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RNU5A-1 Gene

RNA gene   GIFtS: 17
GCID: GC15P065763

RNA, U5A Small Nuclear 1

(Previous names: RNA, U5C small nuclear, RNA, U5A small nuclear)
(Previous symbols: RNU5C, RNU5A)
  See RNU5A-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, U5A Small Nuclear 11 2     RNA, U5A Small Nuclear1
RNU5A1 2 5     RNA, U5C Small Nuclear1
RNU5C1 2     U5A2
RNU52 5     U5B12

External Ids:    HGNC: 102111   Entrez Gene: 268312   Ensembl: ENSG000001995687   OMIM: 1806915   
ORGUL members:    fRNAdb10:FR020510 FR221523 FR376319 FR134545 FR029924      
NCBI13:X01691 K03167 K03167 X01691    
NONCODE14:u3881 u4695    
Rfam:RF00020    

Export aliases for RNU5A-1 gene to outside databases

Previous GC identifers: GC15P065590 GC15P065675


(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 RNU5A-1 Gene:
RNU5A-1 (RNA, U5A small nuclear 1) is an RNA gene, and is affiliated with the snRNA class. Diseases associated with RNU5A-1 include poikiloderma with neutropenia.

fRNAdb sequence ontology for RNU5A-1:
U5_snRNA - U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.

View fRNAdb secondary structures for RNU5A-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:
   Search for regulatory transcription factor binding sites for RNU5A-1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNU5A-1


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

Entrez Gene cytogenetic band: 15q22.31   Ensembl cytogenetic band:  15q22.31   HGNC cytogenetic band: 15q22.31

RNU5A-1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU5A-1 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P065763:  view genomic region     (about GC identifiers)

Start:
65,588,389 bp from pter      End:
65,588,505 bp from pter
Size:
117 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNU5A-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., eBioscience, and/or antibodies-online,
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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, 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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4 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000362698(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 RNU5A-1:none

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

RNU5A-1 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 RNU5A-1 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
lizard
(Anolis carolinensis)
Reptilia U56
U5 spliceosomal RNA
85(a)
many ↔ many
4(110081790-110081905)
        Species with no ortholog for RNU5A-1

ENSEMBL Gene Tree for RNU5A-1 (if available)
TreeFam Gene Tree for RNU5A-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 RNU5A-1 (see all 131)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1895308311,2
--65586390(+) AAATCA/GTAGAT 1 -- us2k10--------
rs1829359381,2
--65586431(+) TAACTG/TAAATA 1 -- us2k10--------
rs1507485971,2
--65586437(+) AAATAC/TAAAAA 1 -- us2k10--------
rs1393427221,2
--65586525(+) CAAAAC/TGTGGT 1 -- us2k10--------
rs288957091,2
--65586627(+) GAGGCC/TGAAGC 1 -- us2k10--------
rs1477343501,2
--65586733(+) GCGCAC/TGCCTG 1 -- us2k10--------
rs1410603641,2
--65586755(+) ACTCAC/GGAGAT 1 -- us2k10--------
rs342042891,2
C,F--65586758(+) CAGGAG/AATTGA 1 -- us2k12Minor allele frequency- A:0.50NA 4
rs6805241,2
C,F,H--65586760(+) ggagaT/Ctgagg 1 -- us2k14Minor allele frequency- C:0.25NA WA 8
rs1489509321,2
--65586821(+) GCGCCA/GTTGCA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for RNU5A-1 (65588389 - 65588505 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for RNU5A-1: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RNU5A-1
DNA2.0 Custom Variant and Variant Library Synthesis for RNU5A-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: 180691    OMIM disorders: --

1 disease for RNU5A-1:    
About MalaCards
poikiloderma with neutropenia


Find genes that share disorders with RNU5A-1           About GenesLikeMe


Export disorders for RNU5A-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 RNU5A-1 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with RNU5A-1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Three novel functional variants of human U5 small nuclear RNA. (PubMed id 1310151)1, 3 Sontheimer E.J. and Steitz J.A. (Mol. Cell. Biol. 1992)
  2. Multiple myeloma-associated chromosomal translocation activates orphan snoRNA ACA11 to suppress oxidative stress. (PubMed id 22751105)1 Chu L....Tomasson M.H. (J. Clin. Invest. 2012)
  3. 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)
  4. The multifunctional human p100 protein 'hooks' methylated ligands. (PubMed id 17632523)1 Shaw N....Rao Z. (amp 2007)
  5. High evolutionary conservation of the secondary structure and of certain nucleotide sequences of U5 RNA. (PubMed id 6200827)1 Branlant C....Pousada C. (Nucleic Acids Res. 1983)
  6. The nuclear 5S RNAs from chicken, rat and man. U5 RNAs are encoded by multiple genes. (PubMed id 6164980)1 Krol A....Branlant C. (Nucleic Acids Res. 1981)
  7. (PubMed id 9016512)10 
  8. (PubMed id 8702566)10 
  9. (PubMed id 2339054)10 
  10. (PubMed id 8797828)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: 26831 HGNC: 10211 Ensembl:ENSG00000199568 euGenes: HUgn26831 ECgene: RNU5A-1
H-InvDB: RNU5A-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 RNU5A-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 RNU5A-1 gene:
Search GeneIP for patents involving RNU5A-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, eBioscience, antibodies-online, 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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