small Cajal body-specific RNA 5
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Aliasesfor SCARNA5 gene
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc ,
7 Ensembl ,
8 DME ,
9 miRBase ,
and/or 10 fRNAdb )About This Section Subcategory (RNA class): scaRNAQuality score for this RNA gene is 5 Aliases Small Cajal Body-Specific RNA 5 1 2 U871 2
External Ids: HGNC: 32561 1 Entrez Gene: 677775 2 Ensembl: ENSG00000252010 7 Export aliases for SCARNA5 gene to outside databases Previous GC identifers: GC02P233849 GC02P225985
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Summariesfor SCARNA5 gene (According to Entrez Gene ,
Tocris Bioscience ,
Wikipedia's
Gene Wiki ,
PharmGKB ,UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
About This Section 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
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Genomic Viewsfor SCARNA5 gene
(According to
GeneLoc and/or
HGNC , and/or
Entrez Gene (NCBI build 37) ,miRBase ,UCSC (hg19) and
Ensembl (release 69) ,
Regulatory elements and Epigenetics data according to
QIAGEN ,
SABiosciences , and/or
SwitchGear Genomics )About This Section RefSeq DNA sequence: NC_000002.11 NC_018913.1 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 Search SABiosciences Chromatin IP Primers for SCARNA5 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
Entrez Gene Ensembl 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)
n3891 FR0144271 FR0107633
234184371 234184510 234184649 chr2
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Proteinsfor SCARNA5 gene
(According to
1 UniProtKB ,
HORDE ,
neXtProt ,
Ensembl ,
and/or Reactome ,
Modification sites according to 2 PhosphoSitePlus ,
Specific Peptides from DME ,
Protein expression images according to data from SPIRE MOPED and PaxDb ,
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
Uscn ,
EMD Millipore ,
R&D Systems ,
OriGene ,
GenScript ,
Cell Signaling Technology ,
Enzo Life Sciences , and/or
Uscn ,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene ,
Antibodies by
EMD Millipore ,
R&D Systems ,
GenScript ,
Cell Signaling Technology ,
OriGene ,
Novus Biologicals ,
Thermo Fisher Scientific ,
Abcam , and/or
Uscn )
About This Section UniProtKB: --
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Protein
Domains /for SCARNA5 gene (According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
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Functionfor SCARNA5 gene
(According to 1 UniProtKB ,
Genatlas ,
LifeMap Discovery™ ,
IUBMB , and/or
2 DME ,
Human phenotypes from GenomeRNAi ,
Animal models from MGI Mar 06 2013,
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 ,
Clones from EMD Millipore ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
Sino Biological ,
DNA2.0 ,
and Vector BioLabs ,
Cell Lines from GenScript ,
LifeMap BioReagents ,
In Situ Hybridization Assays from Advanced Cell Diagnostics ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene .)
About This Section
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Pathways & Interactionsfor SCARNA5 gene
(Pathways according to
EMD Millipore ,
R&D Systems ,
Cell Signaling Technology ,
KEGG ,
PharmGKB ,
BioSystems ,
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 1 UniProtKB ,
2 MINT ,
3 I2D , and/or
4 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene) .
About This Section Interactions: Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCARNA5
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Drugs & Compoundsfor SCARNA5 gene (Chemical Compounds according to UniProtKB , Enzo Life Sciences ,
EMD Millipore , Tocris Bioscience
HMDB ,
BitterDB , and/or
Novoseek , and Drugs according to
DrugBank ,
Enzo Life Sciences , and/or
PharmGKB , with drugs/clinical trials/news
search links to CenterWatch )
About This Section Browse Tocris compounds for SCARNA5 SCARNA5
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Transcriptsfor SCARNA5 gene (Secondary structures according to
fRNAdb ,Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank , Entrez Gene ,
DOTS (version 10), and/or
AceView ,
transcript ids from Ensembl
with links to UCSC , GeneLoc ,
alternative splicing isoforms according to ASD and/or
ECgene ,EMD Millipore ,
OriGene ,
QIAGEN ,
shRNA from
OriGene ,
microRNA from QIAGEN ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
DNA2.0 ,
Vector BioLabs ,
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) Additional cDNA sequence: AY077737.1
1 DOTS entry : DT.40251215 GeneLoc Exon Structure
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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 ,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 image BioGPS CGAP TAG: --
About this image SOURCE GeneReport for Unigene cluster: Hs.663619 SABiosciences Custom PCR Arrays for SCARNA5 Primer Browse OriGene genome-wide validated SYBR primer pairs Browse OriGene validated miRNA SYBR primer pairs Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat SCARNA5 Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCARNA5 QIAGEN QuantiFast Probe-based Assays in human mouse rat
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Orthologsfor SCARNA5 gene
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
,
5 MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase ,
and/or
6 Ensembl 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)
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Paralogsfor SCARNA5 gene (Paralogs according to
1 HomoloGene ,2 Ensembl , and 3 SIMAP , Pseudogenes according to 4 Pseudogene.org Build 68)About This Section
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Genomic Variantsfor SCARNA5 gene (SNPs/Variants according to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE ,
UniProtKB , 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
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Disorders
/ Diseasesfor SCARNA5 gene
(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 .)
About This Section About MalaCards About GeneDecksing OMIM gene information: 610767 Export disorders for SCARNA5 gene to outside databases
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Publicationsfor SCARNA5 gene (in
PubMed .
Associations of this gene to articles via
1 Entrez Gene ,
2 UniProtKB/Swiss-Prot ,
3 HGNC ,
4 GAD ,
5 PharmGKB ,
6 HMDB ,
7 DrugBank ,
8 UniProtKB/TrEMBL ,
9 Novoseek , and/or
10 fRNAdb )
About This Section PubMed articles for SCARNA5 gene integrated from 9 sources :(articles sorted by number of sources associating them with SCARNA5) Utopia : connect your pdf to the dynamic
Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs. (PubMed id 12032087) 1 , 3(2002) A common sequence motif determines the Cajal body-spec ific localization of box H/ACA scaRNAs. (PubMed id 12912925) 1 (2003) U87 RNA, a novel C/D box small nucleolar RNA from mammalian cells. (PubMed id 12119114) 1 (2002) (PubMed id 11387227) 10 (PubMed id 16381836) 10 (PubMed id 2431280) 10 (PubMed id 15103394) 10 (PubMed id 18089548) 10 (PubMed id 15608158) 10
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External Searches for SCARNA5 gene
(in PubMed ,
OMIM , and NCBI Bookshelf ) About This Section
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Genome Databases showing SCARNA5 gene
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
Kegg ,
and/or
H-InvDB )
About This Section
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Other Databases showing SCARNA5 gene
(According to HUGE )
About This Section --
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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
Name Description PharmGKB entry for SCARNA5 Pharmacogenomics, SNPs, Pathways
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About This Section Patent Information for SCARNA5 gene: SCARNA5 GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Productsfor SCARNA5 gene (Antibodies, recombinant proteins, and assays from EMD Millipore , R&D Systems , OriGene , QIAGEN , GenScript , Cell Signaling Technology , SABiosciences , Novus Biologicals , Sino Biological , Enzo Life Sciences , Abcam , ProSpec , Uscn , Thermo Fisher Scientific , Gene Editing from DNA2.0 , Clones from EMD Millipore , OriGene , GenScript , Sino Biological , DNA2.0 , SwitchGear Genomics , Vector BioLabs , Cell lines from GenScript and LifeMap BioReagents , PCR Arrays from SABiosciences , Drugs and/or compounds from EMD Millipore , Tocris Bioscience , and/or
Enzo Life Sciences ), In Situ Hybridization Assays from Advanced Cell Diagnostics About This Section
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SCARNA5 Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SCARNA5 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCARNA5 QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human mouse rat QIAGEN QuantiFast Probe-based Assays in human mouse rat Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCARNA5
Search Tocris compounds for SCARNA5
Search ThermoFisher Antibodies for SCARNA5
Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SCARNA5
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