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SCARNA5 Gene

RNA gene   GIFtS: 19
GCID: GC02P234184

Small Cajal Body-Specific RNA 5
  See related disease
at
MalaCards
 

Aliases
for SCARNA5 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): scaRNA

Quality score for this RNA gene is 5

Aliases
Small Cajal Body-Specific RNA 51 2
U872

External Ids:    HGNC: 325611   Entrez Gene: 6777752   Ensembl: ENSG000002520107   OMIM: 6156405   
ORGUL members:    fRNAdb10:FR209117 FR249336 FR144271 FR107633      
H-InvDB12:HIT000383042    
NCBI13:AY077737 AY077737    
NONCODE14:u3476    
Rfam:RF00478    

Export aliases for SCARNA5 gene to outside databases

Previous GC identifers: GC02P233849 GC02P225985


Summaries
for SCARNA5 gene

(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 SCARNA5 Gene:
SCARNA5 (small Cajal body-specific RNA 5) is an RNA gene, and is affiliated with the scaRNA class. Diseases associated with SCARNA5 include crohn's disease.

fRNAdb sequence ontology for SCARNA5:
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.

View fRNAdb secondary structures for SCARNA5

Genomic Views
for SCARNA5 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_000002.12  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCARNA5 gene promoter:
         NF-YB   CBF-B   CBF-A   NF-YA   CP1C   CP1A   NF-Y   CBF-C   CBF(2)   GATA-1   
         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 SCARNA5


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

Entrez Gene cytogenetic band: 2q37.1   Ensembl cytogenetic band:  2q37.1   HGNC cytogenetic band: 2q37.1

SCARNA5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCARNA5 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P234184:  view genomic region     (about GC identifiers)

Start:
 234,184,372 bp from pter      End:
 234,184,649 bp from pter
Size:
 278 bases      Orientation:
 plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SCARNA5

Proteins
for SCARNA5 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 SCARNA5 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:
SCARNA: ncRNAs / Small nucleolar RNAs : Small cajal body-specific

  --

Function
for SCARNA5 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 SCARNA5 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 SCARNA5 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 SCARNA5

Drugs & Compounds
for SCARNA5 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 SCARNA5



Transcripts
for SCARNA5 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:


Unigene Cluster for SCARNA5:

Small Cajal body-specific RNA 5
Hs.663619  [show with all ESTs]
Unigene Representative Sequence: DW427280
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000516201(snoRNA)
miRNA
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Additional mRNA sequence: AY077737.1 

1 DOTS entry:

DT.40251215 

GeneLoc Exon Structure


Expression
for SCARNA5 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 SCARNA5:H-invDB

SCARNA5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SCARNA5 Expression
About this image

SCARNA5 Protein expression data from MOPED1, PaxDb2 and MaxQB3:  --

SOURCE GeneReport for Unigene cluster: Hs.663619
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In Situ
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Orthologs
for SCARNA5 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 SCARNA5 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
chicken
(Gallus gallus)		 Aves SCARNA66
 Small Cajal body specific RNA 6
 55(a)
 1 → many
 9(697936-698207) ENSGALG00000025706
lizard
(Anolis carolinensis)		 Reptilia SCARNA66
 Small Cajal body specific RNA 6
 58(a)
 1 → many
 3(35942651-35942930) ENSACAG00000021910
zebrafish
(Danio rerio)		 Actinopterygii SCARNA66
 Small Cajal body specific RNA 6
 52(a)
 many ↔ many
 15(44821387-44821666) ENSDARG00000083760
        Species with no ortholog for SCARNA5

ENSEMBL Gene Tree for SCARNA5 (if available)
TreeFam Gene Tree for SCARNA5 (if available)

Paralogs
for SCARNA5 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Genomic Variants
for SCARNA5 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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Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SCARNA5
DNA2.0 Custom Variant and Variant Library Synthesis for SCARNA5

Disorders / Diseases
for SCARNA5 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: 615640OMIM information: 610767    
1 disease for SCARNA5:    
About MalaCards
crohn's disease


SCARNA5 for disorders           About GeneDecksing


Export disorders for SCARNA5 gene to outside databases

Publications
for SCARNA5 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 SCARNA5 gene, integrated from 10 sources (see all 14):
(articles sorted by number of sources associating them with SCARNA5)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. (PubMed id 12032087)1, 3 Darzacq X....Kiss T. (EMBO J. 2002)
  2. A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300. (PubMed id 22936669)1 JuliA A....Marsal S. (Gut 2013)
  3. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PubMed id 22412388)1 Kenny E.E....Peter I. (PLoS Genet. 2012)
  4. Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. (PubMed id 20570966)1 McGovern D.P....Rotter J.I. (Hum. Mol. Genet. 2010)
  5. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. (PubMed id 21102463)1 Franke A....Parkes M. (Nat. Genet. 2010)
  6. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. (PubMed id 17435756)1 Rioux J.D....Brant S.R. (Nat. Genet. 2007)
  7. A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs. (PubMed id 12912925)1 Richard P....Kiss T. (EMBO J. 2003)
  8. U87 RNA, a novel C/D box small nucleolar RNA from mammalian cells. (PubMed id 12119114)1 Gogolevskaya I.K....Kramerov D.A. (Gene 2002)
  9. (PubMed id 2431280)10 
  10. (PubMed id 15103394)10 

External Searches for SCARNA5 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 SCARNA5 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 677775 HGNC: 32561 Ensembl:ENSG00000252010 euGenes: HUgn677775 ECgene: SCARNA5
H-InvDB: SCARNA5

Other Databases showing SCARNA5 gene

(According to HUGE)
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Specialized Databases showing SCARNA5 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 SCARNA5 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SCARNA5 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 SCARNA5 gene:
Search GeneIP for patents involving SCARNA5

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



Products
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