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SNORA23 Gene

RNA gene   GIFtS: 18
GCID: GC11P009450

Small Nucleolar RNA, H/ACA Box 23

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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 6

Aliases
Small Nucleolar RNA, H/ACA Box 231 2
ACA232

External Ids:    HGNC: 326131   Entrez Gene: 6778082   Ensembl: ENSG000002019987   
ORGUL members:    fRNAdb10:FR159063 FR137466 FR030197 FR137466 FR069259      
H-InvDB12:HIT000382984    
NCBI13:AJ609438 AJ295844 AC132192 AJ609438 AJ609438    
NONCODE14:u3303    
Rfam:RF00319    
RNAdb15:SNO1494    

Export aliases for SNORA23 gene to outside databases

Previous GC identifers: GC11P009408 GC11P009121


(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 SNORA23 Gene:
SNORA23 (small nucleolar RNA, H/ACA box 23) is an RNA gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontology for SNORA23:
H_ACA_box_snoRNA - Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.

View fRNAdb secondary structures for SNORA23

(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 SNORA23 gene promoter:
         GATA-3   CBF-C   GATA-1   GATA-2   C/EBPalpha   AREB6   FOXO4   FOXJ2 (long isoform)   FOXJ2   CBF(2)   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORA23


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

Entrez Gene cytogenetic band: 11p15.4   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.4

SNORA23 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORA23 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P009450:  view genomic region     (about GC identifiers)

Start:
9,450,313 bp from pter      End:
9,450,501 bp from pter
Size:
189 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNORA23

(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,
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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:
SNORA: ncRNAs / Small nucleolar RNAs : H/ACA 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:
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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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(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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(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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4 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000365128(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 SNORA23:H-invDB

SNORA23 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CGGCCAAAGA
SNORA23 Expression
About this image

SNORA23 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 SNORA23 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Snora235 small nucleolar RNA, H/ACA box 23   --   7 (57.70 cM) 110046364 
chicken
(Gallus gallus)
Aves SNORA236
Small nucleolar RNA SNORA23
77(a)
1 ↔ 1
5(8816827-8817008) ENSGALG00000017862
lizard
(Anolis carolinensis)
Reptilia SNORA236
Small nucleolar RNA SNORA23
73(a)
1 ↔ 1
1(64214370-64214550) ENSACAG00000020807
zebrafish
(Danio rerio)
Actinopterygii SNORA236
SNORA236
Small nucleolar RNA SNORA23
66(a)
63(a)
many → 1
many → 1
7(67012725-67012905) ENSDARG00000082611
7(67001908-67002086) ENSDARG00000083454


ENSEMBL Gene Tree for SNORA23 (if available)
TreeFam Gene Tree for SNORA23 (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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Selected SNPs for SNORA23 (see all 58)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1899075351,2
--9372674(+) CTGTCA/TCCCAG 1 -- us2k10--------
rs1816544301,2
--9372709(+) GGCTCA/GCTGCA 1 -- us2k10--------
rs127996721,2
C,F--9372746(+) ttctcC/Atgcct 1 -- us2k14Minor allele frequency- A:0.50NA 8
rs110423491,2
C,F,A--9372809(+) GGAGTG/ACAGTG 1 -- us2k16Minor allele frequency- A:0.46NA EA 248
rs108402371,2
C,F,A--9372884(+) CTGCCC/ACCAGC 1 -- us2k110Minor allele frequency- A:0.46NA WA CSA EA 371
rs1450119621,2
C--9372908(+) TTTTAC/GTAGAG 1 -- us2k10--------
rs128008021,2
C,F--9372927(+) ttgccG/Atgttg 1 -- us2k1 tfbs34Minor allele frequency- A:0.25NA 8
rs1119697611,2
C,F--9373019(+) ACTGTG/CCCTGG 1 -- us2k12Minor allele frequency- C:0.02CSA WA 120
rs1862234471,2
--9373087(+) TTTACA/GTTCTA 1 -- us2k10--------
rs71017451,2
C--9373133(+) ATTGTA/GTCttt 1 -- us2k1 tfbs312Minor allele frequency- G:0.08NA WA CSA EA 374

HapMap Linkage Disequilibrium report for SNORA23 (9450313 - 9450501 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for SNORA23:    About this table    
Variant IDTypeSubtypePubMed ID
nsv499766OTHER Inversion21111241
nsv7215OTHER Inversion18451855

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNORA23
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(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: 605586 194071 604499 607967 609270 609470    

Find genes that share disorders with SNORA23           About GenesLikeMe


Export disorders for SNORA23 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 SNORA23 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with SNORA23)
    Utopia: connect your pdf to the dynamic
world of online information

  1. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. (PubMed id 16381836)1, 3 Lestrade L. and Weber M.J. (Nucleic Acids Res. 2006)
  2. Human box H/ACA pseudouridylation guide RNA machinery. (PubMed id 15199136)1, 3 Kiss A.M....Kiss T. (Mol. Cell. Biol. 2004)
  3. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PubMed id 19446021)1 Dieci G....Montanini B. (Genomics 2009)
  4. (PubMed id 12007400)10 
  5. (PubMed id 11387227)10 
  6. (PubMed id 15103394)10 
  7. (PubMed id 8797828)10 
  8. (PubMed id 10736225)10 
  9. (PubMed id 18089548)10 
  10. (PubMed id 15608158)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: 677808 HGNC: 32613 Ensembl:ENSG00000201998 euGenes: HUgn677808 ECgene: SNORA23
H-InvDB: SNORA23

(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 SNORA23 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 SNORA23 gene:
Search GeneIP for patents involving SNORA23

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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