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Aliases for RNU4-39P Gene

Subcategory (RNA class) for RNU4-39P Gene

snRNA

Aliases for RNU4-39P Gene

  • RNA, U4 Small Nuclear 39, Pseudogene 2 3 5

External Ids for RNU4-39P Gene

ORGUL Members for RNU4-39P Gene

Previous GeneCards Identifiers for RNU4-39P Gene

  • GC11M066386

Summaries for RNU4-39P Gene

GeneCards Summary for RNU4-39P Gene

RNU4-39P (RNA, U4 Small Nuclear 39, Pseudogene) is a Pseudogene, and is affiliated with the snRNA class.

fRNAdb sequence ontologies for RNU4-39P Gene - the ORGUL cluster for this gene includes several descriptions:

  • 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.

  • U4 spliceosomal RNA: 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 re-fold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.

View fRNAdb secondary structures for RNU4-39P

Additional gene information for RNU4-39P 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 RNU4-39P Gene

Genomics for RNU4-39P Gene

GeneHancer (GH) Regulatory Elements for RNU4-39P Gene

Promoters and enhancers for RNU4-39P 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
GH11I066636 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.4 -23.2 -23246 3.8 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 RBM4 ACTN3 EIF1AD RBM14 KDM2A SART1 ENSG00000255320 ENSG00000258297 CORO1B RELA
GH11I066676 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.7 -62.7 -62731 2.8 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 GC11P066677 RBM4B RN7SL12P SPTBN2 C11orf80 LRFN4 PC ACTN3 ZDHHC24 RBM14-RBM4
GH11I066578 Enhancer 1 Ensembl ENCODE 11.2 +35.8 35807 0.7 ATF1 RB1 ARID4B SIN3A ZNF2 ZBTB7B RAD21 EGR1 ZNF143 FOS ZDHHC24 ACTN3 RBM4B LOC101928069 DPP3 MRPL11 PELI3 RBM14 RBM14-RBM4 RNU4-39P
GH11I066685 Enhancer 0.2 ENCODE 10.4 -71.4 -71425 2 RN7SL12P SPTBN2 C11orf80 LRFN4 PC ACTN3 ZDHHC24 RBM14-RBM4 LOC100505504 RBM14
GH11I066686 Enhancer 0.2 ENCODE 10.4 -70.3 -70295 0.2 RN7SL12P SPTBN2 C11orf80 LRFN4 PC ZDHHC24 ACTN3 RBM14-RBM4 RBM14 RNU4-39P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNU4-39P on UCSC Golden Path with GeneCards custom track

Genomic Locations for RNU4-39P Gene

Genomic Locations for RNU4-39P Gene
chr11:66,614,964-66,615,090
(GRCh38/hg38)
Size:
127 bases
Orientation:
Minus strand
chr11:66,382,435-66,382,561
(GRCh37/hg19)

Genomic View for RNU4-39P Gene

Genes around RNU4-39P on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNU4-39P Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNU4-39P Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNU4-39P Gene

ORGUL Member Location for RNU4-39P Gene

ORGUL Member Location for RNU4-39P gene

Proteins for RNU4-39P Gene

Post-translational modifications for RNU4-39P Gene

No Post-translational modifications

No data available for DME Specific Peptides for RNU4-39P Gene

Domains & Families for RNU4-39P 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 RNU4-39P Gene

Function for RNU4-39P 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 RNU4-39P Gene

Localization for RNU4-39P 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 RNU4-39P Gene

Pathways & Interactions for RNU4-39P Gene

SuperPathways for RNU4-39P Gene

No Data Available

Interacting Proteins for RNU4-39P Gene

Gene Ontology (GO) - Biological Process for RNU4-39P Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RNU4-39P Gene

Drugs & Compounds for RNU4-39P Gene

No Compound Related Data Available

Transcripts for RNU4-39P Gene

fRNAdb Secondary structures for RNU4-39P Gene

  • RF00015;U4;AADB02282093.1/304-194

mRNA/cDNA for RNU4-39P Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for RNU4-39P Gene

No ASD Table

Relevant External Links for RNU4-39P Gene

GeneLoc Exon Structure for
RNU4-39P
ECgene alternative splicing isoforms for
RNU4-39P

Expression for RNU4-39P Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNU4-39P Gene

genes like me logo Genes that share expression patterns with RNU4-39P: 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 RNU4-39P Gene

Orthologs for RNU4-39P Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNU4-39P Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia U4 34
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia U4 34
  • 76 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia U4 34
  • 59 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Gm25135 34
  • 57 (a)
OneToMany
dog
(Canis familiaris)
Mammalia U4 34
  • 50 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia U4 34
  • 73 (a)
OneToMany
Species where no ortholog for RNU4-39P 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • zebrafish (Danio rerio)

Evolution for RNU4-39P Gene

ENSEMBL:
Gene Tree for RNU4-39P (if available)
TreeFam:
Gene Tree for RNU4-39P (if available)

Paralogs for RNU4-39P Gene

No data available for Paralogs for RNU4-39P Gene

Variants for RNU4-39P Gene

Additional Variant Information for RNU4-39P Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNU4-39P

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 RNU4-39P Gene

Disorders for RNU4-39P Gene

No disorders were found for RNU4-39P Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for RNU4-39P Gene

Publications for RNU4-39P Gene

  1. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. (PMID: 11163207) Vidovic I … Ficner R (Molecular cell 2000) 1
  2. A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles. (PMID: 9452384) Raghunathan PL … Guthrie C (Science (New York, N.Y.) 1998) 1
  3. The uRNA database. (PMID: 9016512) Zwieb C (Nucleic acids research 1997) 1
  4. The spliceosomal snRNAs of Caenorhabditis elegans. (PMID: 2339054) Thomas J … Blumenthal T (Nucleic acids research 1990) 1

Products for RNU4-39P Gene

Sources for RNU4-39P Gene

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