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RNU1-2 Gene

RNA gene   GIFtS: 17
GCID: GC01P017233

RNA, U1 Small Nuclear 2

(Previous names: RNA, U1C1 small nuclear, RNA, U1C2 small nuclear)
(Previous symbols: RNU1C1, RNU1C2)
  Search for RNU1-2
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, U1 Small Nuclear 21 2     RNA, U1C2 Small Nuclear1
RNU1C11 2     U1C12
RNU1C21 2     U1C212
RNA, U1C1 Small Nuclear1     

External Ids:    HGNC: 101231   Entrez Gene: 268702   Ensembl: ENSG000002070057   
ORGUL members:    fRNAdb10:FR065763 FR251069 FR135896 FR067322 FR005262      
NCBI13:K00788 M28011 M14586 M14385 M14386 M14587 M14585 AK026936 AC006359 V00590
               M25190
see top 5    
NONCODE14:u3829 u4044    
Rfam:RF00003    

Export aliases for RNU1-2 gene to outside databases

Previous GC identifers: GC01U902390 GC01P017224 GC01P017227


(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 RNU1-2 Gene:
RNU1-2 (RNA, U1 small nuclear 2) is an RNA gene, and is affiliated with the snRNA class.

fRNAdb sequence ontologies for RNU1-2 - the ORGUL cluster for this gene includes several descriptions:
snRNA - A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
U1_snRNA - U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.

View fRNAdb secondary structures for RNU1-2

(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 RNU1-2
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNU1-2


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

Entrez Gene cytogenetic band: 1p36.1   Ensembl cytogenetic band:  1p36.13   HGNC cytogenetic band: 1p36.13

RNU1-2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU1-2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P017233:  view genomic region     (about GC identifiers)

Start:
17,222,475 bp from pter      End:
17,222,638 bp from pter
Size:
164 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNU1-2

(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 RNU1-2 About    
See pathways by source

SuperPathContained pathways About
1Spliceosomal Splicing Cycle
Spliceosomal Splicing Cycle

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for RNU1-2
    Spliceosomal Splicing Cycle


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Interactions:

    Search GeneGlobe Interaction Network for RNU1-2

(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 RNU1-2



(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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5/7 fRNAdb Secondary structures (see all 7):


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000384278(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 RNU1-2:none

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

RNU1-2 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 mammals.

Orthologs for RNU1-2 gene from Selected species (see all 3)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
dog
(Canis familiaris)
Mammalia U16
U1 spliceosomal RNA
99(a)
1 → many
18(50902588-50902751) ENSCAFG00000030934


ENSEMBL Gene Tree for RNU1-2 (if available)
TreeFam Gene Tree for RNU1-2 (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 RNU1-2 (see all 153)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs112033491,2
C,F,A,H--17220490(+) gattgC/Gtttga 1 -- us2k15Minor allele frequency- G:0.42NA CSA 12
rs74181591,2
C,F--17220522(+) atgtcG/Atggct 1 -- us2k13Minor allele frequency- A:0.09NA WA 122
rs112033501,2
C,F,A,H--17220539(+) tgtcaG/Atgaaa 1 -- us2k14Minor allele frequency- A:0.44NA CSA 9
rs74181811,2
C,H--17220614(+) catcaG/Cgtagt 1 -- us2k16Minor allele frequency- C:0.00NS EA NA 416
rs2005758071,2
C--17220652(+) TCCACA/GAAGGC 1 -- us2k10--------
rs1440892011,2
--17220665(+) GTCAGA/TTACCC 1 -- us2k10--------
rs73663501,2
C,F,A,H--17220670(+) ATACCC/TAGAAA 1 -- us2k14Minor allele frequency- T:0.40NA WA 10
rs1474186741,2
C--17220704(+) CAATGG/TGTCTC 1 -- us2k10--------
rs74185821,2
C--17220724(+) CTCCAG/AGGAAT 1 -- us2k1 tfbs32Minor allele frequency- A:0.00NA 4
rs3699624171,2
C--17220738(+) GCCTGA/GTCAAG 1 -- us2k10--------

HapMap Linkage Disequilibrium report for RNU1-2 (17222475 - 17222638 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RNU1-2: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RNU1-2
DNA2.0 Custom Variant and Variant Library Synthesis for RNU1-2

(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 RNU1-2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RNU1-2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition. (PubMed id 3837185)1, 3 Bernstein L.B....Weiner A.M. (Mol. Cell. Biol. 1985)
  2. (PubMed id 8797828)10 
  3. (PubMed id 9016512)10 
  4. (PubMed id 2977088)10 
  5. (PubMed id 15608158)10 
  6. (PubMed id 2405391)10 
  7. (PubMed id 7984237)10 
  8. (PubMed id 11297556)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: 26870 HGNC: 10123 Ensembl:ENSG00000207005 euGenes: HUgn26870 ECgene: RNU1-2
H-InvDB: RNU1-2

(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 RNU1-2 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 RNU1-2 gene:
Search GeneIP for patents involving RNU1-2

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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