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    LRIG3 leucine rich repeats and immunoglobulin like domains 3 [ Homo sapiens (human) ]

    Gene ID: 121227, updated on 9-Dec-2024

    Summary

    Official Symbol
    LRIG3provided by HGNC
    Official Full Name
    leucine rich repeats and immunoglobulin like domains 3provided by HGNC
    Primary source
    HGNC:HGNC:30991
    See related
    Ensembl:ENSG00000139263 MIM:608870; AllianceGenome:HGNC:30991
    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
    LIG3
    Summary
    Predicted to act upstream of or within otolith morphogenesis. Located in extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in thyroid (RPKM 16.5), skin (RPKM 7.2) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LRIG3 in Genome Data Viewer
    Location:
    12q14.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (58872155..58920504, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (58852431..58900780, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (59265937..59314285, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902949 Neighboring gene long intergenic non-protein coding RNA 2388 Neighboring gene uncharacterized LOC100506869 Neighboring gene Sharpr-MPRA regulatory region 8919 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30091 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:59235169-59235668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:59254059-59254582 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:59281329-59282528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4600 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4602 Neighboring gene NANOG hESC enhancer GRCh37_chr12:59318825-59319449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:59327314-59327814 Neighboring gene LRIG3 divergent transcript Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30204 Neighboring gene VISTA enhancer hs1468 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30226 Neighboring gene ribosomal protein S6 pseudogene 22 Neighboring gene methyltransferase like 15 pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Clone Names

    • FLJ26573, FLJ90440, KIAA3016

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in otolith morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    leucine-rich repeats and immunoglobulin-like domains protein 3
    Names
    LIG-3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001136051.3NP_001129523.1  leucine-rich repeats and immunoglobulin-like domains protein 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001129523.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AY358288, AY358295
      Consensus CDS
      CCDS44933.1
      UniProtKB/Swiss-Prot
      Q6UXM1
      Related
      ENSP00000368436.4, ENST00000379141.8
      Conserved Domains (9) summary
      cd05763
      Location:560634
      Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
      smart00408
      Location:651714
      IGc2; Immunoglobulin C-2 Type
      smart00082
      Location:386434
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:202386
      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:543633
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:6386
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:87108
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:252311
      LRR_8; Leucine rich repeat
      pfam13927
      Location:438525
      Ig_3; Immunoglobulin domain
    2. NM_153377.5NP_700356.2  leucine-rich repeats and immunoglobulin-like domains protein 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_700356.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region and represents the use of an alternate promoter, compared to variant 1, which results in a protein (isoform 2) with a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK292857, AY358288
      Consensus CDS
      CCDS8960.1
      UniProtKB/Swiss-Prot
      Q6UXL7, Q6UXM1, Q8NC72
      Related
      ENSP00000326759.3, ENST00000320743.8
      Conserved Domains (9) summary
      TIGR00864
      Location:416494
      PCC; polycystin cation channel protein
      COG4886
      Location:142425
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00031
      Location:123146
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:147168
      LRR_RI; leucine-rich repeat [structural motif]
      pfam07679
      Location:697784
      I-set; Immunoglobulin I-set domain
      pfam13855
      Location:78133
      LRR_8; Leucine rich repeat
      pfam13927
      Location:498585
      Ig_3; Immunoglobulin domain
      cd00096
      Location:705708
      Ig; Ig strand A' [structural motif]
      cd05763
      Location:604694
      IgI_LRIG1-like; Immunoglobulin (Ig)-like ectodomain of the LRIG1 (Leucine-rich Repeats And Immunoglobulin-like Domains Protein 1) and similar proteins; member of the I-set of IgSF domains

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      58872155..58920504 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017018790.3XP_016874279.1  leucine-rich repeats and immunoglobulin-like domains protein 3 isoform X1

      UniProtKB/TrEMBL
      C9K080
      Related
      ENSP00000413143.2, ENST00000433272.6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      58852431..58900780 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371063.1XP_054227038.1  leucine-rich repeats and immunoglobulin-like domains protein 3 isoform X1

      UniProtKB/TrEMBL
      C9K080