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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RNU4-1 Gene

RNA gene   GIFtS: 16
GCID: GC12M120730

RNA, U4 small nuclear 1

(Previous names: RNA, U4B2 small nuclear, RNA, U4A small nuclear )
(Previous symbols: RNU4B2, RNU4A)
  Search for RNU4-1
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for RNU4-1    

Aliases
for RNU4-1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): snRNA

Quality score for this RNA gene is 5

Aliases
RNA, U4 Small Nuclear 11 2     U4BL1 2
RNU4A1 2     RNA, U4A Small Nuclear1
RNU4B21 2     RNA, U4B2 Small Nuclear1
U41 2     

External Ids:    HGNC: 101921   Entrez Gene: 268352   Ensembl: ENSG000002007957   
ORGUL members:    fRNAdb10:FR291801 FR292932 FR080402 FR280117 FR292932      
NCBI:X59361 V00592 M15956 M15956 AC004263 see all 15    
NONCODE:u4679 u4054 u3850 u3846 u4921    
Rfam:RF00015    

Export aliases for RNU4-1 gene to outside databases

Previous GC identifers: GC12U900787 GC12M119218 GC12M117739


Summaries
for RNU4-1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
fRNAdb sequence ontology for RNU4-1:
U4_snRNA - U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.

View fRNAdb secondary structures for RNU4-1

Genomic Views
for RNU4-1 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
 Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RNU4-1 gene promoter:
         STAT1   ATF-2   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   FOXJ2 (long isoform)   STAT3   c-Myb   FOXJ2   c-Jun   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RNU4-1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RNU4-1


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

Entrez Gene cytogenetic band: 12q24.31   Ensembl cytogenetic band:  12q24.31   HGNC cytogenetic band: 12q24.31

RNU4-1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU4-1 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M120730:  view genomic region     (about GC identifiers)

Start:
 120,730,897 bp from pter      End:
 120,731,040 bp from pter
Size:
 144 bases      Orientation:
 minus strand
ORGUL member locations:
Legend (see complete legend)

  • FR0251263
  • FR0280117
  • FR0292932
  • FR0216443
  • FR0291801
  • FR0266745
120730896 120730968 120731040 chr12

Proteins
for RNU4-1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for RNU4-1 gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for RNU4-1 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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Pathways & Interactions
for RNU4-1 gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways  About this table 
See pathways by source

Super-pathwaycontained gene-specific pathways
1Spliceosomal Splicing Cycle
Spliceosomal Splicing Cycle1.00

1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for RNU4-1
    Spliceosomal Splicing Cycle


Interactions:

    SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for RNU4-1

Drugs & Compounds
for RNU4-1 gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for RNU4-1
Search CenterWatch for drugs/clinical trials and news about RNU4-1 

Transcripts
for RNU4-1 gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
 5/7 fRNAdb Secondary structures (see all 7):


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000363925(snRNA)

miRNA
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Inhib. RNA
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Primer
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GeneLoc Exon Structure


Expression
for RNU4-1 gene

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for RNU4-1:none

RNU4-1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image    SABiosciences Custom PCR Arrays for RNU4-1
Primer
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In Situ
Assay Products: 
 		Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for RNU4-1

Orthologs
for RNU4-1 gene

(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)
About This Section
   --

ENSEMBL Gene Tree for RNU4-1 (if available)
TreeFam Gene Tree for RNU4-1 (if available) 

Paralogs
for RNU4-1 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for RNU4-1 gene
RNU4-10P2  ENSG000001993252  ENSG000002525012  ENSG000002010762  ENSG000001996722  ENSG000002227602  ENSG000001997092  ENSG000002225602  
ENSG000001994832  ENSG000002220572  ENSG000001999202  ENSG000002002742  ENSG000002024712  ENSG000002014392  ENSG000002530482  ENSG000002522372  
ENSG000002011842  RNU4-6P2  ENSG000002010702  RNU4-5P2  RNU4-7P2  ENSG000002014352  ENSG000002225012  ENSG000002016072  
ENSG000002227952  RNU4-9P2  ENSG000002013792  ENSG000002011642  ENSG000002226092  ENSG000001994582  RNU4-22  ENSG000002023392  
ENSG000002222022  ENSG000002226862  ENSG000002229902  RNU4-8P2  ENSG000002016092  ENSG000002014912  ENSG000002221462  ENSG000002013172  
ENSG000002232122  ENSG000002012962  ENSG000002020692  ENSG000002021032  ENSG000002024292  ENSG000002004312  ENSG000002227902  ENSG000002517522  
ENSG000002013422  ENSG000002223632  ENSG000001993132  ENSG000002016482  ENSG000002000342  ENSG000002228082  ENSG000002000622  ENSG000002024682  
ENSG000002016082  RNU4-4P2  ENSG000001996342  ENSG000002520672  ENSG000002021812  ENSG000002228212  ENSG000002012212  ENSG000002226632  
ENSG000002000702  ENSG000002517892  ENSG000002221772  ENSG000002016142  ENSG000002220672  ENSG000002073092  ENSG000002227272  ENSG000002006532  
ENSG000002021572  ENSG000002012312  ENSG000002232452  ENSG000002231522  ENSG000002525602  ENSG000002011862  ENSG000002069382  ENSG000002224052  
ENSG000002227502  ENSG000002069362  ENSG000002231752  ENSG000002015452  ENSG000002228722  ENSG000002015702  ENSG000002009742  ENSG000002008892  
ENSG000002518892  ENSG000001996432  

RNU4-1 for paralogs           About GeneDecksing



Genomic Variants
for RNU4-1 gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/17 NCBI SNPs in RNU4-1 are shown (see all 17)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 12 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs1904402661,2
--120731720(+) AGAATA/CATGTT 1 -- us2k10--------
rs1381826491,2
--120731823(+) TTTTT-/GAG   
  ATGGAGTTTTT 		1 -- us2k10--------
rs1825172401,2
--120731963(+) CACCAC/GTCTTT 1 -- us2k10--------
rs1492070431,2
--120732163(+) GCGCAA/GTGGCG 1 -- us2k10--------
rs79729141,2
C,--120732246(+) gtagaC/Gacggg 1 -- us2k10--------
rs1489234211,2
--120732334(+) GATTA-/CCAGCC 1 -- us2k10--------
rs1389861171,2
--120732349(+) GCCACC/TGCGCC 1 -- us2k10--------
rs1876279891,2
--120732482(+) CAGCTC/GGATAC 1 -- us2k10--------
rs1421217731,2
--120732667(+) GCTCTA/GTTGCC 1 -- us2k10--------
rs1463424921,2
--120732779(+) CAGGTC/GCGTGC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for RNU4-1 (120730897 - 120731040 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for RNU4-1: --

SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RNU4-1
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Disorders / Diseases
for RNU4-1 gene

(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.)
About This Section
   --

Publications
for RNU4-1 gene

(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)
About This Section

PubMed articles for RNU4-1 gene, integrated from 9 sources (see all 16):
(articles sorted by number of sources associating them with RNU4-1)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Genes for human U4 small nuclear RNA. (PubMed id 3582982)1, 3 Bark C....Pettersson U. (1986)
  2. Implication of the SMN complex in the biogenesis and s teady state level of the signal recognition particle. (PubMed id 23221635)1 Piazzon N....Massenet S. (2013)
  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. (2012)
  4. Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes. (PubMed id 17332742)1 Behzadnia N.... Luehrmann R. (2007)
  5. U4 small nuclear RNA can function in both the major and minor spliceosomes. (PubMed id 14691257)1 Shukla G.C. and Padgett R.A. (2004)
  6. NMR structure of the 3' stem-loop from human U4 snRNA. (PubMed id 12384583)1 Comolli L.R....Gmeiner W.H. (2002)
  7. Toward a complete human genome sequence. (PubMed id 9847074)1 Wilson R. (1998)
  8. Evidence for base-pairing between mammalian U2 and U6 small nuclear ribonucleoprotein particles. (PubMed id 2176635)1 Hausner T.P....Weiner A.M. (1990)
  9. Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs. (PubMed id 6169000)1 Krol A....Jacob M. (1981)
  10. (PubMed id 9016512)10 

External Searches for RNU4-1 gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing RNU4-1 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 26835 HGNC: 10192 Ensembl:ENSG00000200795 euGenes: HUgn26835 ECgene: RNU4-1
H-InvDB: RNU4-1

Other Databases showing RNU4-1 gene

(According to HUGE)
About This Section
   --

Specialized Databases showing RNU4-1 gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for RNU4-1 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for RNU4-1 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for RNU4-1 gene:
Search GeneIP for patents involving RNU4-1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



Products
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von Willebrand factor
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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