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    LRIT1 leucine rich repeat, Ig-like and transmembrane domains 1 [ Homo sapiens (human) ]

    Gene ID: 26103, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LRIT1provided by HGNC
    Official Full Name
    leucine rich repeat, Ig-like and transmembrane domains 1provided by HGNC
    Primary source
    HGNC:HGNC:23404
    See related
    Ensembl:ENSG00000148602 MIM:616103; AllianceGenome:HGNC:23404
    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
    PAL; LRRC21; FIGLER9
    Summary
    Predicted to be involved in visual perception. Predicted to be located in dendrite; endoplasmic reticulum; and membrane. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 2.4) See more
    Orthologs
    mouse all
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    Genomic context

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    See LRIT1 in Genome Data Viewer
    Location:
    10q23.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (84231520..84241546, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (85110046..85120066, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (85991276..86001302, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963048-85963548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963549-85964049 Neighboring gene cadherin related family member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85974015-85974538 Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:86004955-86005454 Neighboring gene retinal G protein coupled receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2553 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:86028972-86030171 Neighboring gene long intergenic non-protein coding RNA 858

    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. Molecular cloning of a novel membrane glycoprotein, pal, specifically expressed in photoreceptor cells of the retina and containing leucine-rich repeat. Gomi F, et al. J Neurosci, 2000 May 1. PMID 10777785, Free PMC Article
    2. Mapping of transcription start sites of human retina expressed genes. Roni V, et al. BMC Genomics, 2007 Feb 7. PMID 17286855, Free PMC Article
    3. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. Flachsbart F, et al. Mutat Res, 2010 Dec 10. PMID 20800603
    4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Grupe A, et al. Am J Hum Genet, 2006 Jan. PMID 16385451, Free PMC Article
    5. New genetic associations detected in a host response study to hepatitis B vaccine. Davila S, et al. Genes Immun, 2010 Apr. PMID 20237496

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp434K091

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 9
    leucine rich repeat containing 21
    leucine-rich repeat, immunoglobulin-like and transmembrane domains 1
    leucine-rich repeat-containing protein 21
    photoreceptor-associated LRR superfamily protein
    retina-specific protein PAL

    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_015613.3 → NP_056428.1  leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_056428.1

      Status: VALIDATED

      Source sequence(s)
      AB031547, AC022389
      Consensus CDS
      CCDS7373.1
      UniProtKB/Swiss-Prot
      Q0QD41, Q9P2V4, Q9Y4N7
      Related
      ENSP00000361177.3, ENST00000372105.4
      Conserved Domains (7) summary
      smart00060
      Location:431 → 498
      FN3; Fibronectin type 3 domain
      smart00410
      Location:267 → 345
      IG_like; Immunoglobulin like
      sd00031
      Location:61 → 84
      LRR_1; leucine-rich repeat [structural motif]
      pfam12799
      Location:131 → 171
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:131 → 202
      LRR_8; Leucine rich repeat
      cl11960
      Location:267 → 345
      Ig; Immunoglobulin domain
      cl15307
      Location:201 → 240
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      84231520..84241546 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011539626.3 → XP_011537928.1  leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1 isoform X1

      Conserved Domains (4) summary
      smart00060
      Location:236 → 303
      FN3; Fibronectin type 3 domain
      smart00410
      Location:72 → 150
      IG_like; Immunoglobulin like
      cl11960
      Location:72 → 150
      Ig; Immunoglobulin domain
      cl15307
      Location:6 → 45
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      85110046..85120066 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365521.1 → XP_054221496.1  leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P2V4.1 GenPept UniProtKB/Swiss-Prot:Q9P2V4

    Gene LinkOut

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

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools