Aliases for RNU4-1 Gene

Subcategory (RNA class) for RNU4-1 Gene

snRNA

Number of RNA Genes sources:

3 / 17

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
  • RNU4-1 2 5
  • U4BL 2 3
  • U4 2 3
  • RF00015 168
  • RNU4B2 3
  • 6QW6_4 167
  • 5O9Z_4 167
  • 6AHD_I 167
  • 6AH0_I 167
  • 6QX9_4 167
  • 3JCR_M 167
  • RNU4A 3

External Ids 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. Diseases associated with RNU4-1 include Hemometra and Primary Optic Atrophy. Among its related pathways are mRNA Splicing - Major Pathway and RNA transport.

Rfam classification for RNU4-1 Gene

Additional gene information for RNU4-1 Gene

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

Genomics for RNU4-1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RNU4-1 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

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

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
RNU4-1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

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 StructureGene Density

RefSeq DNA sequence for RNU4-1 Gene

Proteins for RNU4-1 Gene

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

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

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

Function for RNU4-1 Gene

Phenotypes From GWAS Catalog for RNU4-1 Gene

Gene Ontology (GO) - Molecular Function for RNU4-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017070 U6 snRNA binding IEA --
genes like me logo Genes that share ontologies with RNU4-1: view

Animal Model Products

CRISPR Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RNU4-1 Gene

Localization for RNU4-1 Gene

Gene Ontology (GO) - Cellular Components for RNU4-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005687 U4 snRNP IEA --
GO:0046540 U4/U6 x U5 tri-snRNP complex IEA --
genes like me logo Genes that share ontologies with RNU4-1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for RNU4-1 Gene

Pathways & Interactions for RNU4-1 Gene

PathCards logo

SuperPathways for RNU4-1 Gene

SuperPathway Contained pathways
1 mRNA Splicing - Major Pathway
.01
2 RNA transport
genes like me logo Genes that share pathways with RNU4-1: view

Pathways by source for RNU4-1 Gene

2 KEGG pathways for RNU4-1 Gene
1 Qiagen pathway for RNU4-1 Gene
  • Spliceosomal Splicing Cycle

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0000244 spliceosomal tri-snRNP complex assembly IEA --
GO:0000353 formation of quadruple SL/U4/U5/U6 snRNP IEA --
genes like me logo Genes that share ontologies with RNU4-1: view

No data available for Interacting Proteins and SIGNOR curated interactions for RNU4-1 Gene

Drugs & Compounds for RNU4-1 Gene

No Compound Related Data Available

Transcripts for RNU4-1 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for RNU4-1 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS00003F07BD_9606 snRNA 144 4

HGNC: 10192,

RefSeq: NR_003925,

PDBe: 6AH0_I, 6AHD_I,

ENA: M15956.1:271..414:ncRNA,

URS0000629D9A_9606 snRNA 141 2

Ensembl: ENST00000363925 (view in UCSC) ,

Rfam: RF00015,

URS0000200C70_9606 snRNA 144 2

PDBe: 5O9Z_4,

ENA: V00592.1:1..145:ncRNA,

URS00004D7446_9606 snRNA 144 1

ENA: K00472.1:1..145:ncRNA,

URS00008FED2D_9606 snRNA 144 1

PDBe: 3JCR_M,

RNU4-1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for RNU4-1 Gene

2 NCBI additional mRNA sequence :

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

Expression for RNU4-1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RNU4-1

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
Chimpanzee
(Pan troglodytes)
Mammalia U4 31
  • 99 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Gm24265 31
  • 99 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia U4 31
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia U4 31
  • 98 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia U4 31
  • 97 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii U4 31 31 31
  • 91 (a)
ManyToMany
Species where no ortholog for RNU4-1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

Additional dbSNP identifiers (rs#s) for RNU4-1 Gene

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 , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for RNU4-1 Gene

Disorders for RNU4-1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RNU4-1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
hemometra
  • hematometra
primary optic atrophy
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RNU4-1

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

No data available for 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
  2. High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs. (PMID: 30165668) Ottesen EW … Singh RN (Nucleic acids research 2018) 3
  3. 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
  4. 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
  5. 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

Products for RNU4-1 Gene

Sources for RNU4-1 Gene