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

RNU5A-1 Gene

RNA gene   GIFtS: 16
GCID: GC15P065590

RNA, U5A small nuclear 1

(Previous names: RNA, U5C small nuclear, RNA, U5A small nuclear )
(Previous symbols: RNU5C, RNU5A)
  Search for RNU5A-1
in
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Biological research products
for RNU5A-1    

Aliases
for RNU5A-1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): snRNA

Quality score for this RNA gene is 5

Aliases
RNA, U5A Small Nuclear 11 2     U5B11 2
RNU5A1 2 5     RNU52 5
RNU5C1 2     RNA, U5A Small Nuclear1
U5A1 2     RNA, U5C Small Nuclear1

External Ids:    HGNC: 102111   Entrez Gene: 268312   Ensembl: ENSG000001995687   OMIM: 1806915   
ORGUL members:    fRNAdb10:FR020510 FR029924 FR134545 FR221523 FR376319      
NCBI:X01691 K03167 X01691 K03167    
NONCODE:u4695 u3881    
Rfam:RF00020    

Export aliases for RNU5A-1 gene to outside databases


Summaries
for RNU5A-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 RNU5A-1 - the ORGUL cluster for this gene includes several descriptions:
snRNA - A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
U5_snRNA - U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.

View fRNAdb secondary structures for RNU5A-1

Genomic Views
for RNU5A-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:
   Search SABiosciences Regulatory transcription factor binding sites for RNU5A-1
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RNU5A-1


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

Entrez Gene cytogenetic band: 15q22.31   Ensembl cytogenetic band:  15q22.31   HGNC cytogenetic band: 15q22.31

RNU5A-1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU5A-1 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P065590:  view genomic region     (about GC identifiers)

Start:
 65,588,389 bp from pter      End:
 65,588,505 bp from pter
Size:
 117 bases      Orientation:
 plus strand

Proteins
for RNU5A-1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, 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,
Biochemical Assays by 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: --

Protein Domains /
Families
for RNU5A-1 gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for RNU5A-1 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, 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
miRNA
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Inhib. RNA
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Gene Editing
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In Situ Assay
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Pathways & Interactions
for RNU5A-1 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 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, 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 RNU5A-1

Drugs & Compounds
for RNU5A-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 Small Molecules at EMD Millipore
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Browse Tocris compounds for RNU5A-1
Search CenterWatch for drugs/clinical trials and news about RNU5A-1 

Transcripts
for RNU5A-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 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, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
 4 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000362698(snRNA)

miRNA
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Inhib. RNA
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Clone
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Primer
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GeneLoc Exon Structure


Expression
for RNU5A-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 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 RNU5A-1:none

RNU5A-1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image    SABiosciences Custom PCR Arrays for RNU5A-1
Primer
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In Situ
Assay Products: 
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Orthologs
for RNU5A-1 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 RNU5A-1 (if available)
TreeFam Gene Tree for RNU5A-1 (if available) 

Paralogs
for RNU5A-1 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for RNU5A-1 gene
RNU5E-3P2  RNU5E-7P2  RNU5B-6P2  RNU5E-4P2  RNU5F-6P2  RNU5A-5P2  RNU5B-4P2  RNU5E-6P2  
RNU5E-5P2  RNU5A-2P2  RNU5E-12  RNU5E-8P2  RNU5A-3P2  RNU5D-2P2  RNU5A-6P2  RNU5F-4P2  
RNU5E-2P2  RNU5B-3P2  RNU5D-12  RNU5F-7P2  RNU5A-7P2  RNU5A-8P2  RNU5F-2P2  RNU5B-2P2  
RNU5F-8P2  RNU5E-10P2  RNU5B-12  RNU5A-4P2  RNU5F-12  RNU5E-9P2  RNU5F-3P2  

RNU5A-1 for paralogs           About GeneDecksing



Genomic Variants
for RNU5A-1 gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 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

10/113 NCBI SNPs in RNU5A-1 are shown (see all 113)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 15 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs1895308311,2
--65586390(+) AAATCA/GTAGAT 1 -- us2k10--------
rs1829359381,2
--65586431(+) TAACTG/TAAATA 1 -- us2k10--------
rs1507485971,2
--65586437(+) AAATAC/TAAAAA 1 -- us2k10--------
rs1393427221,2
--65586525(+) CAAAAC/TGTGGT 1 -- us2k10--------
rs288957091,2
--65586627(+) GAGGCC/TGAAGC 1 -- us2k10--------
rs1477343501,2
--65586733(+) GCGCAC/TGCCTG 1 -- us2k10--------
rs1410603641,2
--65586755(+) ACTCAC/GGAGAT 1 -- us2k10--------
rs342042891,2
C,F,--65586758(+) CAGGAG/AATTGA 1 -- us2k12Minor allele frequency- A:0.50NA 4
rs6805241,2
C,F,H,--65586760(+) GGAGAT/CTGAGG 1 -- us2k14Minor allele frequency- C:0.25NA WA 8
rs1489509321,2
--65586821(+) GCGCCA/GTTGCA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for RNU5A-1 (65588389 - 65588505 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for RNU5A-1: --

SABiosciences Cancer Mutation PCR Assays
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Disorders / Diseases
for RNU5A-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.)
About This Section
RNU5A-1 for disorders           About MalaCards

RNU5A-1 for disorders           About GeneDecksing

OMIM gene information: 180691    OMIM disorders: --


Export disorders for RNU5A-1 gene to outside databases

Publications
for RNU5A-1 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 RNU5A-1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with RNU5A-1)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Three novel functional variants of human U5 small nuclear RNA. (PubMed id 1310151)1, 3 Sontheimer E.J. and Steitz J.A. (1992)
  2. High evolutionary conservation of the secondary structure and of certain nucleotide sequences of U5 RNA. (PubMed id 6200827)1 Branlant C....Pousada C. (1983)
  3. The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes. (PubMed id 6164980)1 Krol A....Branlant C. (1981)
  4. (PubMed id 8797828)10 
  5. (PubMed id 9016512)10 
  6. (PubMed id 2977088)10 
  7. (PubMed id 15608158)10 
  8. (PubMed id 8702566)10 
  9. (PubMed id 2339054)10 

External Searches for RNU5A-1 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 RNU5A-1 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 26831 HGNC: 10211 Ensembl:ENSG00000199568 euGenes: HUgn26831 ECgene: RNU5A-1
H-InvDB: RNU5A-1

Other Databases showing RNU5A-1 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing RNU5A-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
NameDescription
PharmGKB entry for RNU5A-1 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for RNU5A-1 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for RNU5A-1 gene:
Search GeneIP for patents involving RNU5A-1

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



Products
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