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

Gene ID: 121227, updated on 3-Nov-2024

Summary

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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, Nov 2024]
Expression
Broad expression in thyroid (RPKM 16.5), skin (RPKM 7.2) and 24 other tissues See more
Orthologs
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Genomic context

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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

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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. Perinuclear leucine-rich repeats and immunoglobulin-like domain proteins (LRIG1-3) as prognostic indicators in astrocytic tumors. Guo D, et al. Acta Neuropathol, 2006 Mar. PMID 16532360
  2. Inhibition of LRIG3 gene expression via RNA interference modulates the proliferation, cell cycle, cell apoptosis, adhesion and invasion of glioblastoma cell (GL15). Cai M, et al. Cancer Lett, 2009 Jun 8. PMID 19200647
  3. Expression of leucine-rich repeats and immunoglobulin-like domains (LRIG) proteins in human ependymoma relates to tumor location, WHO grade, and patient age. Yi W, et al. Clin Neuropathol, 2009 Jan-Feb. PMID 19216216
  4. Effects of RNAi-mediated gene silencing of LRIG3 expression on cell cycle and survival of glioma cells. Cai M, et al. J Huazhong Univ Sci Technolog Med Sci, 2009 Feb. PMID 19224171
  5. Effect of RNAi-mediated LRIG3 gene silencing on proliferation of glioma GL15 cells and expression of PCNA and Ki-67. Cai MJ, et al. Ai Zheng, 2009 Jan. PMID 19448407

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Glioma-derived LRIG3 interacts with NETO2 in tumor-associated macrophages to modulate microenvironment and suppress tumor growth.
    Title: Glioma-derived LRIG3 interacts with NETO2 in tumor-associated macrophages to modulate microenvironment and suppress tumor growth.
  2. Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma.
    Title: Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma.
  3. LRIG3 represses cell motility by inhibiting slug via inactivating ERK signaling in human colorectal cancer.
    Title: LRIG3 represses cell motility by inhibiting slug via inactivating ERK signaling in human colorectal cancer.
  4. miR-196a targeting LRIG3 promotes the proliferation and migration of cervical cancer cells.
    Title: miR-196a targeting LRIG3 promotes the proliferation and migration of cervical cancer cells.
  5. A novel circular RNA circ-LRIG3 facilitates the malignant progression of hepatocellular carcinoma by modulating the EZH2/STAT3 signaling.
    Title: A novel circular RNA circ-LRIG3 facilitates the malignant progression of hepatocellular carcinoma by modulating the EZH2/STAT3 signaling.
  6. LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.
    Title: LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.
  7. I these data of the current study indicated that overexpressed LRIG3 gene expression might inhibit the viability, adhesion, invasion and migration and promote the apoptosis of PC cells.
    Title: Overexpressed LRIG3 gene ameliorates prostate cancer through suppression of cell invasion and migration.
  8. Role of LRIG3 in cancer [review]
    Title: LRIGs: A Prognostically Significant Family with Emerging Therapeutic Competence against Cancers.
  9. This is the first time a haplotype on chromosome 12 containing sequence variants in the genes DCTN2, DNAH10, LRIG3, and MYO1A has been linked to an inherited neuropathy in humans.
    Title: Variants in the genes DCTN2, DNAH10, LRIG3, and MYO1A are associated with intermediate Charcot-Marie-Tooth disease in a Norwegian family.
  10. LRIG3 functions as a tumor suppressor by attenuating EGFR signaling pathway.
    Title: LRIG3 modulates proliferation, apoptosis and invasion of glioblastoma cells as a potent tumor suppressor.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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

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

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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Homology

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

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

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_001136051.3 → NP_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:560 → 634
    Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
    smart00408
    Location:651 → 714
    IGc2; Immunoglobulin C-2 Type
    smart00082
    Location:386 → 434
    LRRCT; Leucine rich repeat C-terminal domain
    cd00116
    Location:202 → 386
    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:543 → 633
    I-set; Immunoglobulin I-set domain
    sd00031
    Location:63 → 86
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:87 → 108
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:252 → 311
    LRR_8; Leucine rich repeat
    pfam13927
    Location:438 → 525
    Ig_3; Immunoglobulin domain

  2. NM_153377.5 → NP_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:416 → 494
    PCC; polycystin cation channel protein
    COG4886
    Location:142 → 425
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:123 → 146
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:147 → 168
    LRR_RI; leucine-rich repeat [structural motif]
    pfam07679
    Location:697 → 784
    I-set; Immunoglobulin I-set domain
    pfam13855
    Location:78 → 133
    LRR_8; Leucine rich repeat
    pfam13927
    Location:498 → 585
    Ig_3; Immunoglobulin domain
    cd00096
    Location:705 → 708
    Ig; Ig strand A' [structural motif]
    cd05763
    Location:604 → 694
    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_017018790.3 → XP_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_054371063.1 → XP_054227038.1  leucine-rich repeats and immunoglobulin-like domains protein 3 isoform X1

    UniProtKB/TrEMBL
    C9K080
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UXM1.1 GenPept UniProtKB/Swiss-Prot:Q6UXM1

Gene LinkOut

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