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RNU11 Gene

RNA gene   GIFtS: 17
GCID: GC01P028975

RNA, U11 Small Nuclear

  Search for RNU11
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): snRNA

Quality score for this RNA gene is 5.4

Aliases
RNA, U11 Small Nuclear1 2
RNU11-12
U112

External Ids:    HGNC: 101081   Entrez Gene: 268242   Ensembl: ENSG000002701037   
ORGUL members:    fRNAdb10:FR274140 FR034640 FR185892 FR132540 FR195561      
H-InvDB12:HIT000383048    
NCBI13:X13707 J04118 X58716 AL840644 X13707 see all 7    
NONCODE14:u4796 u3842    
Rfam:RF00548    
RNAdb15:RNZ1498 EVF1709    

Export aliases for RNU11 gene to outside databases

Previous GC identifers: GC00U990630 GC01U901037 GC01P028849 GC01P027228


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RNU11 Gene:
RNU11 (RNA, U11 small nuclear) is an RNA gene, and is affiliated with the snRNA class.

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.
snRNA - A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
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.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for RNU11

(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   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:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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)

ORGUL Member Locations for RNU11

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
snRNA: ncRNAs / Small nuclear RNAs

  --

(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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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Interactions:

    Search GeneGlobe Interaction Network for RNU11

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for RNU11



(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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5/7 fRNAdb Secondary structures (see all 7):


Unigene Cluster for RNU11:

RNA, U11 small nuclear
Hs.640266
Unigene Representative Sequence: BP873537
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602813(lincRNA) ENST00000387069(lincRNA)(uc009vtj.1)
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Additional mRNA sequence: 

J04118.1 NR_004407.1 

GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for RNU11:H-invDB

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

RNU11 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.640266
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(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)
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This gene was present in the common ancestor of chordates.

Orthologs for RNU11 gene from Selected species (see all 10)    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 
chicken
(Gallus gallus)
Aves U116
U116
U11 spliceosomal RNA
74(a)
62(a)
1 ↔ many
1 ↔ many
23(2216932-2217058) ENSGALG00000024628
4(20313045-20313174) ENSGALG00000025212
lizard
(Anolis carolinensis)
Reptilia U116
U11 spliceosomal RNA
74(a)
1 ↔ 1
GL344007.1(66441-66580)
zebrafish
(Danio rerio)
Actinopterygii U116
U11 spliceosomal RNA
68(a)
many ↔ many
19(15493860-15493995) ENSDARG00000080410


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for RNU11 (see all 139)    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 -- us2k14Minor 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
C--28974241(+) ATTAGC/GCGGGC 1 -- us2k10--------
rs1836592491,2
C--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
      Database of Genomic Variants (DGV) variations for RNU11: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RNU11
DNA2.0 Custom Variant and Variant Library Synthesis for RNU11

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

RNU11 for disorders           About GeneDecksing


Export disorders for RNU11 gene to outside databases

(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)
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PubMed articles for RNU11 gene, integrated from 10 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. (Proc. Natl. Acad. Sci. U.S.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. (Mol. Cell 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. (RNA 2004)
  4. (PubMed id 8797828)10 
  5. (PubMed id 9016512)10 
  6. (PubMed id 2977088)10 
  7. (PubMed id 15608158)10 
  8. (PubMed id 15210936)10 
  9. (PubMed id 16273071)10 
  10. (PubMed id 15608161)10 

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 26824 HGNC: 10108 Ensembl:ENSG00000270103 euGenes: HUgn26824 ECgene: RNU11
H-InvDB: RNU11

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RNU11 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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