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

RNU11 Gene

RNA gene   GIFtS: 18
GCID: GC01P028975

RNA, U11 small nuclear
  Search for RNU11
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 Human Malady Compendium 
Biological research products
for RNU11    

Aliases
for RNU11 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 5.4

Aliases
RNA, U11 Small Nuclear1 2
U111 2

External Ids:    HGNC: 101081   Entrez Gene: 268242   Ensembl: ENSG000002098047   
ORGUL members:    fRNAdb10:FR274140 FR034640 FR185892 FR132540 FR195561      
H-InvDB:HIT000383048    
NCBI:AL840644 X13707 X58716 X13707 J04118 see all 7    
NONCODE:u4796 u3842    
Rfam:RF00548    
RNAdb:RNZ1498 EVF1709    

Export aliases for RNU11 gene to outside databases

Previous GC identifers: GC00U990630 GC01U901037 GC01P028849 GC01P027228


Summaries
for RNU11 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 RNU11 - the ORGUL cluster for this gene includes several descriptions:
U11 spliceosomal RNA - The U11 small nuclear (snRNA), together with U4atac/U6atac, U5, and U12 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
U11_snRNA - U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.

View fRNAdb secondary structures for RNU11

Genomic Views
for RNU11 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
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_004610.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RNU11 gene promoter:
         Pbx1a   Tal-1   MyoD   Lmo2   POU6F1 (c2)   AP-4   CUTL1   E47   GR-alpha   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RNU11


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

Entrez Gene cytogenetic band: 1p35   Ensembl cytogenetic band:  1p35.3   HGNC cytogenetic band: 1p35

RNU11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU11 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P028975:  view genomic region     (about GC identifiers)

Start:
 28,975,112 bp from pter      End:
 28,975,246 bp from pter
Size:
 135 bases      Orientation:
 plus strand
ORGUL member locations:
Legend (see complete legend)

  • FR0195561
  • FR0034640
  • FR0185892
  • FR0274140
  • FR0132540
  • FR0129843
  • FR0341613
  • RF00548
28975111 28975179 28975246 chr1

Proteins
for RNU11 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 RNU11 gene

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

Function
for RNU11 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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In Situ Assay
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Pathways & Interactions
for RNU11 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 RNU11

Drugs & Compounds
for RNU11 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
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for RNU11
Search CenterWatch for drugs/clinical trials and news about RNU11 

Transcripts
for RNU11 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
 5/7 fRNAdb Secondary structures (see all 7):


Unigene Cluster for RNU11:

RNA, U11 small nuclear
Hs.640266
Unigene Representative Sequence: BP873537
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000387069(snRNA)

miRNA
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Inhib. RNA
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Primer
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Additional cDNA sequence: 

J04118.1 NR_004407.1 

GeneLoc Exon Structure


Expression
for RNU11 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 RNU11:H-invDB

RNU11 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
SOURCE GeneReport for Unigene cluster: Hs.640266
    SABiosciences Custom PCR Arrays for RNU11
Primer
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In Situ
Assay Products: 
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Orthologs
for RNU11 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
This gene was present in the common ancestor of human and mouse.

Orthologs for RNU11 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Rnu115 U11 small nuclear RNA   --   4 (65.08 cM) 132270079 


ENSEMBL Gene Tree for RNU11 (if available)
TreeFam Gene Tree for RNU11 (if available) 

Paralogs
for RNU11 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for RNU11 gene
ENSG000002124292  ENSG000002124512  ENSG000002124132  ENSG000002527072  ENSG000002125182  

RNU11 for paralogs           About GeneDecksing



Genomic Variants
for RNU11 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

10/84 NCBI SNPs in RNU11 are shown (see all 84)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 1 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs1864401791,2
--28973312(+) TTCACA/GCCATT 1 -- us2k10--------
rs580695001,2
--28973620(+) GGATTA/GCAGGC 1 -- us2k10--------
rs73681971,2
C,--28973799(+) ATATTG/TTTTTT 1 -- us2k1 tfbs34Minor allele frequency- T:0.17NA EA 244
rs2012488271,2
--28973799(+) ATATT-/GTTTTT 1 -- us2k10--------
rs1917459801,2
--28973930(+) GGGTAC/GCTGGG 1 -- us2k10--------
rs1493447581,2
--28973982(+) TGGGGC/TAGGGA 1 -- us2k10--------
rs1447587391,2
--28973993(+) CGAGGC/TCTCTA 1 -- us2k10--------
rs1454100621,2
--28974241(+) ATTAGC/GCGGGC 1 -- us2k10--------
rs1836592491,2
--28974337(+) GCCGAG/TATCGC 1 -- us2k10--------
rs359866041,2
C--28974386(+) GTCTC-/AAAAAA 1 -- us2k11Minor allele frequency- A:0.00NA 2

HapMap Linkage Disequilibrium report for RNU11 (28975112 - 28975246 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for RNU11: --

SABiosciences Cancer Mutation PCR Assays
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Disorders / Diseases
for RNU11 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
RNU11 for disorders           About MalaCards

RNU11 for disorders           About GeneDecksing

OMIM gene information: 115665 116600 121800 155600 211420 600975 605225 605606 606788 606852 606928 607317 607671 608446 608543 608553 608995    

Export disorders for RNU11 gene to outside databases

Publications
for RNU11 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 RNU11 gene, integrated from 9 sources (see all 13):
(articles sorted by number of sources associating them with RNU11)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Additional low-abundance human small nuclear ribonucleoproteins: U11, U12, etc. (PubMed id 2973606)1, 3 Montzka K.A. and Steitz J.A. (1988)
  2. An ancient mechanism for splicing control: U11 snRNP as an activator of alternative splicing. (PubMed id 20347424)1 Verbeeren J....Frilander M.J. (2010)
  3. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PubMed id 15146077)1 Will C.L.... Luehrmann R. (2004)
  4. (PubMed id 16273071)10 
  5. (PubMed id 15608161)10 
  6. (PubMed id 15210936)10 
  7. (PubMed id 8797828)10 
  8. (PubMed id 9016512)10 
  9. (PubMed id 2977088)10 
  10. (PubMed id 15608158)10 

External Searches for RNU11 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 RNU11 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 26824 HGNC: 10108 Ensembl:ENSG00000209804 euGenes: HUgn26824 ECgene: RNU11
H-InvDB: RNU11

Other Databases showing RNU11 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing RNU11 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 RNU11 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for RNU11 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for RNU11 gene:
Search GeneIP for patents involving RNU11

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



Products
for RNU11 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),
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