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RNU6-66P Gene

RNA gene   GIFtS: 14
GCID: GC13M073690

RNA, U6 Small Nuclear 66, Pseudogene

(Previous names: RNA, U6 small nuclear 66)
(Previous symbol: RNU6-66)
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(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

Aliases
RNA, U6 Small Nuclear 66, Pseudogene1 2
RNU6-661 2
RNA, U6 Small Nuclear 661

External Ids:    HGNC: 425561   Entrez Gene: 1008737702   Ensembl: ENSG000002002677   
ORGUL members:    fRNAdb10:FR011264 FR011264      
NCBI13:AL354720    
Rfam:RF00026    

Export aliases for RNU6-66P gene to outside databases


(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 RNU6-66P Gene:
RNU6-66P (RNA, U6 small nuclear 66, pseudogene) is an RNA gene, and is affiliated with the snRNA class.

fRNAdb sequence ontologies for RNU6-66P - the ORGUL cluster for this gene includes several descriptions:
U6 spliceosomal RNA - U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA [2]. This model hits a large number of sequences in vertebrate genomes, which appear to be U6 derived pseudogenes or repeats. This family has a high significance threshold to minimise this problem, but many annotated pseudogenes remain.
U6_snRNA - U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.

View fRNAdb secondary structures for RNU6-66P

(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for RNU6-66P
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNU6-66P


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

Ensembl cytogenetic band:  13q22.1   HGNC cytogenetic band: 13q22.1

RNU6-66P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU6-66P gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M073690:  view genomic region     (about GC identifiers)

Start:
73,687,052 bp from pter      End:
73,687,155 bp from pter
Size:
104 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNU6-66P

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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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  --

(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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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:

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(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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(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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1 fRNAdb Secondary structure:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000363397(snRNA)
miRNA
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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 RNU6-66P:none

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

RNU6-66P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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 RNU6-66P gene from Selected species (see all 5)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
lizard
(Anolis carolinensis)
Reptilia U66
U6 spliceosomal RNA
72(a)
1 → many
1(142563526-142563627)
        Species with no ortholog for RNU6-66P

ENSEMBL Gene Tree for RNU6-66P (if available)
TreeFam Gene Tree for RNU6-66P (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 RNU6-66P (see all 56)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 13 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs560700341,2
C--73686601(+) TCCACC/GCACCT 1 -- ds50010--------
rs748908121,2
C--73686635(+) ACAGGC/TGCGAT 1 -- ds50010--------
rs1387060201,2
--73686650(+) TGCACA/CTGGCC 1 -- ds50010--------
rs735207611,2
C,F--73686835(+) CTTCAC/TTTTCT 1 -- ds50011Minor allele frequency- T:0.50WA 2
rs619673841,2
F--73687189(+) AGTATC/AGCAAA 1 -- us2k11Minor allele frequency- A:0.00NA 2
rs1143369271,2
F--73687240(+) TGGGTT/AGAAAT 1 -- us2k11Minor allele frequency- A:0.04WA 118
rs1397337571,2
C--73687249(+) ATTCTA/GACTCT 1 -- us2k10--------
rs1430706281,2
--73687371(+) CAAAAC/TGCAAT 1 -- us2k10--------
rs558088751,2
C,F--73687598(+) AAATGT/GTGTAT 1 -- us2k15Minor allele frequency- G:0.18WA CSA EA 243
rs573245471,2
C,F--73687662(+) TGAAAC/ATGAAT 1 -- us2k14Minor allele frequency- A:0.15WA CSA EA 241

HapMap Linkage Disequilibrium report for RNU6-66P (73687052 - 73687155 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RNU6-66P: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RNU6-66P
DNA2.0 Custom Variant and Variant Library Synthesis for RNU6-66P

(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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  --

(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 RNU6-66P gene integrated from 10 sources:
(articles sorted by number of sources associating them with RNU6-66P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. (PubMed id 9016512)10 
  2. (PubMed id 1960724)10 
  3. (PubMed id 2339054)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: 100873770 HGNC: 42556 Ensembl:ENSG00000200267 euGenes: HUgn100873770 ECgene: RNU6-66P
H-InvDB: RNU6-66P

(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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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RNU6-66P gene:
Search GeneIP for patents involving RNU6-66P

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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