Aliases for LRFN4 Gene

Aliases for LRFN4 Gene

  • Leucine Rich Repeat And Fibronectin Type III Domain Containing 4 2 3 5
  • Leucine-Rich Repeat And Fibronectin Type-III Domain-Containing Protein 4 3 4
  • Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 6 2 3
  • SALM3 3 4
  • 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. Diseases associated with LRFN4 include Central Nervous System Tuberculosis and Cone-Rod Dystrophy 2. 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 LRFN4 Gene

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

Additional gene information for LRFN4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRFN4 Gene

Genomics for LRFN4 Gene

GeneHancer (GH) Regulatory Elements for LRFN4 Gene

Promoters and enhancers for LRFN4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J066854 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 517 +0.3 270 3.5 HNRNPK ZBTB40 ZNF217 NRF1 TCF12 POLR2G USF1 BCLAF1 GTF2E2 ZNF10 LRFN4 RBM4 ENSG00000254461 ENSG00000254855 RCE1 KDM2A MUS81 SF3B2 ENSG00000245156 ENSG00000255038
GH11J066855 Promoter/Enhancer 0.6 Ensembl dbSUPER 500.7 -1.9 -1879 0.4 POLR2A LRFN4 CDK2AP2 HSALNG0085087 PC
GH11J066889 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 23.5 +35.6 35620 4.6 ZNF217 CTCF TCF12 SP1 JUND FOS ZNF639 REST ZBTB11 AFF1 RAD9A LRFN4 CTSF RCE1 RNU7-23P PC SYT12 ACTN3 CDK2AP2 CLCF1
GH11J066675 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 11.2 -179.4 -179364 4.2 ZNF217 EP300 CTCF SIN3A NRF1 POLR2G SP1 GTF2E2 PHF8 POLR2A RBM4B lnc-RBM4-2 RBM14 RBM4 RAD9A CCS RCE1 SF3B2 ENSG00000245156 EIF1AD
GH11J066901 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.9 +49.1 49056 7.8 EP300 FOXK2 TCF12 POLR2G USF1 NCOR1 ZIC2 KDM6A TCF7 ZNF623 PC C11orf80 RHOD ACTN3 CTSF RIN1 C11orf86 LRFN4 SYT12 ENSG00000254510
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRFN4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRFN4

Top Transcription factor binding sites by QIAGEN in the LRFN4 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • Egr-2
  • HEN1
  • HSF2
  • Pax-5
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for LRFN4 Gene

Genomic Locations for LRFN4 Gene
chr11:66,856,480-66,860,475
(GRCh38/hg38)
Size:
3,996 bases
Orientation:
Plus strand
chr11:66,624,118-66,627,946
(GRCh37/hg19)
Size:
3,829 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

  • Glycosylated.
  • Glycosylation at Asn25, Asn70, Asn324, Asn333, Asn376, and Asn440
  • Modification sites at PhosphoSitePlus

Other Protein References for LRFN4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRFN4 Gene

Domains & Families for LRFN4 Gene

Gene Families for LRFN4 Gene

Protein Domains for LRFN4 Gene

Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin subtype
  • Cysteine-rich flanking region, C-terminal
  • Leucine-rich repeat signature
  • Cysteine-rich flanking region, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LRFN4 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat and fibronectin type-III domain-containing protein 4 (LRFN4_HUMAN)
  • LRFN4 protein (Q6IPL6_HUMAN)
  • LRFN4 protein (Q6PK41_HUMAN)
  • LRFN4 protein (Q7L3C2_HUMAN)

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.
Domain:
  • The PDZ-binding motif is required for neurite outgrowth promotion (By similarity). This motif is also involved in DLG1-, DLG3- and DLG4-binding.
Family:
  • Belongs to the LRFN family.
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).

Phenotypes From GWAS Catalog for LRFN4 Gene

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:
  • Lrfn4 Lrfn4<tm1(KOMP)Vlcg>

Animal Model Products

  • Taconic Biosciences Mouse Models for LRFN4

CRISPR Products

miRNA for LRFN4 Gene

miRTarBase miRNAs that target LRFN4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRFN4

Clone 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
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 LRFN4 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
peroxisome 0
endoplasmic reticulum 0
lysosome 0
golgi apparatus 0

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 IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0098978 glutamatergic synapse IBA 21873635
genes like me logo Genes that share ontologies with LRFN4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRFN4 Gene

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:0099151 regulation of postsynaptic density assembly 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 LRFN4: view

No data available for SIGNOR curated interactions for LRFN4 Gene

Drugs & Compounds for LRFN4 Gene

No Compound Related Data Available

Transcripts for LRFN4 Gene

mRNA/cDNA for LRFN4 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 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 LRFN4

Clone 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

Expression for LRFN4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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 and MOPED for LRFN4 Gene



Protein tissue co-expression partners for LRFN4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRFN4

SOURCE GeneReport for Unigene cluster for LRFN4 Gene:

Hs.209979

Evidence on tissue expression from TISSUES for LRFN4 Gene

  • Lung(4.7)
  • Nervous system(4.5)
  • Eye(4.4)
  • Stomach(3.1)
genes like me logo Genes that share expression patterns with LRFN4: 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 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 31
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LRFN4 31
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LRFN4 31 30
  • 90.68 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRFN4 31 30
  • 90.41 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lrfn4 17 31 30
  • 87.83 (n)
rat
(Rattus norvegicus)
Mammalia Lrfn4 30
  • 87.51 (n)
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 42 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia lrfn2 30
  • 58.29 (n)
zebrafish
(Danio rerio)
Actinopterygii lrfn4b 31 30
  • 60.87 (n)
OneToMany
lrfn4a 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for LRFN4: view image

Paralogs for LRFN4 Gene

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

  • LRFN4_HUMAN
  • E7ENX6_HUMAN
  • Q6IPL6_HUMAN
  • Q6PK41_HUMAN
  • Q7L3C2_HUMAN
genes like me logo Genes that share paralogs with LRFN4: view

Variants for LRFN4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRFN4 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs3741194 - p.Val340Ala

Additional dbSNP identifiers (rs#s) for LRFN4 Gene

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)

Additional Variant Information for LRFN4 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LRFN4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LRFN4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
central nervous system tuberculosis
  • intracranial tuberculoma
cone-rod dystrophy 2
  • cord2
- elite association - COSMIC cancer census association via MalaCards
Search LRFN4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRFN4

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

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

Publications for LRFN4 Gene

  1. 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
  2. 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
  3. 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
  4. High SALM3 Expression in Tumor Cells and Fibroblasts Is Correlated with Poor Prognosis in Gastric Cancer Patients. (PMID: 31089399) Liu Y … Wu H (Disease markers 2019) 3 54
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54

Products for LRFN4 Gene

Sources for LRFN4 Gene