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LINGO4 leucine rich repeat and Ig domain containing 4 [ Homo sapiens (human) ]

Gene ID: 339398, updated on 5-Mar-2024

Summary

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Official Symbol
LINGO4provided by HGNC
Official Full Name
leucine rich repeat and Ig domain containing 4provided by HGNC
Primary source
HGNC:HGNC:31814
See related
Ensembl:ENSG00000213171 MIM:609794; AllianceGenome:HGNC:31814
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LRRN6D; DAAT9248; PRO34002
Summary
Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in adrenal (RPKM 1.2), testis (RPKM 0.4) and 16 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1q21.3
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151800264..151805419, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150923752..150928907, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151772740..151777895, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tudor and KH domain containing Neighboring gene chloride nucleotide-sensitive channel 1A pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1326 Neighboring gene TDRKH antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151781322-151781822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151787417-151787917 Neighboring gene RAR related orphan receptor C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151794559-151795060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151795061-151795560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151797330-151798265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151801527-151802212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151802899-151803586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1327 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1726 Neighboring gene C2CD4D and THEM5 antisense RNA 1 Neighboring gene C2 calcium dependent domain containing 4D

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. No evidence of association between the LINGO4 gene and essential tremor in Chinese Han patients. Liang H, et al. Parkinsonism Relat Disord, 2012 Mar. PMID 22104011
  2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article
  3. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. variants in coding region of the LINGO4 gene may play little or no role in the risk of Essential tremor susceptibility
    Title: No evidence of association between the LINGO4 gene and essential tremor in Chinese Han patients.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 4
Names
leucine-rich repeat neuronal protein 6D

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001004432.4 → NP_001004432.1  leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 4 precursor

    See identical proteins and their annotated locations for NP_001004432.1

    Status: VALIDATED

    Source sequence(s)
    AL589765
    Consensus CDS
    CCDS30855.1
    UniProtKB/Swiss-Prot
    Q6UY18
    Related
    ENSP00000357810.4, ENST00000368820.4
    Conserved Domains (7) summary
    smart00013
    Location:31 → 64
    LRRNT; Leucine rich repeat N-terminal domain
    smart00410
    Location:420 → 501
    IG_like; Immunoglobulin like
    cd00116
    Location:87 → 320
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00031
    Location:350 → 362
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:86 → 109
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:65 → 120
    LRR_8; Leucine rich repeat
    cl11960
    Location:431 → 501
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    151800264..151805419 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    150923752..150928907 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UY18.1 GenPept UniProtKB/Swiss-Prot:Q6UY18

Gene LinkOut

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