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Aliases for RNU4ATAC15P Gene

Subcategory (RNA class) for RNU4ATAC15P Gene

snRNA

Aliases for RNU4ATAC15P Gene

  • RNA, U4atac Small Nuclear 15, Pseudogene 2 3 5

External Ids for RNU4ATAC15P Gene

ORGUL Members for RNU4ATAC15P Gene

Summaries for RNU4ATAC15P Gene

GeneCards Summary for RNU4ATAC15P Gene

RNU4ATAC15P (RNA, U4atac Small Nuclear 15, Pseudogene) is a Pseudogene, and is affiliated with the snRNA class.

fRNAdb sequence ontologies for RNU4ATAC15P Gene - the ORGUL cluster for this gene includes several descriptions:

  • snRNA: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.

  • U4atac minor spliceosomal RNA: U4atac is an essential component of the minor U12-type spliceosome complex which is required for removal of the rarer class of eukaryotic introns (AT-AC, U12-type) [1]. U4atac snRNA is proposed to form a base-paired complex with another spliceosomal RNA U6atac via two stem loop regions. These interacting stem loops have been shown to be required for in vivo splicing [2]. U4atac also contains an 3' Sm protein binding site which has been shown to be essential for splicing activity [2]. U4atac is the functional analog of U4 (Rfam:RF00015) in the major U2-type spliceosomal complex [2]. The drosophila U4atac snRNA has an additional predicted 3' stem loop terminal to the Sm binding site [3] which is not included in this model.

  • U4atac minor spliceosomal RNA: U4atac is an essential component of the minor U12-type spliceosome complex which is required for removal of the rarer class of eukaryotic introns (AT-AC, U12-type) [1]. U4atac snRNA is proposed to form a base-paired complex with another spliceosomal RNA U6atac via two stem loop regions. These interacting stem loops have been shown to be required for in vivo splicing [2]. U4atac also contains an 3' Sm protein binding site which has been shown to be essential for splicing activity [2]. U4atac is the functional analog of U4 (Rfam:RF00015) in the major U2-type spliceosomal complex [2]. The drosophila U4atac snRNA has an additional predicted 3' stem loop terminal to the Sm binding site [3] which is not included in this model.

View fRNAdb secondary structures for RNU4ATAC15P

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary and piRNA Summary for RNU4ATAC15P Gene

Genomics for RNU4ATAC15P Gene

Regulatory Elements for RNU4ATAC15P Gene

Enhancers for RNU4ATAC15P Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09G033133 1.5 Ensembl ENCODE dbSUPER 12 -34.0 -34036 12.9 HDGF MLX WRNIP1 ZFP64 ARID4B DMAP1 ZNF48 YY1 FOS SP5 B4GALT1 B4GALT1-AS1 RNU4ATAC15P SPINK4 SMU1 BAG1 CHMP5 OSTCP8
GH09G033226 1.5 Ensembl ENCODE dbSUPER 11.8 +57.8 57822 11.0 PKNOX1 FOXA2 ARID4B SIN3A BRCA1 ZBTB7B ZNF121 GLIS2 FOS DEK NFX1 BAG1 CHMP5 B4GALT1 B4GALT1-AS1 SMU1 RNU4ATAC15P DFFBP1 SPINK4 GC09P033251
GH09G033202 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.7 +28.6 28558 1.2 CTCF EBF1 RELA POLR2A EED RELB IKZF2 CREM CHD2 MAZ RNU4ATAC15P B4GALT1-AS1 B4GALT1 SMU1 SPINK4 GC09P033176
GH09G033149 1.4 Ensembl ENCODE dbSUPER 12.1 -23.5 -23468 3.4 HDAC1 CREB3L1 KLF17 INSM2 SIN3A ZNF2 TCF12 ZNF366 ZSCAN5C FOS SMU1 B4GALT1 RNU4ATAC15P APTX B4GALT1-AS1
GH09G033225 1.4 Ensembl ENCODE dbSUPER 11.8 +51.6 51645 1.0 HDGF PKNOX1 ZNF2 RAD21 RFX5 ZNF335 SIRT6 FOS MIXL1 ZNF654 B4GALT1-AS1 B4GALT1 SMU1 RNU4ATAC15P APTX DNAJA1 SPINK4 GC09P033251
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RNU4ATAC15P on UCSC Golden Path with GeneCards custom track

Genomic Location for RNU4ATAC15P Gene

Chromosome:
9
Start:
33,174,170 bp from pter
End:
33,174,295 bp from pter
Size:
126 bases
Orientation:
Plus strand

Genomic View for RNU4ATAC15P Gene

Genes around RNU4ATAC15P on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNU4ATAC15P Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNU4ATAC15P Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNU4ATAC15P Gene

ORGUL Member Location for RNU4ATAC15P Gene

ORGUL Member Location for RNU4ATAC15P gene

Proteins for RNU4ATAC15P Gene

Post-translational modifications for RNU4ATAC15P Gene

No Post-translational modifications

No data available for DME Specific Peptides for RNU4ATAC15P Gene

Domains & Families for RNU4ATAC15P Gene

Graphical View of Domain Structure for InterPro Entry

No data available for Gene Families , Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for RNU4ATAC15P Gene

Function for RNU4ATAC15P Gene

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RNU4ATAC15P Gene

Localization for RNU4ATAC15P Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for RNU4ATAC15P Gene

Pathways & Interactions for RNU4ATAC15P Gene

SuperPathways for RNU4ATAC15P Gene

No Data Available

Interacting Proteins for RNU4ATAC15P Gene

Gene Ontology (GO) - Biological Process for RNU4ATAC15P Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RNU4ATAC15P Gene

Drugs & Compounds for RNU4ATAC15P Gene

No Compound Related Data Available

Transcripts for RNU4ATAC15P Gene

fRNAdb Secondary structures for RNU4ATAC15P Gene

  • RF00618;U4atac;ADDF012530914.1/189-73

mRNA/cDNA for RNU4ATAC15P Gene

(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for RNU4ATAC15P Gene

No ASD Table

Relevant External Links for RNU4ATAC15P Gene

GeneLoc Exon Structure for
RNU4ATAC15P
ECgene alternative splicing isoforms for
RNU4ATAC15P

Expression for RNU4ATAC15P Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNU4ATAC15P Gene

NURSA nuclear receptor signaling pathways regulating expression of RNU4ATAC15P Gene:

RNU4ATAC15P
genes like me logo Genes that share expression patterns with RNU4ATAC15P: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNU4ATAC15P Gene

Orthologs for RNU4ATAC15P Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNU4ATAC15P Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia U4atac 35 35
  • 98 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia U4atac 35
  • 82 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia U4atac 35
  • 75 (a)
OneToMany
dog
(Canis familiaris)
Mammalia U4atac 35
  • 67 (a)
ManyToMany
chicken
(Gallus gallus)
Aves U4atac 35
  • 69 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia U4atac 35 35 35
  • 75 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii U4atac 35
  • 57 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea U4atac 35
  • 55 (a)
OneToMany
Species where no ortholog for RNU4ATAC15P was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RNU4ATAC15P Gene

ENSEMBL:
Gene Tree for RNU4ATAC15P (if available)
TreeFam:
Gene Tree for RNU4ATAC15P (if available)

Paralogs for RNU4ATAC15P Gene

No data available for Paralogs for RNU4ATAC15P Gene

Variants for RNU4ATAC15P Gene

Relevant External Links for RNU4ATAC15P Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNU4ATAC15P

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations from dbSNP and Humsavar , Structural Variations from Database of Genomic Variants (DGV) and Variation tolerance for RNU4ATAC15P Gene

Disorders for RNU4ATAC15P Gene

No disorders were found for RNU4ATAC15P Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for RNU4ATAC15P Gene

Publications for RNU4ATAC15P Gene

  1. Evolutionary conservation of minor U12-type spliceosome between plants and humans. (PMID: 15987817) Lorkovic Z.J. … Barta A. (RNA 2005) 1
  2. A revised model for U4atac/U6atac snRNA base pairing. (PMID: 11911359) Padgett R.A. … Shukla G.C. (RNA 2002) 1
  3. Domains of human U4atac snRNA required for U12-dependent splicing in vivo. (PMID: 12409455) Shukla G.C. … Padgett R.A. (Nucleic Acids Res. 2002) 1

Products for RNU4ATAC15P Gene

Sources for RNU4ATAC15P Gene

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