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SNORA12 Gene

RNA gene   GIFtS: 20
GCID: GC10M102002

Small Nucleolar RNA, H/ACA Box 12
  Search for SNORA12
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Aliases
for SNORA12 gene

(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, H/ACA Box 121 2
U1082

External Ids:    HGNC: 326001   Entrez Gene: 6778002   Ensembl: ENSG000002124647   OMIM: 6113305   
ORGUL members:    fRNAdb10:FR274478 FR274478      
H-InvDB12:HIT000383037 HIT000383037    
NCBI13:AM055730 AL138921    
Rfam:RF00586    
RNAdb15:SNO1555    

Export aliases for SNORA12 gene to outside databases

Previous GC identifers: GC10M101986 GC10M095625 GC10M101998


Summaries
for SNORA12 gene

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SNORA12 Gene:
Small nucleolar RNAs (snoRNAs) are small noncoding RNAs involved in RNA processing. Box H/ACA snoRNAs, such as
SNORA12, direct the conversion of uridine to pseudouridine at specific residues of ribosomal RNAs or small
nuclear RNAs (snRNAs) (Gu et al., 2005).(supplied by OMIM, Mar 2008)

GeneCards Summary for SNORA12 Gene:
SNORA12 (small nucleolar RNA, H/ACA box 12) is an RNA gene, and is affiliated with the snoRNA class.



fRNAdb sequence ontologies for SNORA12 - the ORGUL cluster for this gene includes several descriptions:
Small nucleolar RNA SNORA12 - U108 belongs to the H/ACA family of snoRNAs. The sequence is predicted to guide the pseudouridylation of the U372 residue in the 28S rRNA subunit. However it has not been reported as a pseudouridylation site.
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 SNORA12

Genomic Views
for SNORA12 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000010.11  NC_018921.2  NT_030059.14  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNORA12 gene promoter:
         Pbx1a   Pax-5   MyoD   LCR-F1   RORalpha1   CREB   PPAR-gamma1   deltaCREB   c-Myb   PPAR-gamma2   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORA12


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

Entrez Gene cytogenetic band: 10q24.31   Ensembl cytogenetic band:  10q24.31   HGNC cytogenetic band: 10q24.31

SNORA12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORA12 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M102002:  view genomic region     (about GC identifiers)

Start:
 101,996,913 bp from pter      End:
 101,997,059 bp from pter
Size:
 147 bases      Orientation:
 minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNORA12

Proteins
for SNORA12 gene

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB: --

Domains /
Families
for SNORA12 gene

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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TryGeneCards Plus		 HGNC Gene Families:
SNORA: ncRNAs / Small nucleolar RNAs : H/ACA box containing

  --

Function
for SNORA12 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Localization
for SNORA12 gene

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Pathways & Interactions
for SNORA12 gene

(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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Interactions:

    Search GeneGlobe Interaction Network for SNORA12

Drugs & Compounds
for SNORA12 gene

(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 SNORA12



Transcripts
for SNORA12 gene

(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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TryGeneCards Plus		 1 fRNAdb Secondary structure:


Unigene Cluster for SNORA12:

Small nucleolar RNA, H/ACA box 12
Hs.662165  [show with all ESTs]
Unigene Representative Sequence: AA378382
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000391162(snoRNA)
miRNA
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Additional mRNA sequence: 

AM055730.1 NR_002954.1 

2 DOTS entries:

DT.92416738  DT.99932366 

GeneLoc Exon Structure


Expression
for SNORA12 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™, 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 SNORA12:H-invDB

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --


SNORA12 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Bone (Muscoskeletal System)    fully expand to see all 2 entries
         HyStem+BMP4-induced 4D20.8 cells
 
 Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
         HyStem+BMP4-induced 4D20.8 cells
SNORA12 Protein expression data from MOPED1, PaxDb2 and MaxQB3:  --

SOURCE GeneReport for Unigene cluster: Hs.662165
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Orthologs
for SNORA12 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)
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This gene was present in the common ancestor of chordates.

Orthologs for SNORA12 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
chicken
(Gallus gallus)		 Aves SNORA126
 Small nucleolar RNA SNORA12
 53(a)
 1 → many
 6(8825056-8825198) ENSGALG00000025583
        Species with no ortholog for SNORA12

ENSEMBL Gene Tree for SNORA12 (if available)
TreeFam Gene Tree for SNORA12 (if available)

Paralogs
for SNORA12 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Genomic Variants
for SNORA12 gene

(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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TryGeneCards Plus		Structural Variations
     Database of Genomic Variants (DGV) 2 variations for SNORA12:    About this table    
Variant IDTypeSubtypePubMed ID
nsv516860CNV Loss19592680
nsv895922CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
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Disorders / Diseases
for SNORA12 gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 611330OMIM information: 603188 607499    

SNORA12 for disorders           About GeneDecksing


Export disorders for SNORA12 gene to outside databases

Publications
for SNORA12 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)
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PubMed articles for SNORA12 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNORA12)		    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. A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes. (PubMed id 16361266)1, 3 Gu A.D....Qu L.H. (Nucleic Acids Res. 2005)
  3. Identification of VKORC1 interaction partners by split-ubiquitin system and coimmunoprecipitation. (PubMed id 21103663)1 Schaafhausen A....MA1ller C.R. (Thromb. Haemost. 2011)
  4. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PubMed id 19446021)1 Dieci G....Montanini B. (Genomics 2009)
  5. (PubMed id 15103394)10 
  6. (PubMed id 18089548)10 
  7. (PubMed id 15608161)10 

External Searches for SNORA12 gene

(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)

Genome Databases showing SNORA12 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 677800 HGNC: 32600 Ensembl:ENSG00000212464 euGenes: HUgn677800 ECgene: SNORA12
H-InvDB: SNORA12

Other Databases showing SNORA12 gene

(According to HUGE)
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Specialized Databases showing SNORA12 gene

(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 SNORA12 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SNORA12 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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TryGeneCards Plus		Patent Information for SNORA12 gene:
Search GeneIP for patents involving SNORA12

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



Products
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