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    LINGO3 leucine rich repeat and Ig domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 645191, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINGO3provided by HGNC
    Official Full Name
    leucine rich repeat and Ig domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:21206
    See related
    Ensembl:ENSG00000220008 MIM:609792; AllianceGenome:HGNC:21206
    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
    LERN2; LRRN6B
    Summary
    Predicted to be located in membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in spleen (RPKM 1.7), brain (RPKM 0.7) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LINGO3 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2287164..2308154, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2260807..2281793, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2287163..2308153, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2269184-2269798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2275050-2275984 Neighboring gene ornithine decarboxylase antizyme 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13675 Neighboring gene PEAK family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9783 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9784 Neighboring gene uncharacterized LOC101928572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13680 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2328300-2328954 Neighboring gene LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13683 Neighboring gene signal peptide peptidase like 2B

    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
    • 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. LINGO3 regulates mucosal tissue regeneration and promotes TFF2 dependent recovery from colitis. Zullo KM, et al. Scand J Gastroenterol, 2021 Jul. PMID 33941035, Free PMC Article
    2. LRRN6A/LERN1 (leucine-rich repeat neuronal protein 1), a novel gene with enriched expression in limbic system and neocortex. Carim-Todd L, et al. Eur J Neurosci, 2003 Dec. PMID 14686891
    3. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    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. LINGO3 regulates mucosal tissue regeneration and promotes TFF2 dependent recovery from colitis.
      Title: LINGO3 regulates mucosal tissue regeneration and promotes TFF2 dependent recovery from colitis.
    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)

    General gene information

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    Homology

    Clone Names

    • FLJ34476

    Gene Ontology Provided by GOA

    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 3
    Names
    leucine rich repeat neuronal 6B
    leucine-rich repeat neuronal protein 2
    leucine-rich repeat neuronal protein 6B

    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_001101391.3 → NP_001094861.1  leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 3 precursor

      See identical proteins and their annotated locations for NP_001094861.1

      Status: VALIDATED

      Source sequence(s)
      AC004152, AC005258
      Consensus CDS
      CCDS45905.1
      UniProtKB/Swiss-Prot
      P0C6S8
      Related
      ENSP00000513689.1, ENST00000698372.1
      Conserved Domains (7) summary
      smart00013
      Location:24 → 58
      LRRNT; Leucine rich repeat N-terminal domain
      cd00116
      Location:111 → 286
      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 ...
      pfam07679
      Location:407 → 497
      I-set; Immunoglobulin I-set domain
      sd00033
      Location:59 → 79
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:59 → 95
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:247 → 303
      LRR_8; Leucine rich repeat
      cl11960
      Location:422 → 490
      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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      2287164..2308154 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      2260807..2281793 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0C6S8.1 GenPept UniProtKB/Swiss-Prot:P0C6S8

    Gene LinkOut

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

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