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

    Gene ID: 339398, updated on 2-Nov-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 located in membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
    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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    See LINGO4 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151800264..151805419, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150923752..150928907, complement)
    RS_2024_09 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

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    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. Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4-Associated Factors, Cellular Functions, and Protein Substrates. Raisch J, et al. Mol Cell Proteomics, 2023 Oct. PMID 37689310, Free PMC Article
    4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    5. 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

    See all (6) citations in PubMed

    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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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