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

Gene ID: 645191, updated on 5-Mar-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 integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in spleen (RPKM 1.7), brain (RPKM 0.7) and 7 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2287164..2308154, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2260807..2281793, complement)
105.20220307 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)

Genotypes

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_2023_10

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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