4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRFN4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRFN4 Gene

Disorders for LRFN4 Gene

Relevant External Links for LRFN4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRFN4

No disorders were found for LRFN4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRFN4 Gene

Publications for LRFN4 Gene

  1. A novel family of adhesion-like molecules that interacts with the NMDA receptor. (PMID: 16495444) Wang C.Y. … Wenthold R.J. (J. Neurosci. 2006) 2 3 64
  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 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  5. Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion. (PMID: 26321637) Li Y. … Kim E. (Cell Rep 2015) 3 64

Products for LRFN4 Gene

Sources for LRFN4 Gene

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