LRRC4B Gene (Protein Coding)

Leucine Rich Repeat Containing 4B

GC19M050516
GIFtS:
34
See more...

Aliases for LRRC4B Gene

Aliases for LRRC4B Gene

  • Leucine Rich Repeat Containing 4B 2 3 5
  • Netrin-G3 Ligand 2 3 4
  • Leucine-Rich Repeats And Immunoglobulin-Like Domains 4 2 3
  • Leucine-Rich Repeat-Containing Protein 4B 3 4
  • LRIG4 3 4
  • NGL-3 3 4
  • HSM 2 3
  • DKFZp761A179 2
  • LRRC4B 5

External Ids for LRRC4B Gene

Previous HGNC Symbols for LRRC4B Gene

  • LRIG4

Previous GeneCards Identifiers for LRRC4B Gene

  • GC19M055713
  • GC19M055714
  • GC19M051020
  • GC19M047356

Summaries for LRRC4B Gene

GeneCards Summary for LRRC4B Gene

LRRC4B (Leucine Rich Repeat Containing 4B) is a Protein Coding gene. Among its related pathways are Cell adhesion molecules. Gene Ontology (GO) annotations related to this gene include signaling receptor binding. An important paralog of this gene is LRRC4C.

UniProtKB/Swiss-Prot Summary for LRRC4B Gene

  • Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity).

Additional gene information for LRRC4B Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRC4B Gene

Genomics for LRRC4B Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for LRRC4B 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 LRRC4B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRC4B

Top Transcription factor binding sites by QIAGEN in the LRRC4B gene promoter:
  • AP-4
  • LyF-1
  • MAZR
  • MIF-1
  • NRSF form 1
  • NRSF form 2
  • Pax-2b
  • STAT5B

Genomic Locations for LRRC4B Gene

Latest Assembly
chr19:50,516,892-50,568,435
(GRCh38/hg38)
Size:
51,544 bases
Orientation:
Minus strand

Previous Assembly
chr19:51,020,149-51,071,692
(GRCh37/hg19 by Entrez Gene)
Size:
51,544 bases
Orientation:
Minus strand

chr19:51,020,149-51,071,302
(GRCh37/hg19 by Ensembl)
Size:
51,154 bases
Orientation:
Minus strand

Genomic View for LRRC4B Gene

Genes around LRRC4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC4B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LRRC4B Gene

Proteins for LRRC4B Gene

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  • Protein details for LRRC4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NT99-LRC4B_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 4B
    Protein Accession:
    Q9NT99
    Secondary Accessions:
    • Q3ZCQ4
    • Q58F20

    Protein attributes for LRRC4B Gene

    Size:
    713 amino acids
    Molecular mass:
    76434 Da
    Quaternary structure:
    • Interacts with PTPRF. Interacts with DLG4.
    SequenceCaution:
    • Sequence=AAH19687.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LRRC4B Gene

Protein Expression for LRRC4B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LRRC4B Gene

  • N-glycosylated. O-glycosylated; contains sialic acid.
  • Glycosylation at Asn224, Asn283, Asn333, Asn374, Asn400, Asn422, Asn425, Asn444, and Asn452
  • Modification sites at PhosphoSitePlus

Other Protein References for LRRC4B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRRC4B Gene

Domains & Families for LRRC4B Gene

Gene Families for LRRC4B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for LRRC4B Gene

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

Suggested Antigen Peptide Sequences for LRRC4B Gene

GenScript: Design optimal peptide antigens:
  • LRRC4B protein (A0PJJ4_HUMAN)
  • LRRC4B protein (A2VDK1_HUMAN)
  • Netrin-G3 ligand (LRC4B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NT99

UniProtKB/Swiss-Prot:

LRC4B_HUMAN :
  • The last 4 C-terminal residues bind to the first 2 PDZ domains of DLG4.
Domain:
  • The last 4 C-terminal residues bind to the first 2 PDZ domains of DLG4.
genes like me logo Genes that share domains with LRRC4B: view

Function for LRRC4B Gene

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  6. Cell Lines for research

Molecular function for LRRC4B Gene

UniProtKB/Swiss-Prot Function:
Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity).

Phenotypes From GWAS Catalog for LRRC4B Gene

Gene Ontology (GO) - Molecular Function for LRRC4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LRRC4B: view
genes like me logo Genes that share phenotypes with LRRC4B: view

Animal Models for LRRC4B Gene

MGI Knock Outs for LRRC4B:

Animal Models for research

  • Taconic Biosciences Mouse Models for LRRC4B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC4B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRRC4B Gene

Localization for LRRC4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRC4B Gene

Membrane. Single-pass membrane protein. Cell junction, synapse, presynaptic 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 LRRC4B gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1
lysosome 0

Gene Ontology (GO) - Cellular Components for LRRC4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
GO:0042734 presynaptic membrane IEA --
genes like me logo Genes that share ontologies with LRRC4B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRRC4B Gene

Pathways & Interactions for LRRC4B Gene

PathCards logo

SuperPathways for LRRC4B Gene

SuperPathway Contained pathways
1 Cell adhesion molecules
Cell adhesion molecules
-
genes like me logo Genes that share pathways with LRRC4B: view

Pathways by source for LRRC4B Gene

1 KEGG pathway for LRRC4B Gene

Gene Ontology (GO) - Biological Process for LRRC4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051965 positive regulation of synapse assembly ISS --
GO:0099151 regulation of postsynaptic density assembly IEA --
GO:0099560 synaptic membrane adhesion IEA --
GO:1905606 regulation of presynapse assembly IEA --
genes like me logo Genes that share ontologies with LRRC4B: view

No data available for SIGNOR curated interactions for LRRC4B Gene

Drugs & Compounds for LRRC4B Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for LRRC4B Gene

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mRNA/cDNA for LRRC4B Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC4B

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC4B Gene

No ASD Table

Relevant External Links for LRRC4B Gene

GeneLoc Exon Structure for
LRRC4B

Expression for LRRC4B Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRC4B Gene

mRNA expression in normal human tissues for LRRC4B Gene
mRNA expression by GTEx for LRRC4B Gene

mRNA differential expression in normal tissues according to GTEx for LRRC4B Gene

This gene is overexpressed in Brain - Cortex (x4.6).

Protein differential expression in normal tissues from HIPED for LRRC4B Gene

This gene is overexpressed in Cerebrospinal fluid (24.4), Fetal Brain (23.1), Frontal cortex (9.8), and Vitreous humor (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRRC4B Gene



Protein tissue co-expression partners for LRRC4B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRC4B

SOURCE GeneReport for Unigene cluster for LRRC4B Gene:

Hs.120873

Evidence on tissue expression from TISSUES for LRRC4B Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with LRRC4B: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC4B Gene

Orthologs for LRRC4B Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC4B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia LRRC4B 30 31
  • 99.86 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia LRRC4B 31
  • 99 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia LRRC4B 30 31
  • 93.25 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia LRRC4B 30 31
  • 92.33 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Lrrc4b 30 17 31
  • 88.15 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Lrrc4b 30
  • 87.58 (n)
Lizard
(Anolis carolinensis)
 Reptilia LRRC4B 31
  • 87 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia lrrc4b 30
  • 73.4 (n)
Zebrafish
(Danio rerio)
 Actinopterygii lrrc4ba 31
  • 66 (a)
 OneToMany
lrrc4bb 31
  • 63 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 39 (a)
 OneToMany
Species where no ortholog for LRRC4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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 LRRC4B Gene

ENSEMBL:
Gene Tree for LRRC4B (if available)
TreeFam:
Gene Tree for LRRC4B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC4B: view image

Paralogs for LRRC4B Gene

Paralogs for LRRC4B Gene

(8) SIMAP similar genes for LRRC4B Gene using alignment to 4 proteins:

  • LRC4B_HUMAN
  • A0PJJ4_HUMAN
  • A2VDK1_HUMAN
  • M0R2G0_HUMAN
genes like me logo Genes that share paralogs with LRRC4B: view

Variants for LRRC4B Gene

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dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRRC4B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LRRC4B Gene

Variant ID Type Subtype PubMed ID
esv3556530 CNV deletion 23714750
esv3556531 CNV deletion 23714750
esv994565 CNV deletion 20482838
nsv1072892 CNV deletion 25765185
nsv1121984 CNV deletion 24896259
nsv1133010 OTHER inversion 24896259
nsv1140251 OTHER inversion 24896259
nsv1144879 CNV deletion 24896259
nsv1152956 OTHER inversion 26484159
nsv2530 CNV deletion 18451855
nsv509750 CNV insertion 20534489
nsv953604 CNV deletion 24416366

Variation tolerance for LRRC4B Gene

Residual Variation Intolerance Score: 6.98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.46; 71.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC4B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC4B

SNP Genotyping and Copy Number Assays for research

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 LRRC4B Gene

Disorders for LRRC4B Gene

Additional Disease Information for LRRC4B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for LRRC4B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRC4B Gene

Publications for LRRC4B Gene

  1. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4
  2. 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
  3. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. (PMID: 11441184) Dehal P … Stubbs L (Science (New York, N.Y.) 2001) 2 3
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. MxA interacts with and is modified by the SUMOylation machinery. (PMID: 25447205) Brantis-de-Carvalho CE … Valentini SR (Experimental cell research 2015) 3

ExternalLinks

View latest publications for LRRC4B gene in Mastermind

Products for LRRC4B Gene

Sources for LRRC4B Gene