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SNORA5C Gene

RNA gene   GIFtS: 18
GCID: GC07M045144

Small Nucleolar RNA, H/ACA Box 5C
  Search for SNORA5C
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Aliases
for SNORA5C 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 6

Aliases
Small Nucleolar RNA, H/ACA Box 5C1 2
ACA5c2

External Ids:    HGNC: 325901   Entrez Gene: 6777962   Ensembl: ENSG000002017727   OMIM: 6113355   
ORGUL members:    fRNAdb10:FR332044 FR407601 FR407601 FR332044      
H-InvDB12:HIT000383041    
NCBI13:AM055746 AC013416    
Rfam:RF00392    
RNAdb15:SNO1535    

Export aliases for SNORA5C gene to outside databases

Previous GC identifers: GC07M045111 GC07M045028


Summaries
for SNORA5C 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 SNORA5C Gene:
Small nucleolar RNAs (snoRNAs) are small noncoding RNAs involved in RNA processing. Box H/ACA snoRNAs, such as
SNORA5C, 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 SNORA5C Gene:
SNORA5C (small nucleolar RNA, H/ACA box 5C) is an RNA gene, and is affiliated with the snoRNA class.



fRNAdb sequence ontologies for SNORA5C - the ORGUL cluster for this gene includes several descriptions:
Small nucleolar RNA SNORA5 - ACA5 is a member of the H/ACA class of snoRNA that guide the sites of modification of uridines to pseudouridines [1].
Small nucleolar RNA SNORA5 - ACA5 is a member of the H/ACA class of snoRNA that guide the sites of modification of uridines to pseudouridines [1].
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
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 SNORA5C

Genomic Views
for SNORA5C 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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TryGeneCards Plus		 Regulatory elements:
   Regulatory transcription factor binding sites in the SNORA5C gene promoter:
         E2F-3a   E2F-4   E2F-5   AML1a   XBP-1   E2F-2   E2F   E2F-1   Zic1   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORA5C


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

Entrez Gene cytogenetic band: 7p13   Ensembl cytogenetic band:  7p13   HGNC cytogenetic band: 7p13

SNORA5C Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORA5C gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M045144:  view genomic region     (about GC identifiers)

Start:
 45,144,505 bp from pter      End:
 45,144,641 bp from pter
Size:
 137 bases      Orientation:
 minus strand

1 alternative location:
Chr7-,CRA_TCAG 45,183,675-45,183,811     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNORA5C

Proteins
for SNORA5C 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 SNORA5C 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 SNORA5C 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 SNORA5C 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 SNORA5C 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 SNORA5C

Drugs & Compounds
for SNORA5C 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 SNORA5C



Transcripts
for SNORA5C 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		 2 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000364902(snoRNA)
miRNA
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GeneLoc Exon Structure


Expression
for SNORA5C 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 SNORA5C:H-invDB

SNORA5C expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGCCCTGGGT
SNORA5C Expression
About this image

SNORA5C Protein expression data from MOPED1, PaxDb2 and MaxQB3:  --
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In Situ
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Orthologs
for SNORA5C 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 SNORA5C gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Snora5c5 small nucleolar RNA, H/ACA box 5C   --   11 (4.60 cM) 6620319 
chicken
(Gallus gallus)		 Aves SNORA56
 Small nucleolar RNA SNORA5
 64(a)
 many ↔ many
 2(3998061-3998196) ENSGALG00000026888
lizard
(Anolis carolinensis)		 Reptilia SNORA56
 Small nucleolar RNA SNORA5
 62(a)
 many ↔ many
 GL343515.1(61876-62009) ENSACAG00000019225
zebrafish
(Danio rerio)		 Actinopterygii SNORA56
SNORA56
(see all 4)		 Small nucleolar RNA SNORA5
(see all 4)		 56(a)
55(a)
(see all 4)		 many ↔ many
many ↔ many
(see all 4)		 19(12753171-12753306) ENSDARG00000090466
19(12758862-12758997) ENSDARG00000091065


ENSEMBL Gene Tree for SNORA5C (if available)
TreeFam Gene Tree for SNORA5C (if available)

Paralogs
for SNORA5C gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Genomic Variants
for SNORA5C 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) 1 variation for SNORA5C:    About this table    
Variant IDTypeSubtypePubMed ID
nsv888001CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
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Disorders / Diseases
for SNORA5C 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: 611335OMIM information: 611325    

SNORA5C for disorders           About GeneDecksing


Export disorders for SNORA5C gene to outside databases

Publications
for SNORA5C 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 SNORA5C gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNORA5C)		    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. A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes. (PubMed id 16361266)1 Gu A.D....Qu L.H. (Nucleic Acids Res. 2005)
  5. (PubMed id 18089548)10 
  6. (PubMed id 15103394)10 
  7. (PubMed id 11387227)10 
  8. (PubMed id 3342024)10 
  9. (PubMed id 15608161)10 

External Searches for SNORA5C 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 SNORA5C gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 677796 HGNC: 32590 Ensembl:ENSG00000201772 euGenes: HUgn677796 ECgene: SNORA5C
H-InvDB: SNORA5C

Other Databases showing SNORA5C gene

(According to HUGE)
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Specialized Databases showing SNORA5C 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 SNORA5C Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SNORA5C 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 SNORA5C gene:
Search GeneIP for patents involving SNORA5C

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



Products
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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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