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RNU6-1 Gene

RNA gene   GIFtS: 20
GCID: GC15M068132

RNA, U6 Small Nuclear 1

(Previous names: RNA, U6A small nuclear)
(Previous symbol: RNU6A)
  See RNU6-1-related disease
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

Aliases
RNA, U6 Small Nuclear 11 2
RNU6A1 2 5
RNU62 5
RNA, U6A Small Nuclear1
U62
U6-12

External Ids:    HGNC: 102271   Entrez Gene: 268272   Ensembl: ENSG000002066257   OMIM: 1806925   
ORGUL members:    fRNAdb10:FR198675 FR080027 FR027467 FR014903 FR196212      
NCBI13:BX648500 AL731658 AC109280 AL671671 AC100400 see all 84    
NONCODE14:u3878 u4045 u4779    
Rfam:RF00026    

Export aliases for RNU6-1 gene to outside databases

Previous GC identifers: GC15U900950 GC15M065922 GC07M122819


(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 RNU6-1 Gene:
RNU6-1 (RNA, U6 small nuclear 1) is an RNA gene, and is affiliated with the snRNA class. Diseases associated with RNU6-1 include poikiloderma with neutropenia.

fRNAdb sequence ontology for RNU6-1:
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 RNU6-1

(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:
   Regulatory transcription factor binding sites in the RNU6-1 gene promoter:
         SRF   ER-alpha   LHX3b/Lhx3b   SRF (504 AA)   CUTL1   Arnt   GATA-1   Chx10   LHX3a/Lhx3a   c-Myb   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RNU6-1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNU6-1


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

Entrez Gene cytogenetic band: 15q23   Ensembl cytogenetic band:  15q23   HGNC cytogenetic band: 15q23

RNU6-1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU6-1 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M068132:  view genomic region     (about GC identifiers)

Start:
68,132,277 bp from pter      End:
68,132,383 bp from pter
Size:
107 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNU6-1

(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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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, 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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SuperPaths for RNU6-1 About    
See pathways by source

SuperPathContained pathways About
1Spliceosomal Splicing Cycle
Spliceosomal Splicing Cycle

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for RNU6-1
    Spliceosomal Splicing Cycle


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RNU6-1
Interactions:

    GeneGlobe Interaction Network for RNU6-1

(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 Small Molecules at EMD Millipore
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Browse Tocris compounds for RNU6-1



(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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5 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000383898(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 RNU6-1:none

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

RNU6-1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for RNU6-1
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In Situ
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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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  --

ENSEMBL Gene Tree for RNU6-1 (if available)
TreeFam Gene Tree for RNU6-1 (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 RNU6-1 (see all 80)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1452642901,2
--68131792(+) TATTTC/TAATGA 1 -- ds50010--------
rs1901076011,2
--68131816(+) CCCTTC/GACATA 1 -- ds50010--------
rs112894101,2
C--68131847(+) GTGGC-/TTTTTT 1 -- ds50010--------
rs561247781,2
C--68131861(+) TTTTT-/T/TT  
        
GATTC
1 -- ds50011NA 2
rs1849259811,2
C--68131870(+) TCAAAA/GGATTC 1 -- ds50010--------
rs588156951,2
C--68132084(+) CAGAGA/TTGAAT 1 -- ds50014Minor allele frequency- T:0.15WA NA EA 360
rs1476198531,2
--68132128(+) CTAGGA/TCTACT 1 -- ds50010--------
rs1421434311,2
C--68132277(+) GATGTA/GAAAAT 1 -- ds50010--------
rs1501671551,2
--68132279(+) TGTAAA/GAATAT 1 -- nc-transcript-variant0--------
rs1141644771,2
F--68132281(+) TAAAAA/GTATGG 1 -- nc-transcript-variant1Minor allele frequency- G:0.02WA 118

HapMap Linkage Disequilibrium report for RNU6-1 (68132277 - 68132383 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RNU6-1: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RNU6-1
DNA2.0 Custom Variant and Variant Library Synthesis for RNU6-1

(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 gene information: 180692    OMIM disorders: --

1 disease for RNU6-1:    
About MalaCards
poikiloderma with neutropenia


Find genes that share disorders with RNU6-1           About GenesLikeMe

Genetic Association Database (GAD): RNU6-1

Export disorders for RNU6-1 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 RNU6-1 gene, integrated from 10 sources (see all 19):
(articles sorted by number of sources associating them with RNU6-1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Common genetic variation and performance on standardized cognitive tests. (PubMed id 20125193)1, 4 Cirulli E.T....Goldstein D.B. (Eur. J. Hum. Genet. 2010)
  2. Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies. (PubMed id 12711679)1, 3 Domitrovich A.M. and Kunkel G.R. (Nucleic Acids Res. 2003)
  3. Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used. (PubMed id 3360322)1, 3 Kunkel G.R. and Pederson T. (amp 1988)
  4. Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex. (PubMed id 23426875)1 Zhao C....Greenbaum N.L. (RNA 2013)
  5. Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. (PubMed id 23319000)1 Luykx J.J....Ophoff R.A. (Mol. Psychiatry 2013)
  6. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre. (PubMed id 22246180)1 Rasche N....Luhrmann R. (EMBO J. 2012)
  7. Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA. (PubMed id 23022480)1 Shchepachev V....Azzalin C.M. (Cell Rep 2012)
  8. Composition and three-dimensional EM structure of double affinity- purified, human prespliceosomal A complexes. (PubMed id 17332742)1 Behzadnia N.... Luehrmann R. (EMBO J. 2007)
  9. The multifunctional human p100 protein 'hooks' methylated ligands. (PubMed id 17632523)1 Shaw N....Rao Z. (amp 2007)
  10. CK2 phosphorylation of Bdp1 executes cell cycle-specific RNA polymerase III transcription repression. (PubMed id 15469824)1 Hu P.... Hernandez N. (Mol. Cell 2004)

(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: 26827 HGNC: 10227 Ensembl:ENSG00000206625 euGenes: HUgn26827 ECgene: RNU6-1
H-InvDB: RNU6-1

(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 RNU6-1 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 RNU6-1 gene:
Search GeneIP for patents involving RNU6-1

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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