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LRIG1 leucine rich repeats and immunoglobulin like domains 1 [ Homo sapiens (human) ]

Gene ID: 26018, updated on 10-Dec-2024

Summary

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Official Symbol
LRIG1provided by HGNC
Official Full Name
leucine rich repeats and immunoglobulin like domains 1provided by HGNC
Primary source
HGNC:HGNC:17360
See related
Ensembl:ENSG00000144749 MIM:608868; AllianceGenome:HGNC:17360
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
LIG1; LIG-1
Summary
Predicted to act upstream of or within several processes, including innervation; otolith morphogenesis; and sensory perception of sound. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in brain (RPKM 61.1), fat (RPKM 28.0) and 23 other tissues See more
Orthologs
mouse all
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Genomic context

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See LRIG1 in Genome Data Viewer
Location:
3p14.1
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (66378797..66501121, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (66423367..66545661, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (66429221..66551545, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 26 Neighboring gene RNA, 7SL, cytoplasmic 482, pseudogene Neighboring gene developmental pluripotency associated 4 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:66433119-66433620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:66433621-66434120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20043 Neighboring gene NANOG hESC enhancer GRCh37_chr3:66472381-66472906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:66486139-66486729 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:66486730-66487319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:66491627-66492374 Neighboring gene HNF4 motif-containing MPRA enhancer 188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14504 Neighboring gene Sharpr-MPRA regulatory region 8313 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66550542-66551042 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66551043-66551543 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:66582385-66583210 Neighboring gene Sharpr-MPRA regulatory region 1089 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:66604132-66605331 Neighboring gene uncharacterized LOC105377141 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:66622461-66623375 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:66623376-66624289 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:66663707-66663920 Neighboring gene TCEAL8 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Upregulation of LRIG1 suppresses malignant glioma cell growth by attenuating EGFR activity. Ye F, et al. J Neurooncol, 2009 Sep. PMID 19300910
  2. LRIG1 modulates aggressiveness of head and neck cancers by regulating EGFR-MAPK-SPHK1 signaling and extracellular matrix remodeling. Sheu JJ, et al. Oncogene, 2014 Mar 13. PMID 23624915
  3. LRIG1 enhances cisplatin sensitivity of glioma cell lines. Wang X, et al. Oncol Res, 2012. PMID 23581227
  4. Expression of LRIG1 is associated with good prognosis and human papillomavirus status in oropharyngeal cancer. Lindquist D, et al. Br J Cancer, 2014 Apr 2. PMID 24548859, Free PMC Article
  5. LRIG1 as a potential novel marker for neoplastic transformation in ocular surface squamous neoplasia. Nagata M, et al. PLoS One, 2014. PMID 24709893, Free PMC Article

See all (106) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LRIG1 engages ligand VISTA and impairs tumor-specific CD8[+] T cell responses.
    Title: LRIG1 engages ligand VISTA and impairs tumor-specific CD8(+) T cell responses.
  2. Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is downregulated in Invasive ductal carcinoma and potential prognostic marker of breast cancer.
    Title: Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is downregulated in Invasive ductal carcinoma and potential prognostic marker of breast cancer.
  3. Dysregulation and antimetastatic function of circLRIG1 modulated by miR-214-3p/LRIG1 axis in bladder carcinoma.
    Title: Dysregulation and antimetastatic function of circLRIG1 modulated by miR-214-3p/LRIG1 axis in bladder carcinoma.
  4. Aberrant promoter methylation contributes to LRIG1 silencing in basal/triple-negative breast cancer.
    Title: Aberrant promoter methylation contributes to LRIG1 silencing in basal/triple-negative breast cancer.
  5. The transmembrane protein LRIG1 triggers melanocytic tumor development following chemically induced skin carcinogenesis.
    Title: The transmembrane protein LRIG1 triggers melanocytic tumor development following chemically induced skin carcinogenesis.
  6. LRIG1 is a positive prognostic marker in Merkel cell carcinoma and Merkel cell carcinoma expresses epithelial stem cell markers.
    Title: LRIG1 is a positive prognostic marker in Merkel cell carcinoma and Merkel cell carcinoma expresses epithelial stem cell markers.
  7. LRIG1 is a conserved EGFR regulator involved in melanoma development, survival and treatment resistance.
    Title: LRIG1 is a conserved EGFR regulator involved in melanoma development, survival and treatment resistance.
  8. Potential Novel Genes for Late-Onset Alzheimer's Disease in East-Asian Descent Identified by APOE-Stratified Genome-Wide Association Study.
    Title: Potential Novel Genes for Late-Onset Alzheimer's Disease in East-Asian Descent Identified by APOE-Stratified Genome-Wide Association Study.
  9. Aryl Hydrocarbon Receptor Defect Attenuates Mitogen-Activated Signaling through Leucine-Rich Repeats and Immunoglobulin-like Domains 1 (LRIG1)-Dependent EGFR Degradation.
    Title: Aryl Hydrocarbon Receptor Defect Attenuates Mitogen-Activated Signaling through Leucine-Rich Repeats and Immunoglobulin-like Domains 1 (LRIG1)-Dependent EGFR Degradation.
  10. microRNA-1246-containing extracellular vesicles from acute myeloid leukemia cells promote the survival of leukemia stem cells via the LRIG1-meditated STAT3 pathway.
    Title: microRNA-1246-containing extracellular vesicles from acute myeloid leukemia cells promote the survival of leukemia stem cells via the LRIG1-meditated STAT3 pathway.
Submit: New GeneRIF Correction See all GeneRIFs (81)

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
Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction.
EBI GWAS Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
EBI GWAS Catalog
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
EBI GWAS Catalog
Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp586O1624

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 hair cycle process IEA
Inferred from Electronic Annotation
more info
  
involved_in innervation IEA
Inferred from Electronic Annotation
more info
  
involved_in otolith morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of sound 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 plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
leucine-rich repeats and immunoglobulin-like domains protein 1
Names
leucine-rich repeat protein LRIG1
ortholog of mouse integral membrane glycoprotein LIG-1

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_001377344.1 → NP_001364273.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC092034, AC099665, AC126122
    UniProtKB/TrEMBL
    Q5XWD3
    Conserved Domains (9) summary
    smart00082
    Location:417 → 465
    LRRCT; Leucine rich repeat C-terminal domain
    COG4886
    Location:67 → 303
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:116 → 139
    LRR_RI; leucine-rich repeat [structural motif]
    pfam07679
    Location:668 → 755
    I-set; Immunoglobulin I-set domain
    pfam13855
    Location:358 → 417
    LRR_8; Leucine rich repeat
    pfam13927
    Location:469 → 556
    Ig_3; Immunoglobulin domain
    cd00096
    Location:685 → 689
    Ig; Ig strand B [structural motif]
    cd05763
    Location:575 → 665
    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
    cd21340
    Location:187 → 374
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  2. NM_001377345.1 → NP_001364274.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC092034, AC099665, AC126122
    Conserved Domains (7) summary
    smart00082
    Location:182 → 230
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:3 → 24
    LRR_RI; leucine-rich repeat [structural motif]
    pfam07679
    Location:433 → 520
    I-set; Immunoglobulin I-set domain
    pfam13855
    Location:80 → 134
    LRR_8; Leucine rich repeat
    pfam13927
    Location:234 → 321
    Ig_3; Immunoglobulin domain
    cd00096
    Location:450 → 454
    Ig; Ig strand B [structural motif]
    cd05763
    Location:340 → 430
    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

  3. NM_001377346.1 → NP_001364275.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC092034, AC099665, AC126122
    Conserved Domains (7) summary
    smart00082
    Location:182 → 230
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:3 → 24
    LRR_RI; leucine-rich repeat [structural motif]
    pfam07679
    Location:433 → 520
    I-set; Immunoglobulin I-set domain
    pfam13855
    Location:80 → 134
    LRR_8; Leucine rich repeat
    pfam13927
    Location:234 → 321
    Ig_3; Immunoglobulin domain
    cd00096
    Location:450 → 454
    Ig; Ig strand B [structural motif]
    cd05763
    Location:340 → 430
    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

  4. NM_001377347.1 → NP_001364276.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC092034, AC099665, AC126122
    Related
    ENST00000496559.6
    Conserved Domains (8) summary
    smart00082
    Location:108 → 156
    LRRCT; Leucine rich repeat C-terminal domain
    sd00031
    Location:50 → 73
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:126 → 153
    LRR_RI; leucine-rich repeat [structural motif]
    pfam07679
    Location:359 → 446
    I-set; Immunoglobulin I-set domain
    pfam13855
    Location:49 → 108
    LRR_8; Leucine rich repeat
    pfam13927
    Location:160 → 247
    Ig_3; Immunoglobulin domain
    cd00096
    Location:376 → 380
    Ig; Ig strand B [structural motif]
    cd05763
    Location:266 → 356
    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

  5. NM_001377348.1 → NP_001364277.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC092034, AC099665, AC126122
    Conserved Domains (8) summary
    smart00082
    Location:99 → 147
    LRRCT; Leucine rich repeat C-terminal domain
    sd00031
    Location:41 → 64
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:117 → 144
    LRR_RI; leucine-rich repeat [structural motif]
    pfam07679
    Location:350 → 437
    I-set; Immunoglobulin I-set domain
    pfam13855
    Location:40 → 99
    LRR_8; Leucine rich repeat
    pfam13927
    Location:151 → 238
    Ig_3; Immunoglobulin domain
    cd00096
    Location:367 → 371
    Ig; Ig strand B [structural motif]
    cd05763
    Location:257 → 347
    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

  6. NM_001377349.1 → NP_001364278.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC092034, AC099665, AC126122
    Conserved Domains (5) summary
    smart00082
    Location:14 → 62
    LRRCT; Leucine rich repeat C-terminal domain
    pfam07679
    Location:265 → 352
    I-set; Immunoglobulin I-set domain
    pfam13927
    Location:66 → 153
    Ig_3; Immunoglobulin domain
    cd00096
    Location:273 → 276
    Ig; Ig strand A' [structural motif]
    cd05763
    Location:172 → 262
    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

  7. NM_015541.3 → NP_056356.2  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_056356.2

    Status: VALIDATED

    Source sequence(s)
    AB050468, AC099665, AF381545, BC014276
    Consensus CDS
    CCDS33783.1
    UniProtKB/Swiss-Prot
    Q6IQ51, Q96CF9, Q96JA1, Q9BYB8, Q9UFI4
    UniProtKB/TrEMBL
    Q5XWD3
    Related
    ENSP00000273261.3, ENST00000273261.8
    Conserved Domains (9) summary
    cd00096
    Location:512 → 586
    Ig; Immunoglobulin domain
    cd05763
    Location:616 → 690
    Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
    smart00408
    Location:707 → 770
    IGc2; Immunoglobulin C-2 Type
    smart00082
    Location:442 → 490
    LRRCT; Leucine rich repeat C-terminal domain
    cd00116
    Location:131 → 416
    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:599 → 689
    I-set; Immunoglobulin I-set domain
    sd00031
    Location:117 → 140
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:141 → 164
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:211 → 271
    LRR_8; Leucine rich repeat

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    66378797..66501121 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447939.1 → XP_047303895.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform X2

    UniProtKB/TrEMBL
    Q5XWD3

  2. XM_011533578.3 → XP_011531880.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform X1

    UniProtKB/TrEMBL
    Q5XWD3
    Conserved Domains (9) summary
    cd00096
    Location:464 → 538
    Ig; Immunoglobulin domain
    cd05763
    Location:568 → 642
    Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
    smart00408
    Location:659 → 722
    IGc2; Immunoglobulin C-2 Type
    smart00082
    Location:394 → 442
    LRRCT; Leucine rich repeat C-terminal domain
    cd00116
    Location:73 → 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 ...
    pfam07679
    Location:551 → 641
    I-set; Immunoglobulin I-set domain
    sd00033
    Location:141 → 164
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:360 → 391
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:211 → 271
    LRR_8; Leucine rich repeat

  3. XM_017006135.2 → XP_016861624.2  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform X3

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_012132916.1 Reference GRCh38.p14 PATCHES

    Range
    355693..371107 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    66423367..66545661 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346123.1 → XP_054202098.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform X2

    UniProtKB/TrEMBL
    Q5XWD3

  2. XM_054346122.1 → XP_054202097.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform X1

    UniProtKB/TrEMBL
    Q5XWD3

  3. XM_054346124.1 → XP_054202099.1  leucine-rich repeats and immunoglobulin-like domains protein 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JA1.2 GenPept UniProtKB/Swiss-Prot:Q96JA1

Gene LinkOut

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