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    KLRA1P killer cell lectin like receptor A1, pseudogene [ Homo sapiens (human) ]

    Gene ID: 10748, updated on 17-Sep-2024

    Summary

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    Official Symbol
    KLRA1Pprovided by HGNC
    Official Full Name
    killer cell lectin like receptor A1, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:6372
    See related
    MIM:604274; AllianceGenome:HGNC:6372
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Ly49; KLRA1; LY49L; KLRAP1; Ly-49L
    Annotation information
    Note: This locus was originally considered to be protein coding, but has been reclassified as a transcribed pseudogene because all associated transcripts are candidates for nonsense-mediated decay (NMD). PMID: 10369937 and 16492762 also state that this locus is likely to be a pseudogene. [13 Feb 2013]
    Expression
    Ubiquitous expression in skin (RPKM 2.9), lymph node (RPKM 2.6) and 23 other tissues See more
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    Genomic context

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    See KLRA1P in Genome Data Viewer
    Location:
    12p13.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10588478..10599835, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (10461894..10473161, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10741077..10752434, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SLC25A39 pseudogene 2 Neighboring gene long intergenic non-protein coding RNA 2446 Neighboring gene uncharacterized LOC105376675 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:10724334-10724939 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:10733376-10734575 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:10765265-10766144 and GRCh37_chr12:10766145-10767022 Neighboring gene mago homolog B, exon junction complex subunit Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene Y-box binding protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4238 Neighboring gene uncharacterized LOC124902876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4240

    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. Identification of a human member of the Ly-49 multigene family. Westgaard IH, et al. Eur J Immunol, 1998 Jun. PMID 9645365
    2. Ly49D-mediated ITAM signaling in immature thymocytes impairs development by bypassing the pre-TCR checkpoint. Merck E, et al. J Immunol, 2011 Jul 1. PMID 21632721
    3. The human Ly-49L gene. Barten R, et al. Immunogenetics, 1999 Jul. PMID 10369937
    4. Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals. Hao L, et al. Proc Natl Acad Sci U S A, 2006 Feb 28. PMID 16492762, Free PMC Article
    5. Comparative genomics of natural killer cell receptor gene clusters. Kelley J, et al. PLoS Genet, 2005 Aug. PMID 16132082, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ly49 family receptors are required for cancer immunosurveillance mediated by natural killer cells.
      Title: Ly49 family receptors are required for cancer immunosurveillance mediated by natural killer cells.
    2. Thymic cellularity is greatly reduced in LY49D transgenic mice due to an impaired transition from double-negative to double-positive stages (the pre-T cell receptor checkpoint).
      Title: Ly49D-mediated ITAM signaling in immature thymocytes impairs development by bypassing the pre-TCR checkpoint.
    3. Natural killer (NK) cell licensing through Ly49 involves specific interactions with its transgenic histocompatibility complex (self-MHC) ligand that are similar to those involved in effector inhibition.
      Title: Ly49-dependent NK cell licensing and effector inhibition involve the same interaction site on MHC ligands.
    4. 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.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide SNP genotyping study using pooled DNA to identify candidate markers mediating susceptibility to end-stage renal disease attributed to Type 1 diabetes.
    7. biochemical analysis of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors
      Title: Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    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

    Other Names

    • killer cell lectin-like receptor subfamily A pseudogene 1
    • killer cell lectin-like receptor subfamily A, member 1, pseudogene

    Clone Names

    • MGC126520, MGC126522

    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.

    RNA

    1. NR_028045.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC021049, BC069672, BC069697, BX950927, CN269037, DA776936

    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
      10588478..10599835 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      10461894..10473161 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_006611.2: Suppressed sequence

      Description
      NM_006611.2: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
    Nucleotide Protein
    Heading Accession and Version

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    Research Materials