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    GAR1 GAR1 ribonucleoprotein [ Homo sapiens (human) ]

    Gene ID: 54433, updated on 27-Nov-2024

    Summary

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    Official Symbol
    GAR1provided by HGNC
    Official Full Name
    GAR1 ribonucleoproteinprovided by HGNC
    Primary source
    HGNC:HGNC:14264
    See related
    Ensembl:ENSG00000109534 MIM:606468; AllianceGenome:HGNC:14264
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NOLA1
    Summary
    This gene is a member of the H/ACA snoRNPs (small nucleolar ribonucleoproteins) gene family. snoRNPs are involved in various aspects of rRNA processing and modification and have been classified into two families: C/D and H/ACA. The H/ACA snoRNPs also include the DKC1, NOLA2 and NOLA3 proteins. These four H/ACA snoRNP proteins localize to the dense fibrillar components of nucleoli and to coiled (Cajal) bodies in the nucleus. Both 18S rRNA production and rRNA pseudouridylation are impaired if any one of the four proteins is depleted. These four H/ACA snoRNP proteins are also components of the telomerase complex. The encoded protein of this gene contains two glycine- and arginine-rich domains and is related to Saccharomyces cerevisiae Gar1p. Two splice variants have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in colon (RPKM 10.2), bone marrow (RPKM 9.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GAR1 in Genome Data Viewer
    Location:
    4q25
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (109815510..109824737)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (113117572..113126796)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (110736666..110745893)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21812 Neighboring gene GAR1 divergent transcript Neighboring gene retinal pigment epithelium-derived rhodopsin homolog Neighboring gene leucine rich repeat, Ig-like and transmembrane domains 3

    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. H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation. Bellodi C, et al. Cell Rep, 2013 May 30. PMID 23707062, Free PMC Article
    2. SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization. MacNeil DE, et al. Mol Cell Biol, 2021 Mar 24. PMID 33526451, Free PMC Article
    3. The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. Hamma T, et al. J Biol Chem, 2010 Jan 8. PMID 19917616, Free PMC Article
    4. NOLA1 gene mutations in acquired aplastic anemia. Pigullo S, et al. Pediatr Blood Cancer, 2009 Mar. PMID 18989882
    5. Stable preparation of aldose reductase isoenzymes from human placenta. Fujii Y, et al. Protein Expr Purif, 1991 Oct-Dec. PMID 1821816

    See all (125) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization.
      Title: SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization.
    2. The deregulated expression and function of H/ACA snoRNPs may underlie specific pathological features of human disease.
      Title: H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation.
    3. The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.
      Title: The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.
    4. heterozygous point mutations in NOLA1 gene are not responsible for aplastic anemia in our patients at least acting via telomere
      Title: NOLA1 gene mutations in acquired aplastic anemia.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
    6. Genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart 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

    EBI GWAS Catalog

    Description
    Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables box H/ACA snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables box H/ACA snoRNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables telomerase RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in snoRNA guided rRNA pseudouridine synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in telomere maintenance via telomerase IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in telomere maintenance via telomerase NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in telomere maintenance via telomerase TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of box H/ACA scaRNP complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of box H/ACA snoRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of box H/ACA snoRNP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of box H/ACA snoRNP complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of box H/ACA telomerase RNP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of box H/ACA telomerase RNP complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in chromosome, telomeric region HDA PubMed 
    colocalizes_with chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of telomerase holoenzyme complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of telomerase holoenzyme complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of telomerase holoenzyme complex TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    H/ACA ribonucleoprotein complex subunit 1
    Names
    GAR1 homolog, ribonucleoprotein
    GAR1 ribonucleoprotein homolog
    nucleolar protein family A member 1
    nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs)
    snoRNP protein GAR1

    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_018983.4 → NP_061856.1  H/ACA ribonucleoprotein complex subunit 1

      See identical proteins and their annotated locations for NP_061856.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains a region of additional sequence in the 5' UTR when compared to variant 2. The encoded protein is identical for both transcript variants.
      Source sequence(s)
      AJ276003, BC003413, CN428426
      Consensus CDS
      CCDS34050.1
      UniProtKB/Swiss-Prot
      Q5MJQ2, Q9NY12
      Related
      ENSP00000226796.6, ENST00000226796.7
      Conserved Domains (1) summary
      pfam04410
      Location:63 → 159
      Gar1; Gar1/Naf1 RNA binding region

    2. NM_032993.2 → NP_127460.1  H/ACA ribonucleoprotein complex subunit 1

      See identical proteins and their annotated locations for NP_127460.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a region of sequence in the 5' UTR when compared to variant 1. The encoded protein is identical for both transcript variants.
      Source sequence(s)
      AJ276003, BC003413, CN428426
      Consensus CDS
      CCDS34050.1
      UniProtKB/Swiss-Prot
      Q5MJQ2, Q9NY12
      Related
      ENSP00000378127.3, ENST00000394631.7
      Conserved Domains (1) summary
      pfam04410
      Location:63 → 159
      Gar1; Gar1/Naf1 RNA binding region

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      109815510..109824737
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047415789.1 → XP_047271745.1  H/ACA ribonucleoprotein complex subunit 1 isoform X1

      UniProtKB/Swiss-Prot
      Q5MJQ2, Q9NY12

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      113117572..113126796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350198.1 → XP_054206173.1  H/ACA ribonucleoprotein complex subunit 1 isoform X1

      UniProtKB/Swiss-Prot
      Q5MJQ2, Q9NY12
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NY12.1 GenPept UniProtKB/Swiss-Prot:Q9NY12

    Gene LinkOut

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

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