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Aliases for SNORD46 Gene

Subcategory (RNA class) for SNORD46 Gene


Quality Score for this RNA gene is


Aliases for SNORD46 Gene

  • Small Nucleolar RNA, C/D Box 46 2 3 5
  • RNA, U40 Small Nuclear 2 3
  • RNA, U46 Small Nuclear 2 3
  • RNA, U40 Small Nucleolar 3
  • U40 Small Nucleolar RNA 3
  • U40 SnoRNA 3
  • RNU40 3
  • RNU46 3
  • U40 3
  • U46 3

External Ids for SNORD46 Gene

Previous HGNC Symbols for SNORD46 Gene

  • RNU46
  • RNU40

Previous GeneCards Identifiers for SNORD46 Gene

  • GC01P045015
  • GC01P045242
  • GC01P043355
  • GC01P044777
  • GC01P044782
  • GC01P044833
  • GC01P044787
  • GC01P044790
  • GC01P044796
  • GC01P044804
  • GC01P044805
  • GC01P044816
  • GC01P044823

Summaries for SNORD46 Gene

GeneCards Summary for SNORD46 Gene

SNORD46 (Small Nucleolar RNA, C/D Box 46) is an RNA Gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontologies for SNORD46 Gene - the ORGUL cluster for this gene includes several descriptions:

  • nc_conserved_region: Non-coding region of sequence similarity by descent from a common ancestor.

  • C_D_box_snoRNA: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.

  • Small nucleolar RNA SNORD46: U40 is a C/D box small nucleolar RNA, also known as snoZ153 in plants. The human sequence has also been annotated in the sequence databases as U46. U40 is encoded in intron 2 of the ribosomal protein S8 gene in human, and is hypothesised to guide methylation of 2'-O-ribose residues on 28S ribosomal RNA [1].

View fRNAdb secondary structures for SNORD46

Additional gene information for SNORD46 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for SNORD46 Gene

Genomics for SNORD46 Gene

GeneHancer (GH) Regulatory Elements for SNORD46 Gene

Promoters and enhancers for SNORD46 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
GH01J044774 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 600.7 -0.3 -272 3.7 ZNF652 SP1 CC2D1A ZFX ELF3 MNT ZNF148 NKRF POLR2A MLLT1 RPS8 ENSG00000225721 GC01P044811 GC01P044848 GC01P044849 GC01P044850 GC01P044853 SNORD46 SNORD55 SNORD38A
GH01J044805 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 11.3 +34.0 33961 10.7 CC2D1A SP1 ZFX ELF3 ZKSCAN8 MNT ZNF148 NKRF MLLT1 ZNF121 TOE1 GPBP1L1 RPS8 HECTD3 MUTYH ENSG00000234329 RPS15AP10 ENSG00000225721 UROD BEST4
GH01J044746 Promoter/Enhancer 0.7 EPDnew Ensembl 12 -29.9 -29889 0.8 KIF2C RPS8 ENSG00000225721 SNORD46 SNORD38A RNU5F-1 PLK3 BTBD19 TCTEX1D4 ARMH1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SNORD46 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNORD46 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • E47
  • Hand1
  • LyF-1
  • MyoD
  • Nkx2-5
  • SRF
  • SRF (504 AA)

Genomic Locations for SNORD46 Gene

Genomic Locations for SNORD46 Gene
104 bases
Plus strand
104 bases
Plus strand

Genomic View for SNORD46 Gene

Genes around SNORD46 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNORD46 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNORD46 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNORD46 Gene

ORGUL Member Location for SNORD46 Gene

ORGUL Member Location for SNORD46 gene

Proteins for SNORD46 Gene

Post-translational modifications for SNORD46 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SNORD46 Gene

Domains & Families for SNORD46 Gene

Gene Families for SNORD46 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNORD46: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SNORD46 Gene

Function for SNORD46 Gene

Animal Model Products

CRISPR Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SNORD46 Gene

Localization for SNORD46 Gene

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 SNORD46 gene
Compartment Confidence
cytosol 1

Gene Ontology (GO) - Cellular Components for SNORD46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with SNORD46: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SNORD46 Gene

Pathways & Interactions for SNORD46 Gene

PathCards logo

SuperPathways for SNORD46 Gene

No Data Available

Interacting Proteins for SNORD46 Gene

Gene Ontology (GO) - Biological Process for SNORD46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with SNORD46: view

No data available for Pathways by source and SIGNOR curated interactions for SNORD46 Gene

Drugs & Compounds for SNORD46 Gene

No Compound Related Data Available

Transcripts for SNORD46 Gene

fRNAdb Secondary structures for SNORD46 Gene

  • FR048365

mRNA/cDNA for SNORD46 Gene

(1) Additional mRNA sequences :
(485) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(2) RNA Central transcripts :

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNORD46 Gene

No ASD Table

Relevant External Links for SNORD46 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SNORD46 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNORD46 Gene

NURSA nuclear receptor signaling pathways regulating expression of SNORD46 Gene:

genes like me logo Genes that share expression patterns with SNORD46: view

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 , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNORD46 Gene

Orthologs for SNORD46 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SNORD46 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SNORD46 35
  • 100 (a)
(Mus musculus)
Mammalia Gm26330 35
  • 91 (a)
(Bos Taurus)
Mammalia SNORD46 35
  • 90 (a)
(Canis familiaris)
Mammalia SNORD46 35
  • 88 (a)
(Anolis carolinensis)
Reptilia SNORD46 35
  • 66 (a)
(Danio rerio)
Actinopterygii SNORD46 35
  • 69 (a)
Species where no ortholog for SNORD46 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SNORD46 Gene

Gene Tree for SNORD46 (if available)
Gene Tree for SNORD46 (if available)

Paralogs for SNORD46 Gene

No data available for Paralogs for SNORD46 Gene

Variants for SNORD46 Gene

Sequence variations from dbSNP and Humsavar for SNORD46 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1002100619 -- 44,776,212(+) C/A upstream_transcript_variant
rs1002496332 -- 44,774,649(+) C/G upstream_transcript_variant
rs1003081053 -- 44,775,795(+) G/T upstream_transcript_variant
rs1004247964 -- 44,776,238(+) G/C upstream_transcript_variant
rs1005196463 -- 44,774,739(+) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SNORD46 Gene

Variant ID Type Subtype PubMed ID
nsv461406 CNV loss 19166990
nsv546145 CNV loss 21841781
nsv998871 CNV loss 25217958

Additional Variant Information for SNORD46 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SNORD46 Gene

Disorders for SNORD46 Gene

Additional Disease Information for SNORD46

No disorders were found for SNORD46 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SNORD46 Gene

Publications for SNORD46 Gene

  1. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. (PMID: 8674114) Kiss-László Z … Kiss T (Cell 1996) 1 2 3 58
  2. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs. (PMID: 8764399) Nicoloso M … Bachellerie JP (Journal of molecular biology 1996) 1 2 3 58
  3. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PMID: 19446021) Dieci G … Montanini B (Genomics 2009) 3 58
  4. A study of the transfer of insulin-requiring diabetic patients from U-40 to U-100 Lente insulin. (PMID: 1606943) Abdulkadir J … Bekele G (Ethiopian medical journal 1992) 23 58
  5. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. (PMID: 18089548) Genome Information Integration Project And H-Invitational 2 … Gojobori T (Nucleic acids research 2008) 1

Products for SNORD46 Gene

Sources for SNORD46 Gene

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