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Aliases for GAR1 Gene

Aliases for GAR1 Gene

  • GAR1 Ribonucleoprotein 2 3 5
  • Nucleolar Protein Family A, Member 1 (H/ACA Small Nucleolar RNPs) 2 3
  • Nucleolar Protein Family A Member 1 3 4
  • SnoRNP Protein GAR1 3 4
  • NOLA1 3 4
  • H/ACA Ribonucleoprotein Complex Subunit 1 3
  • GAR1 Ribonucleoprotein Homolog (Yeast) 2
  • GAR1 Homolog, Ribonucleoprotein 3
  • GAR1 Ribonucleoprotein Homolog 3

External Ids for GAR1 Gene

Previous HGNC Symbols for GAR1 Gene

  • NOLA1

Previous GeneCards Identifiers for GAR1 Gene

  • GC04P110957
  • GC04P110736
  • GC04P106468

Summaries for GAR1 Gene

Entrez Gene Summary for GAR1 Gene

  • 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]

GeneCards Summary for GAR1 Gene

GAR1 (GAR1 Ribonucleoprotein) is a Protein Coding gene. Diseases associated with GAR1 include Dyskeratosis Congenita and Spinal Muscular Atrophy. Among its related pathways are Ribosome biogenesis in eukaryotes and rRNA processing in the nucleus and cytosol. GO annotations related to this gene include poly(A) RNA binding and cation channel activity.

UniProtKB/Swiss-Prot for GAR1 Gene

  • Required for ribosome biogenesis and telomere maintenance. Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ("psi") residues, which may serve to stabilize the conformation of rRNAs. May also be required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme.

Gene Wiki entry for GAR1 Gene

Additional gene information for GAR1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GAR1 Gene

Genomics for GAR1 Gene

Regulatory Elements for GAR1 Gene

Enhancers for GAR1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04H110192 1.8 FANTOM5 ENCODE dbSUPER 20.7 +380.9 380855 6 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 GAR1 SEC24B ENSG00000250511 ELOVL6 ENSG00000248200
GH04H109727 1.3 ENCODE dbSUPER 20.8 -85.8 -85757 4 HDGF PKNOX1 ATF1 ARID4B SIN3A DMAP1 GTF3C2 ZNF766 GLIS2 ZNF143 PLA2G12A GAR1 SEC24B SEC24B-AS1 CDC42P4 CFI SETP20 CASP6
GH04H109734 1.2 ENCODE dbSUPER 9.8 -79.3 -79250 2 HDAC1 PKNOX1 ARNT NFRKB YY1 TCF12 ATF7 ZBTB2 ZBTB11 CEBPB PLA2G12A CFI GAR1
GH04H109184 1 Ensembl ENCODE 11.2 -630.6 -630596 1 TBP HDGF KLF1 ATF1 TAL1 JUN TCF12 CTBP1 POLR2A GATA2 GAR1 GC04P109269 GC04P109270 GC04M108908
GH04H109422 1.1 Ensembl ENCODE 10.1 -392.8 -392819 0 HDGF CTCF PKNOX1 ATF1 ZNF2 RAD21 TEAD3 CC2D1A SMC3 ZNF143 SEC24B CDC42P4 SETP20 CASP6 GAR1 OSTC PLA2G12A LRIT3 PIR37678
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GAR1 on UCSC Golden Path with GeneCards custom track

Promoters for GAR1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000171855 390 2201 FOXA2 ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF766 CBX5 ZNF207 SP3

Genomic Location for GAR1 Gene

Chromosome:
4
Start:
109,815,510 bp from pter
End:
109,824,740 bp from pter
Size:
9,231 bases
Orientation:
Plus strand

Genomic View for GAR1 Gene

Genes around GAR1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GAR1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GAR1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GAR1 Gene

Proteins for GAR1 Gene

  • Protein details for GAR1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY12-GAR1_HUMAN
    Recommended name:
    H/ACA ribonucleoprotein complex subunit 1
    Protein Accession:
    Q9NY12
    Secondary Accessions:
    • Q5MJQ2

    Protein attributes for GAR1 Gene

    Size:
    217 amino acids
    Molecular mass:
    22348 Da
    Quaternary structure:
    • Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which contains NHP2/NOLA2, GAR1/NOLA1, NOP10/NOLA3, and DKC1/NOLA4, which is presumed to be the catalytic subunit. The complex contains a stable core formed by binding of one or two NOP10-DKC1 heterodimers to NHP2; GAR1 subsequently binds to this core via DKC1. The complex binds a box H/ACA small nucleolar RNA (snoRNA), which may target the specific site of modification within the RNA substrate. The complex also interacts with TERC, which contains a 3-terminal domain related to the box H/ACA snoRNAs. Specific interactions with snoRNAs or TERC are mediated by GAR1 and NHP2. Associates with NOLC1/NOPP140. H/ACA snoRNPs interact with the SMN complex, consisting of SMN1 or SMN2, GEMIN2/SIP1, DDX20/GEMIN3, and GEMIN4. This is mediated by interaction between GAR1 and SMN1 or SMN2. The SMN complex may be required for correct assembly of the H/ACA snoRNP complex. Component of the telomerase holoenzyme complex at least composed of TERT, DKC1, WRAP53/TCAB1, NOP10, NHP2, GAR1, TEP1, EST1A, POT1 and a telomerase RNA template component (TERC).

    Alternative splice isoforms for GAR1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GAR1 Gene

Post-translational modifications for GAR1 Gene

  • Ubiquitination at isoforms=2150
  • Modification sites at PhosphoSitePlus

Other Protein References for GAR1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GAR1 Gene

Domains & Families for GAR1 Gene

Gene Families for GAR1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for GAR1 Gene

Suggested Antigen Peptide Sequences for GAR1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NY12

UniProtKB/Swiss-Prot:

GAR1_HUMAN :
  • Interaction with SMN1 requires at least one of the RGG-box regions.
  • Belongs to the GAR1 family.
Domain:
  • Interaction with SMN1 requires at least one of the RGG-box regions.
Family:
  • Belongs to the GAR1 family.
genes like me logo Genes that share domains with GAR1: view

Function for GAR1 Gene

Molecular function for GAR1 Gene

UniProtKB/Swiss-Prot Function:
Required for ribosome biogenesis and telomere maintenance. Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ("psi") residues, which may serve to stabilize the conformation of rRNAs. May also be required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme.

Phenotypes From GWAS Catalog for GAR1 Gene

Gene Ontology (GO) - Molecular Function for GAR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IPI 10757788
GO:0005515 protein binding IPI 11509230
GO:0034513 box H/ACA snoRNA binding IPI 10757788
GO:0070034 telomerase RNA binding IPI 10757788
genes like me logo Genes that share ontologies with GAR1: view
genes like me logo Genes that share phenotypes with GAR1: view

Animal Model Products

CRISPR Products

miRNA for GAR1 Gene

miRTarBase miRNAs that target GAR1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GAR1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GAR1 Gene

Localization for GAR1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GAR1 Gene

Nucleus, nucleolus. Nucleus, Cajal body. Note=Also localized to Cajal bodies (coiled bodies).

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GAR1 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GAR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000784 colocalizes_with nuclear chromosome, telomeric region IDA 24270157
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005697 telomerase holoenzyme complex TAS 22527283
genes like me logo Genes that share ontologies with GAR1: view

Pathways & Interactions for GAR1 Gene

genes like me logo Genes that share pathways with GAR1: view

Pathways by source for GAR1 Gene

Gene Ontology (GO) - Biological Process for GAR1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000454 snoRNA guided rRNA pseudouridine synthesis IBA --
GO:0001522 pseudouridine synthesis IEA --
GO:0006364 rRNA processing IEA --
GO:0007004 telomere maintenance via telomerase TAS 22527283
GO:0031118 rRNA pseudouridine synthesis TAS --
genes like me logo Genes that share ontologies with GAR1: view

No data available for SIGNOR curated interactions for GAR1 Gene

Drugs & Compounds for GAR1 Gene

(2) Drugs for GAR1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for GAR1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with GAR1: view

Transcripts for GAR1 Gene

Unigene Clusters for GAR1 Gene

GAR1 ribonucleoprotein homolog (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GAR1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for GAR1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7
SP1: - -
SP2: -
SP3:

Relevant External Links for GAR1 Gene

GeneLoc Exon Structure for
GAR1
ECgene alternative splicing isoforms for
GAR1

Expression for GAR1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GAR1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GAR1 Gene



Protein tissue co-expression partners for GAR1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GAR1 Gene:

GAR1

SOURCE GeneReport for Unigene cluster for GAR1 Gene:

Hs.69851
genes like me logo Genes that share expression patterns with GAR1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for GAR1 Gene

Orthologs for GAR1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GAR1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GAR1 33 34
  • 99.39 (n)
cow
(Bos Taurus)
Mammalia GAR1 34
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gar1 34
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GAR1 34
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GAR1 34
  • 78 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GAR1 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves GAR1 34
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GAR1 34
  • 82 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii gar1 34
  • 78 (a)
OneToOne
zgc56086 33
fruit fly
(Drosophila melanogaster)
Insecta CG4038 34
  • 56 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y66H1A.4 34
  • 56 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GAR1 34 36
  • 55 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1115 34
  • 64 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4306 33
Species where no ortholog for GAR1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for GAR1 Gene

ENSEMBL:
Gene Tree for GAR1 (if available)
TreeFam:
Gene Tree for GAR1 (if available)

Paralogs for GAR1 Gene

Pseudogenes.org Pseudogenes for GAR1 Gene

genes like me logo Genes that share paralogs with GAR1: view

No data available for Paralogs for GAR1 Gene

Variants for GAR1 Gene

Sequence variations from dbSNP and Humsavar for GAR1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs1000272685 -- 109,822,468(+) AGGTG(C/G)CAGAG reference, missense
rs1000340980 -- 109,815,376(+) TGCTT(C/T)AGTTC upstream-variant-2KB
rs10003826 -- 109,818,483(+) tctct(C/T)tctct intron-variant
rs10004390 -- 109,822,037(+) TACCC(A/G)ATGCA intron-variant
rs1000662726 -- 109,820,667(+) CAAAA(C/G)GCTGC intron-variant

Variation tolerance for GAR1 Gene

Residual Variation Intolerance Score: 64.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.35; 26.74% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GAR1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GAR1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for GAR1 Gene

Disorders for GAR1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for GAR1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
dyskeratosis congenita
  • zinsser-cole-engman syndrome
spinal muscular atrophy
  • juvenile spinal muscular atrophy
aplastic anemia
  • pulmonary fibrosis, idiopathic
- elite association - COSMIC cancer census association via MalaCards
Search GAR1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for GAR1

Human Genome Epidemiology (HuGE) Navigator
GAR1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GAR1
genes like me logo Genes that share disorders with GAR1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GAR1 Gene

Publications for GAR1 Gene

  1. In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAs. (PMID: 10757788) Dragon F … Filipowicz W (Molecular and cellular biology 2000) 2 3 4 22 60
  2. Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1. (PMID: 12244096) Whitehead SE … Terns MP (The Journal of biological chemistry 2002) 3 4 22 60
  3. The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1. (PMID: 11509230) Pellizzoni L … Dreyfuss G (Current biology : CB 2001) 3 4 22 60
  4. Specificity and stoichiometry of subunit interactions in the human telomerase holoenzyme assembled in vivo. (PMID: 20351177) Egan ED … Collins K (Molecular and cellular biology 2010) 3 22 60
  5. NOLA1 gene mutations in acquired aplastic anemia. (PMID: 18989882) Pigullo S … Dufour C (Pediatric blood & cancer 2009) 3 22 60

Products for GAR1 Gene

Sources for GAR1 Gene

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