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SNORD3A Gene

RNA gene   GIFtS: 19
GCID: GC17P019091

Small Nucleolar RNA, C/D Box 3A

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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): lncRNA

Quality score for this RNA gene is 3

Aliases
Small Nucleolar RNA, C/D Box 3A1 2
RNU32 5
U32

External Ids:    HGNC: 331891   Entrez Gene: 7808512   Ensembl: ENSG000002639347   OMIM: 1807105   
ORGUL members:         

Export aliases for SNORD3A gene to outside databases

Previous GC identifers: GC17U900799 GC17P019032


(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 SNORD3A Gene:
U3 RNA, an abundant small nucleolar RNA (snoRNA), is thought to play a role in the processing of ribosomal RNA
precursors (Bernstein et al., 1983 (PubMed 6186397)).(supplied by OMIM, Jun 2009)

GeneCards Summary for SNORD3A Gene:
SNORD3A (small nucleolar RNA, C/D box 3A) is an RNA gene, and is affiliated with the lncRNA class.




(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:
   Search for regulatory transcription factor binding sites for SNORD3A
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORD3A


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

Entrez Gene cytogenetic band: 17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

SNORD3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORD3A gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P019091:  view genomic region     (about GC identifiers)

Start:
19,091,329 bp from pter      End:
19,092,027 bp from pter
Size:
699 bases      Orientation:
plus strand

(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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(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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SuperPaths for SNORD3A About    
See pathways by source

SuperPathContained pathways About
1RNA transport
RNA transport
2Ribosome biogenesis in eukaryotes
Ribosome biogenesis in eukaryotes


Find genes that share SuperPaths with SNORD3A           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



2 Kegg Pathways  (Kegg details for SNORD3A):
    Ribosome biogenesis in eukaryotes
RNA transport

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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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000584923(lincRNA)(uc021trx.1) ENST00000365494(lincRNA)
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 SNORD3A:none

SNORD3A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SNORD3A Expression
About this image

SNORD3A 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 human and chimp.

Orthologs for SNORD3A gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia U36
U36
Small nucleolar RNA U3
94(a)
94(a)
many ↔ many
many ↔ many
GL392668.1(3619-3834) ENSPTRG00000042492
17(36817854-36818069) ENSPTRG00000027110


ENSEMBL Gene Tree for SNORD3A (if available)
TreeFam Gene Tree for SNORD3A (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 SNORD3A (see all 55)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1994995511,2
C--19091144(+) AACAAC/TTTTTA 1 -- us2k10--------
rs2017788631,2
C--19091418(+) AGAGAG/ATAGCG 1 -- nc-transcript-variant1Minor allele frequency- A:0.00EU 559
rs1995854481,2
C,F--19091429(+) GTTTTC/GTCCTG 1 -- nc-transcript-variant1Minor allele frequency- G:0.03EU 589
rs1905862261,2
C--19091434(+) CTCCTC/GAGCGT 1 -- nc-transcript-variant0--------
rs2014694511,2
C,F--19091443(+) GTGAAG/ACCGGC 1 -- nc-transcript-variant1Minor allele frequency- A:0.01EU 585
rs2016854391,2
C,F--19091445(+) GAAGCC/TGGCTT 1 -- nc-transcript-variant1Minor allele frequency- T:0.01EU 579
rs726392031,2
C,F--19091452(+) GCTTTC/TTGGCG 1 -- nc-transcript-variant1Minor allele frequency- T:0.11EU 535
rs2016990251,2
F--19091453(+) CTTTCA/G/TGGCGT 2 -- nc-transcript-variant1EU 568
rs1996624901,2
F--19091457(+) CTGGCG/ATTGCT 1 -- nc-transcript-variant1Minor allele frequency- A:0.01EU 569
rs2007090231,2
C,F--19091464(+) TGCTTA/C/GGCTGC 2 -- nc-transcript-variant1EU 528

HapMap Linkage Disequilibrium report for SNORD3A (19091329 - 19092027 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SNORD3A: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SNORD3A
DNA2.0 Custom Variant and Variant Library Synthesis for SNORD3A

(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: 180710    OMIM disorders: --


Find genes that share disorders with SNORD3A           About GenesLikeMe


Export disorders for SNORD3A 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 SNORD3A gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNORD3A)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human genes encoding U3 snRNA associate with coiled bodies in interphase cells and are clustered on chromosome 17p11.2 in a complex inverted repeat structure. (PubMed id 9365252)1, 3 Gao L....Matera A.G. (Nucleic Acids Res. 1997)
  2. A weak C' box renders U3 snoRNA levels dependent on hU3-55K binding. (PubMed id 21505065)1 Knox A.A....Watkins N.J. (Mol. Cell. Biol. 2011)
  3. PHAX and CRM1 are required sequentially to transport U3 snoRNA to nucleoli. (PubMed id 15574332)1 Boulon S.... Bertrand E. (Mol. Cell 2004)
  4. Assembly and maturation of the U3 snoRNP in the nucleoplasm in a large dynamic multiprotein complex. (PubMed id 15574333)1 Watkins N.J.... Luehrmann R. (Mol. Cell 2004)
  5. In humans all U3 genes map to chromosome 17p12--&gt;p11, but in mouse the U3A and U3B genes are located on different chromosomes. (PubMed id 8440138)1 Mazan S....Bachellerie J.P. (Cytogenet. Cell Genet. 1993)
  6. U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. (PubMed id 2531075)1 Tyc K. and Steitz J.A. (EMBO J. 1989)
  7. Genes for human U3 small nucleolar RNA contain highly conserved flanking sequences. (PubMed id 2719960)1 Yuan Y. and Reddy R. (Biochim. Biophys. Acta 1989)
  8. Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. (PubMed id 6186397)1 Bernstein L.B....Weiner A.M. (Cell 1983)

(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: 780851 HGNC: 33189 Ensembl:ENSG00000263934 euGenes: HUgn780851 ECgene: SNORD3A Kegg: 780851
H-InvDB: SNORD3A

(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 SNORD3A 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 SNORD3A gene:
Search GeneIP for patents involving SNORD3A

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



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