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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SNORD42A Gene

RNA gene   GIFtS: 15
GCID: GC17P027050

small nucleolar RNA, C/D box 42A

(Previous names: RNA, U42A small nuclear )
(Previous symbol: RNU42A)
  Search for SNORD42A
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for SNORD42A    

Aliases
for SNORD42A gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): snoRNA

Quality score for this RNA gene is 6

Aliases
Small Nucleolar RNA, C/D Box 42A1 2
RNU42A1 2
U421 2
RNA, U42A Small Nuclear1
U42A2

External Ids:    HGNC: 101801   Entrez Gene: 268092   Ensembl: ENSG000002386497   
ORGUL members:    fRNAdb10:FR294723 FR074416 FR292342 FR216100 FR292342      
H-InvDB:HIT000383089    
NCBI:AF001689 X96641 X96641 AF001689 AC010761    
NONCODE:u569 u5065    
Rfam:RF00150    
RNAdb:SNO1428    

Export aliases for SNORD42A gene to outside databases

Previous GC identifers: GC17P024093 GC17P024098 GC17P024102 GC17P024106 GC17P024110 GC17P024114 GC17P024118 GC17P024122 GC17P023259


Summaries
for SNORD42A gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
fRNAdb sequence ontologies for SNORD42A - the ORGUL cluster for this gene includes several descriptions:
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].
snoRNA - A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
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'.

View fRNAdb secondary structures for SNORD42A

Genomic Views
for SNORD42A gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
 Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SNORD42A gene promoter:
         HFH-3   ATF-2   Tal-1beta   E47   CRE-BP1   FOXI1   PPAR-gamma1   c-Jun   PPAR-gamma2   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNORD42A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q11   Ensembl cytogenetic band:  17q11.2   HGNC cytogenetic band: 17q11.2

SNORD42A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORD42A gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P027050:  view genomic region     (about GC identifiers)

Start:
 27,050,447 bp from pter      End:
 27,050,510 bp from pter
Size:
 64 bases      Orientation:
 plus strand
ORGUL member locations:
Legend (see complete legend)

  • FR0070518
  • FR0294723
  • RF00150
  • FR0074416
  • FR0216100
  • FR0292342
27050446 27050478 27050510 chr17

Proteins
for SNORD42A gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for SNORD42A gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for SNORD42A gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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In Situ Assay
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Pathways & Interactions
for SNORD42A gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SNORD42A

Drugs & Compounds
for SNORD42A gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SNORD42A
Search CenterWatch for drugs/clinical trials and news about SNORD42A 

Transcripts
for SNORD42A gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
 5 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000459584(snoRNA)

miRNA
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Inhib. RNA
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Primer
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24/3749 AceView cDNA sequences (see all 3749):

AW516764 BE293105 AI656436 BE465359 BM839028 BG337174 BQ058928 CD242385 
BG325832 BQ636857 BU186032 BM987496 BG341092 BQ953016 BM749252 BG398391 
CB117736 AW615397 BU849090 BF975432 BF433216 BE409276 BF663688 AV716453 

GeneLoc Exon Structure


Expression
for SNORD42A gene

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for SNORD42A:H-invDB

SNORD42A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image    SABiosciences Custom PCR Arrays for SNORD42A
Primer
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In Situ
Assay Products: 
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Orthologs
for SNORD42A gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
This gene was present in the common ancestor of human and mouse.

Orthologs for SNORD42A gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Snord42a5 small nucleolar RNA, C/D box 42A   --   11 (46.74 cM) 78181302 


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

Paralogs
for SNORD42A gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for SNORD42A gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SNORD42A
DNA2.0 Custom Variant and Variant Library Synthesis for SNORD42A

Disorders / Diseases
for SNORD42A gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
SNORD42A for disorders           About MalaCards

SNORD42A for disorders           About GeneDecksing

OMIM gene information: 215500 601202 601251 605809 606579 607464 608631 609432 610185    

Export disorders for SNORD42A gene to outside databases

Publications
for SNORD42A gene

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for SNORD42A gene, integrated from 9 sources (see all 13):
(articles sorted by number of sources associating them with SNORD42A)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. (PubMed id 8674114)1, 3 Kiss-Laszlo Z....Kiss T. (1996)
  2. Eukaryotic snoRNAs: a paradigm for gene expression fl exibility. (PubMed id 19446021)1 Dieci G....Montanini B. (2009)
  3. Cloning, sequencing, gene organization, and localization of the human ribosomal protein RPL23A gene. (PubMed id 9417910)1 Fan W.... Lennon G. (1997)
  4. (PubMed id 8797828)10 
  5. (PubMed id 10736225)10 
  6. (PubMed id 15608158)10 
  7. (PubMed id 16381836)10 
  8. (PubMed id 15608161)10 
  9. (PubMed id 12215523)10 
  10. (PubMed id 11387227)10 

External Searches for SNORD42A gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing SNORD42A gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 26809 HGNC: 10180 AceView: RPL23A Ensembl:ENSG00000238649 euGenes: HUgn26809
ECgene: SNORD42A H-InvDB: SNORD42A

Other Databases showing SNORD42A gene

(According to HUGE)
About This Section
   --

Specialized Databases showing SNORD42A gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for SNORD42A Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SNORD42A gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SNORD42A gene:
Search GeneIP for patents involving SNORD42A

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



Products
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