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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SCARNA5 Gene

RNA gene   GIFtS: 17
GCID: GC02P234184

Small Cajal Body-Specific RNA 5
  Search for SCARNA5
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)
About This Section
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   
ORGUL members:    fRNAdb10:FR209117 FR249336 FR144271 FR107633      
H-InvDB12:HIT000383042    
NCBI13:AY077737 AY077737    
NONCODE14:u3476 n3891      
Rfam:RF00478    

Export aliases for SCARNA5 gene to outside databases

Previous GC identifers: GC02P233849 GC02P225985


Summaries
for SCARNA5 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
GeneCards Summary for SCARNA5 Gene: 
SCARNA5 (small Cajal body-specific RNA 5) is an RNA gene, and is affiliated with the scaRNA class.

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.2  NT_005120.16  
Regulatory elements:
   SABiosciences 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

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section
UniProtKB: --

Protein Domains /
Families
for SCARNA5 gene

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
 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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section
Animal Models:
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miRNA
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Pathways & Interactions
for SCARNA5 gene

(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCARNA5

Drugs & Compounds
for SCARNA5 gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Search CenterWatch for drugs/clinical trials and news about 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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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


SOURCE GeneReport for Unigene cluster: Hs.663619
    SABiosciences Custom PCR Arrays for SCARNA5
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In Situ
Assay Products: 
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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)
About This Section
   --

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)
About This Section
  --

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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
SABiosciences Cancer Mutation 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.)
About This Section
SCARNA5 for disorders           About MalaCards
OMIM information: 610767    

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)
About This Section

PubMed articles for SCARNA5 gene, integrated from 9 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. (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. (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. (2012)
  4. Fucosyltransferase 2 (FUT2) non-secretor status is as sociated with Crohn's disease. (PubMed id 20570966)1 McGovern D.P....Rotter J.I. (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. (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. (2007)
  7. A common sequence motif determines the Cajal body-spec ific localization of box H/ACA scaRNAs. (PubMed id 12912925)1 Richard P....Kiss T. (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. (2002)
  9. (PubMed id 2431280)10 
  10. (PubMed id 15103394)10 

External Searches for SCARNA5 gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 677775 HGNC: 32561 Ensembl:ENSG00000252010 euGenes: HUgn677775 ECgene: SCARNA5
H-InvDB: SCARNA5

Other Databases showing SCARNA5 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing SCARNA5 gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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
for SCARNA5 gene

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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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