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Aliases for RNU4ATAC16P Gene

Subcategory (RNA class) for RNU4ATAC16P Gene

snRNA

Aliases for RNU4ATAC16P Gene

  • RNA, U4atac Small Nuclear 16, Pseudogene 2 3 5

External Ids for RNU4ATAC16P Gene

ORGUL Members for RNU4ATAC16P Gene

Previous GeneCards Identifiers for RNU4ATAC16P Gene

  • GC12P000893

Summaries for RNU4ATAC16P Gene

GeneCards Summary for RNU4ATAC16P Gene

RNU4ATAC16P (RNA, U4atac Small Nuclear 16, Pseudogene) is a Pseudogene, and is affiliated with the snRNA class.

fRNAdb sequence ontologies for RNU4ATAC16P 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 RNU4ATAC16P

Additional gene information for RNU4ATAC16P 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 RNU4ATAC16P Gene

Genomics for RNU4ATAC16P Gene

GeneHancer (GH) Regulatory Elements for RNU4ATAC16P Gene

Promoters and enhancers for RNU4ATAC16P 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
GH12J000779 Promoter/Enhancer 1.5 Ensembl ENCODE dbSUPER 600.7 -1.1 -1064 2.5 CEBPG ZSCAN21 MAFK SP7 SP1 HNF1A PRDM1 MLLT1 IKZF1 ZNF600 RNU4ATAC16P RAD52 NINJ2 GC12M000775 WNK1
GH12J000716 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.5 -64.5 -64532 2 CBFA2T2 ZNF121 TRIM24 PRDM1 SMARCA4 DPF2 ATF1 PKNOX1 LEF1 EP300 NINJ2 LINC02455 WNK1 RNU4ATAC16P B4GALNT3
GH12J000805 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 12.8 +26.1 26080 2.6 ZNF121 CEBPG ZNF384 SP7 ZNF174 SP1 PRDM1 MLLT1 MZF1 IKZF1 RAD52 WASH8P WNK1 RNU4ATAC16P LOC101929384 ENSG00000261799 KDM5A ENSG00000285704
GH12J000722 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.5 -54.1 -54133 9.6 SP1 CC2D1A ZNF121 ZNF687 NCOA3 RELA PRDM1 MLLT1 IKZF1 ZNF600 WNK1 NINJ2 IQSEC3 RNU4ATAC16P ENSG00000177406 LINC02455
GH12J000814 Enhancer 1.1 Ensembl ENCODE dbSUPER 12.8 +33.3 33267 0.4 ZNF384 CTCF SP7 ZNF174 MLLT1 RAD21 RXRA REST ZEB2 TRIM22 WNK1 RNU4ATAC16P RAD52 ENSG00000285704
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNU4ATAC16P on UCSC Golden Path with GeneCards custom track

Genomic Locations for RNU4ATAC16P Gene

Genomic Locations for RNU4ATAC16P Gene
chr12:781,133-781,258
(GRCh38/hg38)
Size:
126 bases
Orientation:
Plus strand
chr12:890,299-890,424
(GRCh37/hg19)
Size:
126 bases
Orientation:
Plus strand

Genomic View for RNU4ATAC16P Gene

Genes around RNU4ATAC16P on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNU4ATAC16P Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNU4ATAC16P Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNU4ATAC16P Gene

ORGUL Member Location for RNU4ATAC16P Gene

ORGUL Member Location for RNU4ATAC16P gene

Proteins for RNU4ATAC16P Gene

Post-translational modifications for RNU4ATAC16P Gene

No Post-translational modifications

No data available for DME Specific Peptides for RNU4ATAC16P Gene

Domains & Families for RNU4ATAC16P 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 RNU4ATAC16P Gene

Function for RNU4ATAC16P Gene

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RNU4ATAC16P Gene

Localization for RNU4ATAC16P 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 RNU4ATAC16P Gene

Pathways & Interactions for RNU4ATAC16P Gene

PathCards logo

SuperPathways for RNU4ATAC16P Gene

No Data Available

Interacting Proteins for RNU4ATAC16P Gene

Gene Ontology (GO) - Biological Process for RNU4ATAC16P Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RNU4ATAC16P Gene

Drugs & Compounds for RNU4ATAC16P Gene

No Compound Related Data Available

Transcripts for RNU4ATAC16P Gene

fRNAdb Secondary structures for RNU4ATAC16P Gene

  • RF00618;U4atac;DAAB015139891.1/656-542

mRNA/cDNA for RNU4ATAC16P Gene

(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for RNU4ATAC16P Gene

No ASD Table

Relevant External Links for RNU4ATAC16P Gene

GeneLoc Exon Structure for
RNU4ATAC16P
ECgene alternative splicing isoforms for
RNU4ATAC16P

Expression for RNU4ATAC16P Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNU4ATAC16P Gene

NURSA nuclear receptor signaling pathways regulating expression of RNU4ATAC16P Gene:

RNU4ATAC16P
genes like me logo Genes that share expression patterns with RNU4ATAC16P: 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 RNU4ATAC16P Gene

Orthologs for RNU4ATAC16P Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNU4ATAC16P Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia U4atac 35
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia U4atac 35
  • 83 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia U4atac 35
  • 74 (a)
OneToMany
dog
(Canis familiaris)
Mammalia U4atac 35
  • 69 (a)
ManyToMany
chicken
(Gallus gallus)
Aves U4atac 35
  • 68 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia U4atac 35 35 35
  • 70 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii U4atac 35
  • 55 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea U4atac 35
  • 55 (a)
OneToMany
Species where no ortholog for RNU4ATAC16P 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 RNU4ATAC16P Gene

ENSEMBL:
Gene Tree for RNU4ATAC16P (if available)
TreeFam:
Gene Tree for RNU4ATAC16P (if available)

Paralogs for RNU4ATAC16P Gene

No data available for Paralogs for RNU4ATAC16P Gene

Variants for RNU4ATAC16P Gene

Additional Variant Information for RNU4ATAC16P Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNU4ATAC16P

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 RNU4ATAC16P Gene

Disorders for RNU4ATAC16P Gene

No disorders were found for RNU4ATAC16P Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for RNU4ATAC16P Gene

Publications for RNU4ATAC16P 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. A revised model for U4atac/U6atac snRNA base pairing. (PMID: 11911359) Padgett RA … Shukla GC (RNA (New York, N.Y.) 2002) 1
  3. Domains of human U4atac snRNA required for U12-dependent splicing in vivo. (PMID: 12409455) Shukla GC … Padgett RA (Nucleic acids research 2002) 1

No data available for External Links for RNU4ATAC16P Gene

Products for RNU4ATAC16P Gene

Sources for RNU4ATAC16P Gene

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