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RNU4-1 Gene(RNA Gene)

RNA, U4 Small Nuclear 1

GCID:
GC12M120293
GIFtS:
15
Genes Participants
UDN Logo

Aliases for RNU4-1 Gene

Subcategory (RNA class) for RNU4-1 Gene

snRNA

Quality Score for this RNA gene is

13

Aliases for RNU4-1 Gene

  • RNA, U4 Small Nuclear 1 2 3 5
  • RNA, U4B2 Small Nuclear 2 3
  • RNA, U4A Small Nuclear 2 3
  • RNU4B2 3
  • RNU4A 3
  • U4BL 3
  • U4 3

External Ids for RNU4-1 Gene

ORGUL Members for RNU4-1 Gene

Previous HGNC Symbols for RNU4-1 Gene

  • RNU4B2
  • RNU4A

Previous GeneCards Identifiers for RNU4-1 Gene

  • GC12U900787
  • GC12M119218
  • GC12M120730
  • GC12M117739

Summaries for RNU4-1 Gene

GeneCards Summary for RNU4-1 Gene

RNU4-1 (RNA, U4 Small Nuclear 1) is an RNA Gene, and is affiliated with the snRNA class. Among its related pathways are Spliceosomal Splicing Cycle.

Additional gene information for RNU4-1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNU4-1 Gene

Genomics for RNU4-1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for RNU4-1 Gene

Promoters and enhancers for RNU4-1 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
GH12J120290 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.0 1007 3.4 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SIRT4 GC12M120292 GC12M120294 RNU4-1 RNU4-2 GCN1 RAB35 PXN RPL31P52 PRKAB1
GH12J120239 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.8 +43.7 43707 19.3 PKNOX1 SMAD1 FOXA2 ARNT ZNF2 ZNF766 E2F8 FOS REST ZNF592 PXN SIRT4 RNU4-1 RNU4-2 RNU6-1088P PLA2G1B P2RX4 BICDL1 RNF10 RAB35
GH12J120223 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 12.3 +61.7 61652 16 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 SP3 PXN-AS1 PXN SIRT4 RAB35 RPLP0 RNU4-1 RNU4-2 RPL31P52 PLA2G1B GCN1
GH12J120220 Enhancer 0.7 ENCODE dbSUPER 11.8 +72.5 72454 1.2 TFAP4 GLIS1 ARID4B KDM1A ZIC2 GC12M120218 PXN GCN1 RNU4-1 RNU4-2 ENSG00000275936
GH12J120222 Enhancer 0.6 ENCODE dbSUPER 11.8 +71.0 71024 0.2 BCOR ZMYM3 KDM1A PXN RNU4-2 RNU4-1 GCN1 ENSG00000275936 GC12M120218
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNU4-1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNU4-1 gene promoter:
  • STAT1
  • STAT3
  • c-Jun
  • ATF-2
  • POU3F2 (N-Oct-5b)
  • POU3F2 (N-Oct-5a)
  • POU3F2
  • c-Myb
  • FOXJ2
  • FOXJ2 (long isoform)

Genomic Locations for RNU4-1 Gene

Genomic Locations for RNU4-1 Gene
chr12:120,293,094-120,293,237
(GRCh38/hg38)
Size:
144 bases
Orientation:
Minus strand
chr12:120,730,897-120,731,040
(GRCh37/hg19)
Size:
144 bases
Orientation:
Minus strand

Genomic View for RNU4-1 Gene

Genes around RNU4-1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNU4-1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNU4-1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RNU4-1 Gene

Proteins for RNU4-1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

Post-translational modifications for RNU4-1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for RNU4-1 Gene

Domains & Families for RNU4-1 Gene

Gene Families for RNU4-1 Gene

HGNC:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RNU4-1: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for RNU4-1 Gene

Function for RNU4-1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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 RNU4-1 Gene

Localization for RNU4-1 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 RNU4-1 Gene

Pathways & Interactions for RNU4-1 Gene

SuperPathways for RNU4-1 Gene

PathCards logo More details on SuperPathways for RNU4-1
SuperPathway Contained pathways
1 Spliceosomal Splicing Cycle
Spliceosomal Splicing Cycle
-
genes like me logo Genes that share pathways with RNU4-1: view

Pathways by source for RNU4-1 Gene

1 Qiagen pathway for RNU4-1 Gene

Interacting Proteins for RNU4-1 Gene

Gene Ontology (GO) - Biological Process for RNU4-1 Gene

None

No data available for SIGNOR curated interactions for RNU4-1 Gene

Drugs & Compounds for RNU4-1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RNU4-1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RNU4-1 Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for RNU4-1 Gene

No ASD Table

Relevant External Links for RNU4-1 Gene

GeneLoc Exon Structure for
RNU4-1
ECgene alternative splicing isoforms for
RNU4-1

Expression for RNU4-1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNU4-1 Gene

mRNA expression in normal human tissues for RNU4-1 Gene
mRNA expression by GTEx for RNU4-1 Gene

mRNA differential expression in normal tissues according to GTEx for RNU4-1 Gene

This gene is overexpressed in Testis (x6.2), Whole Blood (x4.8), and Pancreas (x4.1).
genes like me logo Genes that share expression patterns with RNU4-1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 RNU4-1 Gene

Orthologs for RNU4-1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNU4-1 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
 Mammalia Gm24265 34
  • 99 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia U4 34
  • 99 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia U4 34
  • 98 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia U4 34
  • 98 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia U4 34
  • 97 (a)
 ManyToMany
zebrafish
(Danio rerio)
 Actinopterygii U4 34 34 34
  • 95 (a)
 ManyToMany
Species where no ortholog for RNU4-1 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • 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 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)

Evolution for RNU4-1 Gene

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

Paralogs for RNU4-1 Gene

No data available for Paralogs for RNU4-1 Gene

Variants for RNU4-1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for RNU4-1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000829757 -- 120,293,080(-) ACTGCAAGAAAATTCAGTCTCCGTAGAGACTG/ACTG downstream_transcript_variant, non_coding_transcript_variant
rs1001645897 -- 120,294,373(-) C/T upstream_transcript_variant
rs1001907162 -- 120,294,459(-) G/A/T upstream_transcript_variant
rs1002276069 -- 120,294,087(-) A/T upstream_transcript_variant
rs1002728504 -- 120,293,064(-) /T downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RNU4-1 Gene

Variant ID Type Subtype PubMed ID
nsv560435 CNV loss 21841781
nsv832530 CNV loss 17160897

Additional Variant Information for RNU4-1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNU4-1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for RNU4-1 Gene

Disorders for RNU4-1 Gene

Additional Disease Information for RNU4-1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RNU4-1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNU4-1 Gene

Publications for RNU4-1 Gene

  1. Genes for human U4 small nuclear RNA. (PMID: 3582982) Bark C … Pettersson U (Gene 1986) 2 3 58
  2. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. (PMID: 29117863) Choudhury NR … Michlewski G (BMC biology 2017) 3 58
  3. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. (PMID: 26275778) Bizarro J … Bertrand E (Nucleic acids research 2015) 3 58
  4. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. (PMID: 25263594) Guo R … Shi Y (Molecular cell 2014) 3 58
  5. Inhibition of U4 snRNA in human cells causes the stable retention of polyadenylated pre-mRNA in the nucleus. (PMID: 24796696) Hett A … West S (PloS one 2014) 3 58

Products for RNU4-1 Gene

Sources for RNU4-1 Gene

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