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GAR1 GAR1 ribonucleoprotein [ Homo sapiens (human) ]

Gene ID: 54433, updated on 7-Apr-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
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Genomic context

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Location:
4q25
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (109815510..109824737)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (113117572..113126796)
105.20220307 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. 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
  2. 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
  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 (108) 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)

Genotypes

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_2023_10

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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