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Aliases for NOP56 Gene

Aliases for NOP56 Gene

  • NOP56 Ribonucleoprotein 2 3 5
  • Nucleolar Protein 5A (56kDa With KKE/D Repeat) 2 3
  • NOL5A 3 4
  • Nucleolar Protein 5A (56kD With KKE/D Repeat) 2
  • NOP56 Ribonucleoprotein Homolog (Yeast) 2
  • NOP56 Ribonucleoprotein Homolog 3
  • Spinocerebellar Ataxia 36 2
  • Nucleolar Protein 56 3
  • Nucleolar Protein 5A 4
  • SCA36 3

External Ids for NOP56 Gene

Previous HGNC Symbols for NOP56 Gene

  • NOL5A

Previous GeneCards Identifiers for NOP56 Gene

  • GC20P002606
  • GC20P002611
  • GC20P002618
  • GC20P002636
  • GC20P002646
  • GC20P002656
  • GC20P002670
  • GC20P002681
  • GC20P002689
  • GC20P002698
  • GC20P002708
  • GC20P002723
  • GC20P002736
  • GC20P002755
  • GC20P002757
  • GC20P002778
  • GC20P002738
  • GC20P002765
  • GC20P002835
  • GC20P002838
  • GC20P002853

Summaries for NOP56 Gene

Entrez Gene Summary for NOP56 Gene

  • Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is similar in sequence to Nop56p and is also found in the nucleolus. Expansion of a GGCCTG repeat from 3-8 copies to 1500-2500 copies in an intron of this gene results in spinocerebellar ataxia 36. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jul 2016]

GeneCards Summary for NOP56 Gene

NOP56 (NOP56 Ribonucleoprotein) is a Protein Coding gene. Diseases associated with NOP56 include Spinocerebellar Ataxia 36 and Oromandibular Dystonia. Among its related pathways are rRNA processing in the nucleus and cytosol and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include snoRNA binding.

UniProtKB/Swiss-Prot for NOP56 Gene

  • Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs.

Gene Wiki entry for NOP56 Gene

Additional gene information for NOP56 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NOP56 Gene

Genomics for NOP56 Gene

GeneHancer (GH) Regulatory Elements for NOP56 Gene

Promoters and enhancers for NOP56 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J002651 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 673 +1.1 1060 4.2 HDGF SMAD1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B NOP56 GC20P002890 GC20P002893 GC20P002900 PIR58104 SNORD110 SNORA51 GC20M002651 MIR1292 GC20P002898
GH20J002656 Promoter/Enhancer 1 EPDnew ENCODE 650.7 +3.8 3845 0.2 PAF1 HIC1 POLR2A ZNF837 ZKSCAN1 GC20P002892 GC20P002893 NOP56 PIR58104 SNORA51 SNORD110 PIR58900 SNORD86 SNORD57 SNORD56
GH20J002655 Promoter/Enhancer 0.9 EPDnew ENCODE 650.7 +3.3 3261 0.2 SSRP1 POLR2A GC20P002890 GC20P002892 GC20P002893 GC20P002894 GC20P002896 GC20P002898 GC20P002900 SNORD57 PIR58104 PIR58900
GH20J003172 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 25.8 +522.1 522127 3.3 PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9 LZTS3 GC20P003173 ITPA ENSG00000229539 DDRGK1 ZNF343 VPS16 NOP56 UBOX5-AS1 SNRPB
GH20J002870 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 25.5 +220.5 220473 4.7 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF207 PTPRA VPS16 NOP56 PCED1A TMEM239 ENSG00000241690 C20orf141 CDC25B ITPA GC20M002886
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NOP56 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NOP56 gene promoter:
  • AREB6
  • S8
  • HEN1
  • ZID
  • Pax-6
  • MZF-1
  • IRF-2
  • COMP1
  • GATA-1

Genomic Locations for NOP56 Gene

Genomic Locations for NOP56 Gene
6,249 bases
Plus strand
6,249 bases
Plus strand

Genomic View for NOP56 Gene

Genes around NOP56 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NOP56 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NOP56 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NOP56 Gene

Proteins for NOP56 Gene

  • Protein details for NOP56 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Nucleolar protein 56
    Protein Accession:
    Secondary Accessions:
    • Q2M3T6
    • Q9NQ05

    Protein attributes for NOP56 Gene

    594 amino acids
    Molecular mass:
    66050 Da
    Quaternary structure:
    • Part of a large pre-ribosomal ribonucleoprotein (RNP) complex, that consists of at least 62 ribosomal proteins, 45 nonribosomal proteins and both pre-rRNA and mature rRNA species. Within this complex directly interacts with TCOF1 in an RNA-independent manner. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles; the core proteins SNU13, NOP56, NOP58 and FBL assemble stepwise onto the snoRNA. Interacts NOP1 and NOP58. Interacts with NUFIP1, RUVBL1 and RUVBL2; RUVBL1:RUVBL2 seem to bridge the association of NOP56 with NUFIP1.
    • Sequence=CAA72789.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for NOP56 Gene

Post-translational modifications for NOP56 Gene

  • Ubiquitination at Lys396, Lys375, isoforms=333, isoforms=320, and Lys288
  • Modification sites at PhosphoSitePlus

Other Protein References for NOP56 Gene

No data available for DME Specific Peptides for NOP56 Gene

Domains & Families for NOP56 Gene

Gene Families for NOP56 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NOP5/NOP56 family.
  • Belongs to the NOP5/NOP56 family.
genes like me logo Genes that share domains with NOP56: view

Function for NOP56 Gene

Molecular function for NOP56 Gene

UniProtKB/Swiss-Prot Function:
Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs.

Phenotypes From GWAS Catalog for NOP56 Gene

Gene Ontology (GO) - Molecular Function for NOP56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding TAS,HDA 22658674
GO:0005515 protein binding IPI 17314511
GO:0030515 snoRNA binding IDA 17636026
GO:0045296 cadherin binding IDA 25468996
GO:1990226 histone methyltransferase binding IPI 17636026
genes like me logo Genes that share ontologies with NOP56: view
genes like me logo Genes that share phenotypes with NOP56: view

Human Phenotype Ontology for NOP56 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for NOP56 Gene

miRTarBase miRNAs that target NOP56

Clone Products

  • Addgene plasmids for NOP56

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NOP56 Gene

Localization for NOP56 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NOP56 Gene

Nucleus, nucleolus. Cytoplasm. Nucleus, nucleoplasm.

Subcellular locations from

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 NOP56 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NOP56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus TAS 9372940
GO:0005732 small nucleolar ribonucleoprotein complex IDA 17636026
genes like me logo Genes that share ontologies with NOP56: view

Pathways & Interactions for NOP56 Gene

genes like me logo Genes that share pathways with NOP56: view

Gene Ontology (GO) - Biological Process for NOP56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000154 rRNA modification IBA --
GO:0006364 rRNA processing TAS --
GO:0042254 ribosome biogenesis IEA --
genes like me logo Genes that share ontologies with NOP56: view

No data available for SIGNOR curated interactions for NOP56 Gene

Drugs & Compounds for NOP56 Gene

No Compound Related Data Available

Transcripts for NOP56 Gene

mRNA/cDNA for NOP56 Gene

Unigene Clusters for NOP56 Gene

NOP56 ribonucleoprotein:
Representative Sequences:

Clone Products

  • Addgene plasmids for NOP56

Alternative Splicing Database (ASD) splice patterns (SP) for NOP56 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c · 4d · 4e ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d ·
SP1: - - - - - - - -
SP2: - - - - -
SP3: - - - - - - - - - - - - -
SP4: - - - - - - -
SP5: - -
SP6: - -
SP11: - - - - - - - - - - -
SP12: - - - - -
SP13: - - - - - -
SP14: - - - - - -
SP15: - - - - -
SP16: - -
SP19: - - - -
SP20: - - - - - -
SP26: -

ExUns: 10e ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b · 16c ^ 17a · 17b · 17c ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b · 20c · 20d
SP5: - - - -
SP6: - - - - -
SP7: - - - - -
SP8: - - - - - - -
SP9: - - - - -
SP10: - -
SP17: - - -
SP18: - - -
SP21: -
SP22: - - - - -
SP24: - - - -
SP25: -

Relevant External Links for NOP56 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NOP56 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NOP56 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NOP56 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (11.3) and Tlymphocyte (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NOP56 Gene

Protein tissue co-expression partners for NOP56 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NOP56 Gene:


SOURCE GeneReport for Unigene cluster for NOP56 Gene:


Evidence on tissue expression from TISSUES for NOP56 Gene

  • Nervous system(5)
  • Liver(4.6)
  • Kidney(4.5)
  • Lung(4.3)
  • Intestine(3.8)
  • Skin(3.8)
  • Eye(2.4)
  • Spleen(2.2)
  • Stomach(2.2)
  • Muscle(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NOP56 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • mouth
  • tongue
  • foot
  • lower limb
  • upper limb
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with NOP56: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for NOP56 Gene

Orthologs for NOP56 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NOP56 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NOP56 34 33
  • 99.21 (n)
(Bos Taurus)
Mammalia NOP56 34 33
  • 91.11 (n)
(Canis familiaris)
Mammalia NOP56 34 33
  • 91.03 (n)
(Rattus norvegicus)
Mammalia Nop56 33
  • 87.39 (n)
(Mus musculus)
Mammalia Nop56 16 34 33
  • 86.39 (n)
(Monodelphis domestica)
Mammalia NOP56 34
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia NOP56 34
  • 71 (a)
(Gallus gallus)
Aves NOP56 34 33
  • 74.7 (n)
(Anolis carolinensis)
Reptilia NOP56 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nop56 33
  • 72.36 (n)
Str.8159 33
African clawed frog
(Xenopus laevis)
Amphibia XNop56 33
(Danio rerio)
Actinopterygii nop56 34 33
  • 73.42 (n)
nol5a 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9727 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002063 33
  • 65.98 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nop56 34 33
  • 65.13 (n)
(Caenorhabditis elegans)
Secernentea K07C5.4 34 33
  • 57.91 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL144C 33
  • 56.87 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12254g 33
  • 54.39 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP56 36 34 33
  • 53.98 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons NOP56 33
  • 60.82 (n)
(Glycine max)
eudicotyledons Gma.2258 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3462 33
(Oryza sativa)
Liliopsida Os03g0352300 33
  • 60.74 (n)
(Triticum aestivum)
Liliopsida Ta.9201 33
(Zea mays)
Liliopsida Zm.7010 33
bread mold
(Neurospora crassa)
Ascomycetes NCU06943 33
  • 56.77 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC646.10c 33
  • 55.35 (n)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.3107 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3107 33
Species where no ortholog for NOP56 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for NOP56 Gene

Gene Tree for NOP56 (if available)
Gene Tree for NOP56 (if available)
Evolutionary constrained regions (ECRs) for NOP56: view image

Paralogs for NOP56 Gene

(2) SIMAP similar genes for NOP56 Gene using alignment to 6 proteins:

  • A0PJ92_HUMAN
  • H0Y653_HUMAN
genes like me logo Genes that share paralogs with NOP56: view

No data available for Paralogs for NOP56 Gene

Variants for NOP56 Gene

Sequence variations from dbSNP and Humsavar for NOP56 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs140155681 uncertain-significance, Retinitis Pigmentosa, Recessive 2,658,498(+) A/G downstream_transcript_variant
rs145651330 uncertain-significance, Retinitis Pigmentosa, Recessive 2,658,827(+) C/T downstream_transcript_variant
rs376112899 uncertain-significance, Retinitis Pigmentosa, Recessive 2,658,777(+) C/T downstream_transcript_variant
rs546467756 uncertain-significance, Retinitis Pigmentosa, Recessive 2,658,548(+) A/G downstream_transcript_variant
rs781157150 uncertain-significance, Retinitis Pigmentosa, Recessive 2,658,789(+) TGATGA/TGA downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NOP56 Gene

Variant ID Type Subtype PubMed ID
nsv585266 CNV loss 21841781
nsv470535 CNV gain 18288195
nsv458852 CNV loss 19166990
nsv1057464 CNV gain 25217958
esv3644998 CNV gain 21293372
esv3402776 CNV insertion 20981092

Variation tolerance for NOP56 Gene

Residual Variation Intolerance Score: 43.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.19; 87.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NOP56 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NOP56 Gene

Disorders for NOP56 Gene

MalaCards: The human disease database

(6) MalaCards diseases for NOP56 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spinocerebellar ataxia 36
  • sca36
oromandibular dystonia
cerebellar disease
  • cerebellar dysfunction
  • hypoceruloplasminemia, hereditary
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search NOP56 in MalaCards View complete list of genes associated with diseases


  • Spinocerebellar ataxia 36 (SCA36) [MIM:614153]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA36 is characterized by complicated clinical features, with ataxia as the first symptom, followed by characteristic late-onset involvement of the motor neuron system. Ataxic symptoms, such as gait and truncal instability, ataxic dysarthria, and uncoordinated limbs, start in late forties to fifties. Characteristically, affected individuals exhibit tongue atrophy with fasciculation. Progression of motor neuron involvement is typically limited to the tongue and main proximal skeletal muscles in both upper and lower extremities. {ECO:0000269 PubMed:21683323}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by large hexanucleotide CGCCTG repeat expansions within intron 1. These expansions induce RNA foci and sequester the RNA-binding protein SRSF2. In addition, the transcription of MIR1292, a microRNA gene located just 19 bp 3 of the GGCCTG repeat, is significantly decreased.

Additional Disease Information for NOP56

genes like me logo Genes that share disorders with NOP56: view

No data available for Genatlas for NOP56 Gene

Publications for NOP56 Gene

  1. Expansion of intronic GGCCTG hexanucleotide repeat in NOP56 causes SCA36, a type of spinocerebellar ataxia accompanied by motor neuron involvement. (PMID: 21683323) Kobayashi H … Koizumi A (American journal of human genetics 2011) 2 3 4 58
  2. Evidence that the AAA+ proteins TIP48 and TIP49 bridge interactions between 15.5K and the related NOP56 and NOP58 proteins during box C/D snoRNP biogenesis. (PMID: 19620283) McKeegan KS … Watkins NJ (Molecular and cellular biology 2009) 3 4 22 58
  3. Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. (PMID: 12417735) Watkins NJ … Lührmann R (Molecular and cellular biology 2002) 3 4 22 58
  4. Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. (PMID: 9372940) Gautier T … Hurt E (Molecular and cellular biology 1997) 2 3 4 58
  5. Fibrillarin and Nop56 interact before being co-assembled in box C/D snoRNPs. (PMID: 19331828) Lechertier T … Roussel P (Experimental cell research 2009) 3 22 58

Products for NOP56 Gene

  • Addgene plasmids for NOP56

Sources for NOP56 Gene

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