U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    LRIT2 leucine rich repeat, Ig-like and transmembrane domains 2 [ Homo sapiens (human) ]

    Gene ID: 340745, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    LRIT2provided by HGNC
    Official Full Name
    leucine rich repeat, Ig-like and transmembrane domains 2provided by HGNC
    Primary source
    HGNC:HGNC:23443
    See related
    Ensembl:ENSG00000204033 AllianceGenome:HGNC:23443
    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
    LRRC22
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in skin (RPKM 1.2), brain (RPKM 0.4) and 1 other tissue See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LRIT2 in Genome Data Viewer
    Location:
    10q23.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (84220485..84225589, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (85099011..85104115, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (85980241..85985345, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85936583-85937084 Neighboring gene G protein-coupled receptor 15 ligand Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:85939583-85940403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2551 Neighboring gene cadherin related family member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963048-85963548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85963549-85964049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:85974015-85974538 Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:86004955-86005454 Neighboring gene retinal G protein coupled receptor

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. New genetic associations detected in a host response study to hepatitis B vaccine. Davila S, et al. Genes Immun, 2010 Apr. PMID 20237496
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2
    Names
    leucine rich repeat containing 22
    leucine-rich repeat, immunoglobulin-like and transmembrane domains 2
    leucine-rich repeat-containing protein 22

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001017924.5 → NP_001017924.1  leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001017924.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      BC140765, BX648524
      Consensus CDS
      CCDS31234.1
      UniProtKB/Swiss-Prot
      A6NDA9, B7ZME6
      Related
      ENSP00000361185.3, ENST00000372113.7
      Conserved Domains (9) summary
      smart00408
      Location:267 → 334
      IGc2; Immunoglobulin C-2 Type
      smart00060
      Location:367 → 430
      FN3; Fibronectin type 3 domain
      cd00116
      Location:75 → 164
      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:253 → 344
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:58 → 80
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:37 → 55
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:81 → 119
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:103 → 163
      LRR_8; Leucine rich repeat
      cl15307
      Location:200 → 243
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. NM_001284223.1 → NP_001271152.1  leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001271152.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC022389, BC140765, BX648524
      Consensus CDS
      CCDS60581.1
      UniProtKB/Swiss-Prot
      A6NDA9
      Related
      ENSP00000438264.1, ENST00000538192.5
      Conserved Domains (9) summary
      smart00408
      Location:267 → 344
      IGc2; Immunoglobulin C-2 Type
      smart00060
      Location:377 → 440
      FN3; Fibronectin type 3 domain
      cd00116
      Location:75 → 164
      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:253 → 354
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:58 → 80
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:37 → 55
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:81 → 119
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:103 → 163
      LRR_8; Leucine rich repeat
      cl15307
      Location:200 → 243
      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
      84220485..84225589 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      85099011..85104115 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NDA9.1 GenPept UniProtKB/Swiss-Prot:A6NDA9

    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