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SNORD24 Gene

RNA gene   GIFtS: 19
GCID: GC09P136283

Small Nucleolar RNA, C/D Box 24

(Previous names: RNA, U24 small nucleolar)
(Previous symbol: RNU24)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): snoRNA

Quality score for this RNA gene is 11

Aliases
Small Nucleolar RNA, C/D Box 241 2
RNU241 2
RNA, U24 Small Nucleolar1
U242

External Ids:    HGNC: 101461   Entrez Gene: 268202   Ensembl: ENSG000002066117   
ORGUL members:    fRNAdb10:FR017664 FR393255 FR393255 FR017664      
H-InvDB12:HIT000383125 HIT000383125    
NCBI13:AL158826 AC002107 Z48765 Z48764 X52138 see all 7    
NONCODE14:u5245    
Rfam:RF00069    
RNAdb15:SNO1402    

Export aliases for SNORD24 gene to outside databases

Previous GC identifers: GC09U900790 GC09P135219 GC09P135227 GC09P135232 GC09P135239 GC09P136217 GC09P136247 GC09P136261


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SNORD24 Gene:
SNORD24 (small nucleolar RNA, C/D box 24) is an RNA gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontologies for SNORD24 - the ORGUL cluster for this gene includes several descriptions:
Small nucleolar RNA SNORD24 - U24 is a member of the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs [1]. C/D box snoRNAs have been shown to act as methylation guides for a number of RNA targets [2,3]. U24 is encoded within an intron of the gene for ribosomal protein L7a in mammals, chicken and Fugu [4]. The U76 snoRNA is found in an intron of the uRNA host gene (UHG) growth arrest specific 5 (GAS5) transcript gene [5]. snoRNAs Z20 and U76 snoRNAs show clear similarity to U24.
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 SNORD24

(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the SNORD24 gene promoter:
         ER-alpha   HOXA3   HTF   Pax-2   Pax-2a   FOXL1   Pax-2b   Chx10   Sox9   PPAR-gamma2   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORD24


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

Entrez Gene cytogenetic band: 9q34   Ensembl cytogenetic band:  9q34.2   HGNC cytogenetic band: 9q34.2

SNORD24 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORD24 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P136283:  view genomic region     (about GC identifiers)

Start:
136,216,251 bp from pter      End:
136,216,325 bp from pter
Size:
75 bases      Orientation:
plus strand

1 alternative location:
Chr9+,NW_003315925 175,490-175,564     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNORD24

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
SNORD: ncRNAs / Small nucleolar RNAs : C/D box containing

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for SNORD24

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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SuperPaths for SNORD24 About    
See pathways by source

SuperPathContained pathways About
1CFTR translational fidelity class I mutations
Cytoplasmic Ribosomal Proteins0.60


1 BioSystems Pathway for SNORD24
    Cytoplasmic Ribosomal Proteins


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Interactions:

    Search GeneGlobe Interaction Network for SNORD24

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for SNORD24



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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2 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000383884(snoRNA)
miRNA
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GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for SNORD24:H-invDB

SNORD24 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SNORD24 Expression
About this image


SNORD24 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 NULL (Uncategorized)
         Mesenchymal Progenitor Cells - Passage 2
SNORD24 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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(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)
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This gene was present in the common ancestor of chordates.

Orthologs for SNORD24 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves SNORD246
Small nucleolar RNA SNORD24
84(a)
1 ↔ 1
17(6866555-6866629) ENSGALG00000017832
zebrafish
(Danio rerio)
Actinopterygii SNORD246
Small nucleolar RNA SNORD24
81(a)
1 ↔ 1
5(34904485-34904556)
        Species with no ortholog for SNORD24

ENSEMBL Gene Tree for SNORD24 (if available)
TreeFam Gene Tree for SNORD24 (if available)

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

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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3 SNPs for SNORD24    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1886941891,2
--136229296(+) TCTACC/TAAAAA 1 -- us2k10--------
rs283671411,2
C--136229315(+) TTAGCC/TGGGCG 1 -- us2k10--------
rs675009721,2
----136229324(+) CGTGA-/TGGCA 
 GGCGCCT
GTAAT
1 -- us2k10--------

HapMap Linkage Disequilibrium report for SNORD24 (136216251 - 136216325 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for SNORD24:    About this table    
Variant IDTypeSubtypePubMed ID
esv2739138CNV Deletion23290073
nsv894076CNV Loss21882294
dgv8325n71CNV Loss21882294
nsv894079CNV Loss21882294
nsv894080CNV Loss21882294
nsv894057CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNORD24
DNA2.0 Custom Variant and Variant Library Synthesis for SNORD24

(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.)
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OMIM information: 185640 156240 606613    

Find genes that share disorders with SNORD24           About GenesLikeMe


Export disorders for SNORD24 gene to outside databases

(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)
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PubMed articles for SNORD24 gene, integrated from 10 sources (see all 15):
(articles sorted by number of sources associating them with SNORD24)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human L7a ribosomal protein: sequence, structural organization, and expression of a functional gene. (PubMed id 8482538)1, 3 De Falco S.... Pietropaolo C. (Gene 1993)
  2. Proteomic identification of common SCF ubiquitin ligase FBXO6-interacting glycoproteins in three kinds of cells. (PubMed id 22268729)1 Liu B....Wang L.S. (J. Proteome Res. 2012)
  3. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PubMed id 19446021)1 Dieci G....Montanini B. (Genomics 2009)
  4. Evolution of U24 and U36 snoRNAs encoded within introns of vertebrate rpL7a gene homologs: unique features of mammalian U36 variants. (PubMed id 9703018)1 Gilley J. and Fried M. (DNA Cell Biol. 1998)
  5. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. (PubMed id 8674114)1 Kiss-LA!szlA^ Z....Kiss T. (Cell 1996)
  6. U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA. (PubMed id 7651828)1 Qu L.H....Bachellerie J.P. (Nucleic Acids Res. 1995)
  7. (PubMed id 8764399)10 
  8. (PubMed id 11606788)10 
  9. (PubMed id 8797828)10 
  10. (PubMed id 10736225)10 

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 26820 HGNC: 10146 Ensembl:ENSG00000206611 euGenes: HUgn26820 ECgene: SNORD24
H-InvDB: SNORD24

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SNORD24 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SNORD24 gene:
Search GeneIP for patents involving SNORD24

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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