SNORD3B-1 Gene
RNA gene GIFtS : 15
GCID: GC17 P018965
small nucleolar RNA, C/D box 3B-1 (Previous names: RNA, U3A1 small nucleolar, RNA, U3A1 small nucleolar ) (Previous symbol: RNU3A1 )
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Aliasesfor SNORD3B-1 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): snoRNAQuality score for this RNA gene is 6 Aliases Small Nucleolar RNA, C/D Box 3B-1 1 2 RNU3A11 2 U3a1 2 U3b11 2 U3b21 2 RNA, U3A1 Small Nucleolar, RNA, U3A1 Small Nucleolar1
External Ids: HGNC: 10168 1 Entrez Gene: 26851 2 Ensembl: ENSG00000200229 7 Export aliases for SNORD3B-1 gene to outside databases Previous GC identifers: GC17M018909 GC17U900934 GC17P018907
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Summariesfor SNORD3B-1 gene (According to Entrez Gene ,
Tocris Bioscience ,
Wikipedia's
Gene Wiki ,
PharmGKB ,
UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
About This Section fRNAdb sequence ontologies for SNORD3B-1 - the ORGUL cluster for this gene includes several descriptions: Small nucleolar RNA U3 - Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localisation, stability and hyper-methylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. U3_snoRNA - U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.View fRNAdb secondary structures for SNORD3B-1
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Genomic Viewsfor SNORD3B-1 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 69) ,
Regulatory elements and Epigenetics data according to
QIAGEN ,
SABiosciences , and/or
SwitchGear Genomics )About This Section Regulatory elements: SABiosciences Regulatory transcription factor binding sites in the SNORD3B-1 gene promoter: AREB6 SRY p53 HTF Sox9 GATA-1 Other transcription factors Search SABiosciences Chromatin IP Primers for SNORD3B-1 Epigenetics: QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNORD3B-1
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 SNORD3B-1 Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different) GeneLoc information about chromosome 17 GeneLoc Exon Structure
GeneLoc location for GC17P018965: view genomic region
(about GC identifiers )
Start:
18,965,225 bp from pter
End:
18,965,441 bp from pter
Size:
217 bases
Orientation:
plus strand
ORGUL member locations:Legend (see complete legend)
FR0040496
FR0400495
FR0023212
FR0406489
FR0407136
FR0407050
18965224 18965333 18965441 chr17
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Proteinsfor SNORD3B-1 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
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Biochemical Assays by
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GenScript ,
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Enzo Life Sciences , and/or
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Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene ,
Antibodies by
EMD Millipore ,
R&D Systems ,
GenScript ,
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OriGene ,
Novus Biologicals ,
Thermo Fisher Scientific ,
Abcam , and/or
Uscn )
About This Section UniProtKB: --
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Protein
Domains / Familiesfor SNORD3B-1 gene (According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
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Functionfor SNORD3B-1 gene
(According to 1 UniProtKB ,
Genatlas ,
LifeMap Discovery™ ,
IUBMB , and/or
2 DME ,
Human phenotypes from GenomeRNAi ,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences ,
miRNA Gene Targets from miRTarBase
shRNA from
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and Vector BioLabs ,
Cell Lines from GenScript ,
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Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene .)
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Pathways & Interactionsfor SNORD3B-1 gene
(Pathways according to
EMD Millipore ,
R&D Systems ,
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BioSystems ,
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Tocris Bioscience ,
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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 SNORD3B-1
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Drugs & Compoundsfor SNORD3B-1 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 SNORD3B-1 Search CenterWatch for drugs/clinical trials and news about SNORD3B-1
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Transcriptsfor SNORD3B-1 gene (Secondary structures according to
fRNAdb ,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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
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RNAi Products from
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siRNAs from
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Tagged/untagged cDNA clones from
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)About This Section 5/6 fRNAdb Secondary structures (see all 6 ): 1 Ensembl transcript including schematic representation, and UCSC links where relevant : ENST00000363359(snoRNA) GeneLoc Exon Structure
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Expression for SNORD3B-1 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
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PCR Arrays from
SABiosciences ,
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In Situ Hybridization Assays from Advanced Cell Diagnostics )
About This Section Expression evidence for SNORD3B-1:none
SNORD3B-1 expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this image BioGPS CGAP TAG: --
About this image SABiosciences Custom PCR Arrays for SNORD3B-1 Primer Products: 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 SNORD3B-1 Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SNORD3B-1 QIAGEN QuantiFast Probe-based Assays in human , mouse , rat SNORD3B-1
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Orthologsfor SNORD3B-1 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 SNORD3B-1 (if available)TreeFam Gene Tree for SNORD3B-1 (if available)
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Paralogsfor SNORD3B-1 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 SNORD3B-1 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
Genomic Data Transcription Related Data Allele Frequencies SNP ID Valid Clinical significance Chr 17 pos Sequence # AA Chg Type More # Allele freq Pop Total sample More
HapMap Linkage Disequilibrium report for SNORD3B-1 (18965225 - 18965441 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions) Database of Genomic Variants (DGV) variations for SNORD3B-1: --
SABiosciences Cancer Mutation PCR Assays
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Disorders
/ Diseasesfor SNORD3B-1 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 .)
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Publicationsfor SNORD3B-1 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 SNORD3B-1 gene integrated from 9 sources : (articles sorted by number of sources associating them with SNORD3B-1) Utopia : connect your pdf to the dynamic world of online information
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. (1997) 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. (1989) (PubMed id 9016512) 10 (PubMed id 10567566) 10 (PubMed id 16381836) 10 (PubMed id 15608161) 10
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External Searches for SNORD3B-1 gene
(in PubMed ,
OMIM , and NCBI Bookshelf ) About This Section
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Genome Databases showing SNORD3B-1 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 SNORD3B-1 gene
(According to HUGE )
About This Section --
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Specialized Databases showing SNORD3B-1 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 SNORD3B-1 Pharmacogenomics, SNPs, Pathways
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About This Section Patent Information for SNORD3B-1 gene: Search GeneIP for patents involving SNORD3B-1 GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Productsfor SNORD3B-1 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 SNORD3B-1 Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SNORD3B-1 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNORD3B-1 QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human , mouse , rat SNORD3B-1 QIAGEN QuantiFast Probe-based Assays in human , mouse , rat SNORD3B-1 Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SNORD3B-1
Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SNORD3B-1
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