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Aliases for SNORD42A Gene

Subcategory (RNA class) for SNORD42A Gene


Quality Score for this RNA gene is


Aliases for SNORD42A Gene

  • Small Nucleolar RNA, C/D Box 42A 2 3 5
  • RNA, U42A Small Nuclear 2 3
  • U42 Small Nuclear RNA 3
  • U42A SnoRNA 3
  • RNU42A 3
  • U42A 3
  • U42 3

External Ids for SNORD42A Gene

Previous HGNC Symbols for SNORD42A Gene

  • RNU42A

Previous GeneCards Identifiers for SNORD42A Gene

  • GC17P024093
  • GC17P024098
  • GC17P024102
  • GC17P024106
  • GC17P024110
  • GC17P024114
  • GC17P024118
  • GC17P024122
  • GC17P027050
  • GC17P023259

Summaries for SNORD42A Gene

GeneCards Summary for SNORD42A Gene

SNORD42A (Small Nucleolar RNA, C/D Box 42A) is an RNA Gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontologies for SNORD42A Gene - the ORGUL cluster for this gene includes several descriptions:

  • 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 SNORD42: snoRNA U42 is found in intron 3 of the ribosomal protein L23a (RPL23a) gene in humans and is also present in mice. U42 is a member of the C/D class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs. Although the selection of the target nucleotide requires the antisense element and the conserved box D or D' of the snoRNA, the methyltransferase activity is supposed to reside in one of the protein components [1].

Additional gene information for SNORD42A 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 SNORD42A Gene

Genomics for SNORD42A Gene

GeneHancer (GH) Regulatory Elements for SNORD42A Gene

Promoters and enhancers for SNORD42A 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
GH17J028715 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.5 -505 14.4 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ENSG00000264577 RAB34 RPL23A NEK8 GC17P028744 GC17P028748 GC17P028753 GC17P028756 SNORD42A SNORD4A
GH17J028660 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.3 -61.0 -61004 3.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SUPT6H SDF2 PROCA1 ENSG00000264044 SNORD42A SNORD4B SGK494 SPAG5-AS1 NEK8 TLCD1
GH17J028854 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.7 +131.6 131629 1.7 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 ERAL1 FAM222B FLOT2 DHRS13 SNORD42A SNORD4A SNORD4B PROCA1
GH17J028807 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 11 +87.0 87010 6.8 HDGF PKNOX1 FOXA2 ARNT SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 SUPT6H TRAF4 LOC101927018 ENSG00000264577 ENSG00000265205 NUFIP2 ENSG00000265908 FAM222B ERAL1 PIGS
GH17J028863 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +141.9 141907 3.3 HDGF SMAD1 ARNT ARID4B IRF4 ZNF766 CBX5 JUNB REST ZNF592 DHRS13 RPL23A PROCA1 NUFIP2 SUPT6H PHF12 ENSG00000264577 ENSG00000265908 FLOT2 NEK8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SNORD42A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNORD42A gene promoter:
  • c-Jun
  • ATF-2
  • Tal-1beta
  • E47
  • FOXI1
  • HFH-3
  • PPAR-gamma1
  • PPAR-gamma2
  • CRE-BP1

Genomic Locations for SNORD42A Gene

Genomic Locations for SNORD42A Gene
64 bases
Plus strand
64 bases
Plus strand

Genomic View for SNORD42A Gene

Genes around SNORD42A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNORD42A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNORD42A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNORD42A Gene

ORGUL Member Location for SNORD42A Gene

ORGUL Member Location for SNORD42A gene

Proteins for SNORD42A Gene

Post-translational modifications for SNORD42A Gene

No Post-translational modifications

No data available for DME Specific Peptides for SNORD42A Gene

Domains & Families for SNORD42A Gene

Gene Families for SNORD42A Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNORD42A: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SNORD42A Gene

Function for SNORD42A Gene

Phenotypes From GWAS Catalog for SNORD42A Gene

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SNORD42A Gene

Localization for SNORD42A Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SNORD42A Gene

Pathways & Interactions for SNORD42A Gene

SuperPathways for SNORD42A Gene

No Data Available

Interacting Proteins for SNORD42A Gene

Gene Ontology (GO) - Biological Process for SNORD42A Gene


No data available for Pathways by source and SIGNOR curated interactions for SNORD42A Gene

Drugs & Compounds for SNORD42A Gene

No Compound Related Data Available

Transcripts for SNORD42A Gene

mRNA/cDNA for SNORD42A Gene

(3749) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
(2) RNA Central transcripts :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SNORD42A Gene

No ASD Table

Relevant External Links for SNORD42A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SNORD42A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SNORD42A Gene

NURSA nuclear receptor signaling pathways regulating expression of SNORD42A Gene:

genes like me logo Genes that share expression patterns with SNORD42A: 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 SNORD42A Gene

Orthologs for SNORD42A Gene

This gene was present in the common ancestor of chordates.

Orthologs for SNORD42A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SNORD42 34
  • 100 (a)
(Mus musculus)
Mammalia Snord42a 34
  • 78 (a)
(Canis familiaris)
Mammalia SNORD42 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia SNORD42 34
  • 68 (a)
(Monodelphis domestica)
Mammalia SNORD42 34
  • 61 (a)
(Gallus gallus)
Aves SNORD42 34
  • 55 (a)
(Danio rerio)
Actinopterygii SNORD42 34
  • 54 (a)
Species where no ortholog for SNORD42A 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 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 SNORD42A Gene

Gene Tree for SNORD42A (if available)
Gene Tree for SNORD42A (if available)

Paralogs for SNORD42A Gene

No data available for Paralogs for SNORD42A Gene

Variants for SNORD42A Gene

Sequence variations from dbSNP and Humsavar for SNORD42A Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000340537 -- 28,723,984(+) C/G downstream_transcript_variant
rs1000673498 -- 28,722,930(+) G/C upstream_transcript_variant
rs1001178674 -- 28,721,774(+) TCTTTCTT/TCTT upstream_transcript_variant
rs1001859064 -- 28,721,564(+) T/A upstream_transcript_variant
rs1003818876 -- 28,722,561(+) C/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SNORD42A Gene

Variant ID Type Subtype PubMed ID
nsv1064087 CNV gain 25217958
nsv960457 CNV duplication 23825009

Additional Variant Information for SNORD42A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SNORD42A Gene

Disorders for SNORD42A Gene

Additional Disease Information for SNORD42A

No disorders were found for SNORD42A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SNORD42A Gene

Publications for SNORD42A 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. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PMID: 19446021) Dieci G … Montanini B (Genomics 2009) 3 58
  3. Cloning, sequencing, gene organization, and localization of the human ribosomal protein RPL23A gene. (PMID: 9417910) Fan W … Lennon G (Genomics 1997) 3 58
  4. 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
  5. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. (PMID: 16381836) Lestrade L … Weber MJ (Nucleic acids research 2006) 1

Products for SNORD42A Gene

Sources for SNORD42A Gene

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