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SNORA62 Gene

RNA gene   GIFtS: 20
GCID: GC03P039479

Small Nucleolar RNA, H/ACA Box 62

(Previous names: RNA, U108 small nucleolar)
(Previous symbols: RNE2, RNU108)
  Search for SNORA62
at  

(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 621 2
RNE21 2 5
RNU1081 2 5
RNA, U108 Small Nucleolar1
E22
E2-12

External Ids:    HGNC: 101071   Entrez Gene: 60442   Ensembl: ENSG000002023637   OMIM: 1806465   
ORGUL members:    fRNAdb10:FR143100 FR361189 FR091361 FR143100 FR091361      
H-InvDB12:HIT000383060 HIT000383060    
NCBI13:U43901 U43901 U36484 L07383 L22739 see all 10    
NONCODE14:u3886    
Rfam:RF00091    
RNAdb15:SNO1548    

Export aliases for SNORA62 gene to outside databases

Previous GC identifers: GC03P039430 GC03P039432 GC03P039450 GC03P039454 GC03P039458 GC03P039460 GC03P039466


(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 SNORA62 Gene:
SNORA62 (small nucleolar RNA, H/ACA box 62) is an RNA gene, and is affiliated with the snoRNA class.

fRNAdb sequence ontologies for SNORA62 - the ORGUL cluster for this gene includes several descriptions:
Small nucleolar RNA SNORA62/SNORA6 family - The members of this family belong to the H/ACA class of snoRNAs which are predicted to guide the sites of modification of uridines to pseudouridines [3]. This family includes human snoRNAs E2 (SNORA62), ACA6 (SNORA6) and M2 and mouse MBI-136. In humans both E2 and ACA6 are encoded in the introns on the same host gene (LAMR1)[1,3]. E2 is involved in the processing of eukaryotic pre-rRNA and has regions of complementarity to 28S rRNA [2]. ACA6 is predicted to guide the pseudouridylation of residue U3616 of 28S rRNA [5].
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.
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 SNORA62

(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 SNORA62 gene promoter:
         AhR   NF-YA   CBF-C   Arnt   CBF-A   CBF-B   CP1A   CP1C   NF-Y   CBF(2)   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORA62


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

Entrez Gene cytogenetic band: 3p22.1   Ensembl cytogenetic band:  3p22.1   HGNC cytogenetic band: 3p22.1

SNORA62 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORA62 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P039479:  view genomic region     (about GC identifiers)

Start:
39,452,545 bp from pter      End:
39,452,698 bp from pter
Size:
154 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNORA62

(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, Cloud-Clone Corp, 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:
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, 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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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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SuperPaths for SNORA62 About    
See pathways by source

SuperPathContained pathways About
1CFTR translational fidelity class I mutations
Cytoplasmic Ribosomal Proteins0.60
2Alpha6-Beta4 Integrin Signaling Pathway
Alpha6-Beta4 Integrin Signaling Pathway


2 BioSystems Pathways for SNORA62
    Alpha6-Beta4 Integrin Signaling Pathway
Cytoplasmic Ribosomal Proteins


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Interactions:

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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, Primers from OriGene, and/or QIAGEN )
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3 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000365493(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 SNORA62:H-invDB

SNORA62 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGGGGCAAGT
SNORA62 Expression
About this image

SNORA62 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SNORA62 Protein Expression
    Custom PCR Arrays for SNORA62
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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 SNORA62 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Snora625 small nucleolar RNA, H/ACA box 62   --   9 (71.41 cM) 120130434 
chicken
(Gallus gallus)
Aves SNORA626
Small nucleolar RNA SNORA62/SNORA6 family
71(a)
1 → many
2(44937393-44937548) ENSGALG00000017838
lizard
(Anolis carolinensis)
Reptilia SNORA626
Small nucleolar RNA SNORA62/SNORA6 family
74(a)
1 → many
GL343224.1(2176182-2176339)
zebrafish
(Danio rerio)
Actinopterygii SNORA626
Small nucleolar RNA SNORA62/SNORA6 family
52(a)
1 → many
3(6727639-6727774)


ENSEMBL Gene Tree for SNORA62 (if available)
TreeFam Gene Tree for SNORA62 (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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Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNORA62
DNA2.0 Custom Variant and Variant Library Synthesis for SNORA62

(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 gene information: 180646OMIM information: 117360 600644 252350 601869 606658 607135 608448 608982 609299    

SNORA62 for disorders           About GeneDecksing


Export disorders for SNORA62 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 SNORA62 gene, integrated from 10 sources (see all 19):
(articles sorted by number of sources associating them with SNORA62)
    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. Genes for E1, E2, and E3 small nucleolar RNAs. (PubMed id 8415643)1, 3 Nag M.K....Eliceiri G.L. (Proc. Natl. Acad. Sci. U.S.A. 1993)
  3. Three small nucleolar RNAs of unique nucleotide sequences. (PubMed id 8421699)1, 3 Ruff E.A....Eliceiri G.L. (Proc. Natl. Acad. Sci. U.S.A. 1993)
  4. A Proteomics Strategy for the Identification of FAT10-Modified Sites by Mass Spectrometry. (PubMed id 23862649)1 Leng L....Wang J. (J. Proteome Res. 2014)
  5. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PubMed id 19446021)1 Dieci G....Montanini B. (Genomics 2009)
  6. (PubMed id 8797828)10 
  7. (PubMed id 10736225)10 
  8. (PubMed id 15608158)10 
  9. (PubMed id 8586453)10 
  10. (PubMed id 9144174)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: 6044 HGNC: 10107 Ensembl:ENSG00000202363 euGenes: HUgn6044 ECgene: SNORA62
H-InvDB: SNORA62

(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 SNORA62 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 SNORA62 gene:
Search GeneIP for patents involving SNORA62

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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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 inGenious Targeting Laboratory, genOway)
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