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

    Gene ID: 26018, updated on 27-Nov-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, Nov 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: 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. 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

    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

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

    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

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

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