Aliases for LINGO4 Gene

Aliases for LINGO4 Gene

  • Leucine Rich Repeat And Ig Domain Containing 4 2 3 5
  • Leucine-Rich Repeat And Immunoglobulin-Like Domain-Containing Nogo Receptor-Interacting Protein 4 3 4
  • Leucine-Rich Repeat Neuronal Protein 6D 3 4
  • LRRN6D 3 4
  • Leucine Rich Repeat Neuronal 6D 2
  • DAAT9248 3
  • PRO34002 3

External Ids for LINGO4 Gene

Previous HGNC Symbols for LINGO4 Gene

  • LRRN6D

Previous GeneCards Identifiers for LINGO4 Gene

  • GC01M150041
  • GC01M150042
  • GC01M151775
  • GC01M123149

Summaries for LINGO4 Gene

GeneCards Summary for LINGO4 Gene

LINGO4 (Leucine Rich Repeat And Ig Domain Containing 4) is a Protein Coding gene. Diseases associated with LINGO4 include Essential Tremor. An important paralog of this gene is LINGO3.

Additional gene information for LINGO4 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LINGO4 Gene

Genomics for LINGO4 Gene

GeneHancer (GH) Regulatory Elements for LINGO4 Gene

Promoters and enhancers for LINGO4 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
GH01J151807 Enhancer 0.2 Ensembl 750.6 -1.8 -1847 1.2 LINGO4 TDRKH FLG-AS1 lnc-LINGO4-1 RORC
GH01J151712 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10 +90.9 90877 6.3 ZBTB40 SMARCE1 CTBP1 NR2F6 CC2D1A TEAD4 SP1 ZC3H8 ZNF148 GTF2F1 CELF3 PIP5K1A SETDB1 PI4KB UBE2D3P3 GABPB2 MRPL9 ZNF687 SNX27 POGZ
GH01J151933 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 14 -129.6 -129563 3.6 CTCF CC2D1A RAD21 SP7 PRDM1 ZNF547 ZIC2 ARID2 REST TCF7L2 THEM4 ENSG00000229021 POGZ PIP5K1A PI4KB GABPB2 S100A10 MRPL9 LINGO4 TDRKH
GH01J151822 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 8.5 -21.5 -21468 12 LCORL FOXA1 MLX RBPJ POLR2A HLF MNT MTA3 NFIB ZNF148 RORC AB372574 ZNF687 PIP5K1A SETDB1 LYSMD1 LINGO4 FLG-AS1 THEM4 ENSG00000269621
GH01J151721 Promoter/Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 10 +85.8 85753 3.2 NKRF CBFA2T2 GLIS2 RFX1 POLR2A PKNOX1 RFX3 SCRT2 BMI1 SIN3A lnc-CELF3-1 SNX27 MRPL9 OAZ3 ENSG00000232937 ENSG00000250734 CGN ENSG00000252840 C2CD4D-AS1 C2CD4D
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINGO4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LINGO4 gene promoter:
  • AP-1
  • AREB6
  • c-Myb
  • HOXA5
  • ITF-2
  • p53
  • RORalpha2
  • STAT5A
  • Zic3

Genomic Locations for LINGO4 Gene

Genomic Locations for LINGO4 Gene
chr1:151,800,264-151,806,154
(GRCh38/hg38)
Size:
5,891 bases
Orientation:
Minus strand
chr1:151,772,740-151,778,630
(GRCh37/hg19)
Size:
5,891 bases
Orientation:
Minus strand

Genomic View for LINGO4 Gene

Genes around LINGO4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LINGO4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINGO4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINGO4 Gene

Proteins for LINGO4 Gene

  • Protein details for LINGO4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UY18-LIGO4_HUMAN
    Recommended name:
    Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 4
    Protein Accession:
    Q6UY18

    Protein attributes for LINGO4 Gene

    Size:
    593 amino acids
    Molecular mass:
    63774 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LINGO4 Gene

Post-translational modifications for LINGO4 Gene

  • Glycosylation at Asn191, Asn253, Asn263, Asn492, Asn508, and Asn515
  • Modification sites at PhosphoSitePlus

Other Protein References for LINGO4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LINGO4 Gene

Domains & Families for LINGO4 Gene

Gene Families for LINGO4 Gene

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

Suggested Antigen Peptide Sequences for LINGO4 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat neuronal protein 6D (LIGO4_HUMAN)
genes like me logo Genes that share domains with LINGO4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LINGO4 Gene

Function for LINGO4 Gene

Phenotypes From GWAS Catalog for LINGO4 Gene

genes like me logo Genes that share phenotypes with LINGO4: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LINGO4

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LINGO4

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LINGO4 Gene

Localization for LINGO4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LINGO4 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 LINGO4 gene
Compartment Confidence
extracellular 4
plasma membrane 2
cytoskeleton 0
endoplasmic reticulum 0
cytosol 0

Gene Ontology (GO) - Cellular Components for LINGO4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031012 extracellular matrix IBA 21873635
genes like me logo Genes that share ontologies with LINGO4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LINGO4 Gene

Pathways & Interactions for LINGO4 Gene

PathCards logo

SuperPathways for LINGO4 Gene

No Data Available

Interacting Proteins for LINGO4 Gene

Gene Ontology (GO) - Biological Process for LINGO4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LINGO4 Gene

Drugs & Compounds for LINGO4 Gene

No Compound Related Data Available

Transcripts for LINGO4 Gene

mRNA/cDNA for LINGO4 Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(10) Selected AceView cDNA sequences:
(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 LINGO4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LINGO4 Gene

No ASD Table

Relevant External Links for LINGO4 Gene

GeneLoc Exon Structure for
LINGO4
ECgene alternative splicing isoforms for
LINGO4

Expression for LINGO4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LINGO4 Gene

mRNA differential expression in normal tissues according to GTEx for LINGO4 Gene

This gene is overexpressed in Muscle - Skeletal (x28.1), Brain - Cerebellum (x7.1), and Brain - Cerebellar Hemisphere (x4.3).

NURSA nuclear receptor signaling pathways regulating expression of LINGO4 Gene:

LINGO4

SOURCE GeneReport for Unigene cluster for LINGO4 Gene:

Hs.591477
genes like me logo Genes that share expression patterns with LINGO4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LINGO4 Gene

Orthologs for LINGO4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LINGO4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LINGO4 33 32
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LINGO4 33 32
  • 89.77 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LINGO4 33 32
  • 88.87 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lingo4 17 33 32
  • 88.76 (n)
rat
(Rattus norvegicus)
Mammalia Lingo4 32
  • 87.75 (n)
oppossum
(Monodelphis domestica)
Mammalia LINGO4 33
  • 80 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii lingo4b 33
  • 43 (a)
ManyToMany
Species where no ortholog for LINGO4 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)
  • lizard (Anolis carolinensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LINGO4 Gene

ENSEMBL:
Gene Tree for LINGO4 (if available)
TreeFam:
Gene Tree for LINGO4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LINGO4: view image

Paralogs for LINGO4 Gene

Paralogs for LINGO4 Gene

(4) SIMAP similar genes for LINGO4 Gene using alignment to 1 proteins:

  • LIGO4_HUMAN
genes like me logo Genes that share paralogs with LINGO4: view

Variants for LINGO4 Gene

Sequence variations from dbSNP and Humsavar for LINGO4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs143154971 uncertain-significance, Polymicrogyria 151,801,443(-) C/A/G/T coding_sequence_variant, missense_variant
rs151205204 uncertain-significance, Polymicrogyria 151,801,854(-) G/A coding_sequence_variant, missense_variant
rs1001398538 -- 151,805,067(-) T/A intron_variant
rs1001899209 -- 151,800,404(-) T/C 3_prime_UTR_variant
rs1002271177 -- 151,804,374(-) G/A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LINGO4 Gene

Variant ID Type Subtype PubMed ID
nsv1010398 CNV gain 25217958

Variation tolerance for LINGO4 Gene

Residual Variation Intolerance Score: 40.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.54; 82.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LINGO4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINGO4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LINGO4 Gene

Disorders for LINGO4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LINGO4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
essential tremor
  • tremor, hereditary essential, 1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LINGO4

genes like me logo Genes that share disorders with LINGO4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LINGO4 Gene

Publications for LINGO4 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 56
  2. No evidence of association between the LINGO4 gene and essential tremor in Chinese Han patients. (PMID: 22104011) Liang H … Deng H (Parkinsonism & related disorders 2012) 3 56
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 56
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 4 56
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 56

Products for LINGO4 Gene

Sources for LINGO4 Gene