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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

Additional gene information for RNU4ATAC15P Gene

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

GeneHancer (GH) Regulatory Elements for RNU4ATAC15P Gene

Promoters and enhancers for RNU4ATAC15P Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I033170 Enhancer 1.3 Ensembl ENCODE dbSUPER 550.8 -1.9 -1888 3.1 PKNOX1 FOXA2 ARNT DMAP1 YY1 TCF12 FOS DEK RXRA REST GC09P033176 RNU4ATAC15P B4GALT1 B4GALT1-AS1 GC09M033166 GC09M033167 GC09M033168
GH09I033075 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10.2 -97.7 -97697 2.2 HDGF PKNOX1 ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 ZNF207 ZNF143 SMU1 B4GALT1 NOL6 NFX1 ANXA2P2 BAG1 CHMP5 TOPORS B4GALT1-AS1 RNU4ATAC15P
GH09I033133 Enhancer 1.4 Ensembl ENCODE dbSUPER 12 -34.0 -34036 12.9 HDGF FOXA2 MLX ZFP64 ARID4B DMAP1 IRF4 ZNF48 ETS1 YY1 B4GALT1 B4GALT1-AS1 RNU4ATAC15P SPINK4 SMU1 BAG1 CHMP5 OSTCP8
GH09I033226 Enhancer 1.4 Ensembl ENCODE dbSUPER 11.8 +57.8 57821 11 PKNOX1 CLOCK FOXA2 ARID4B NEUROD1 SIN3A ZBTB7B IRF4 BRCA1 ZNF121 NFX1 SMU1 BAG1 ASS1P12 DFFBP1 TCEA1P4 TOPORS ENSG00000228352 CHMP5 NOL6
GH09I033239 Promoter/Enhancer 1.5 EPDnew ENCODE 10.7 +66.0 66003 1.3 PKNOX1 SMAD1 ATF1 ARNT ARID4B TCF12 ZNF766 GATA2 ATF7 NCOA1 SPINK4 CHMP5 BAG1 SMU1 B4GALT1-AS1 B4GALT1 RNU4ATAC15P NFX1 GC09P033251 GC09M033166
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNU4ATAC15P on UCSC Golden Path with GeneCards custom track

Genomic Locations for RNU4ATAC15P Gene

Genomic Locations for RNU4ATAC15P Gene
chr9:33,174,170-33,174,295
(GRCh38/hg38)
Size:
126 bases
Orientation:
Plus strand
chr9:33,174,168-33,174,293
(GRCh37/hg19)

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

Phenotypes From GWAS Catalog 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 , Subcellular locations from the Human Protein Atlas (HPA) 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 34 34
  • 98 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia U4atac 34
  • 82 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia U4atac 34
  • 75 (a)
OneToMany
dog
(Canis familiaris)
Mammalia U4atac 34
  • 67 (a)
ManyToMany
chicken
(Gallus gallus)
Aves U4atac 34
  • 69 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia U4atac 34 34 34
  • 75 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii U4atac 34
  • 57 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea U4atac 34
  • 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

Additional Variant Information 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 ZJ … Barta A (RNA (New York, N.Y.) 2005) 1
  2. Domains of human U4atac snRNA required for U12-dependent splicing in vivo. (PMID: 12409455) Shukla GC … Padgett RA (Nucleic acids research 2002) 1
  3. A revised model for U4atac/U6atac snRNA base pairing. (PMID: 11911359) Padgett RA … Shukla GC (RNA (New York, N.Y.) 2002) 1

Products for RNU4ATAC15P Gene

Sources for RNU4ATAC15P Gene

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