241 articles
rRNA processing and modification
rRNA processing and modification are the cleavage and site-specific chemical changes that convert a 47S precursor transcript into the mature 18S, 5.8S, and 28S ribosomal RNAs, guided by snoRNPs.
rRNA-processing protein Efg1
rRNA-processing protein Efg1 (Exit from G1 protein 1, YGR272C) is a 233-aa nucleolar assembly factor of yeast 90S pre-ribosomes, required for 18S rRNA processing at A1/A2 sites; distinct from Candida Efg1 and mitochondrial EFG1.
SBDS
SBDS, the Shwachman-Bodian-Diamond syndrome gene on chromosome 7, encodes a 250-amino-acid ribosome maturation factor that with EFL1 releases eIF6 from 60S pre-ribosomes; biallelic mutations cause Shwachman-Diamond syndrome.
Selenocysteine tRNA and selenocysteine decoding
Selenocysteine decoding is the process by which tRNA charged with selenocysteine reads selected UGA stop codons, directed by an mRNA structure called the SECIS element.
Sex-lethal splicing factor
Sex-lethal (Sxl) is the master switch gene of Drosophila sex determination and dosage compensation, encoding a female-specific RNA binding protein that controls splicing of transformer and its own transcript and represses msl-2 translation.
Shapiro Senapathy algorithm
Shapiro Senapathy algorithm: a 1987 position weight matrix method for scoring eukaryotic splice sites, the basis of SpliceSiteFinder and related splice prediction tools.
SILVA ribosomal RNA database
SILVA is a curated, regularly updated database of aligned 16S/18S (SSU) and 23S/28S (LSU) rRNA sequences for Bacteria, Archaea, and Eukarya, hosted by DSMZ; release 144 (2026) holds 905,628 SSU Ref NR99 sequences and ships DADA2, Kraken2, MEGAN, and Qiime2 classifiers.
Site-directed RNA editing
Site-directed RNA editing uses engineered enzymes or guide RNAs to alter individual RNA bases without changing the genome, offering transient, repeatable therapies now in early clinical trials.
SLBP
SLBP (stem-loop binding protein, HBP, gene 7884) is a metazoan RNA-binding protein that binds the 26-nt stem-loop at the 3' end of replication-dependent histone mRNAs, enabling U7 snRNP-dependent 3' end processing, export, translation, and cell cycle-regulated degradation.
Sm-like protein Lsm1
Lsm1 (LSM1, CaSm) is a Sm-like protein forming the cytoplasmic Lsm1-7 heptameric ring that binds deadenylated mRNA 3' ends, protects them, and activates decapping in 5'-to-3' mRNA decay, distinct from the nuclear Lsm2-8 splicing complex.
Small ribosomal subunit protein uS3m, fungi
Small ribosomal subunit protein uS3m, called Var1 in yeast, is the mitochondrially encoded small-subunit mitoribosomal protein of fungi and plants. It forms the mRNA entry channel with uS4 and uS5, has ~30% asparagine from AT-rich mtDNA, and is lost in the yeast CTG clade.
Sof1-like protein
Sof1-like protein (IPR007287, Pfam PF04158) is a conserved eukaryotic protein domain named after yeast SOF1, an essential nucleolar U3 snoRNA-associated factor required for 40S ribosomal subunit biogenesis; orthologs include human DCAF13, distinct from mouse sperm SOF1.
Splice site mutation
Splice site mutation: a DNA change disrupting spliceosome recognition of exon-intron boundaries (GT donor, AG acceptor dinucleotides), causing exon skipping, intron retention, or cryptic site use; a major cause of genetic disease, targetable by splice-switching antisense oligonucleotides.
Splice-site recognition and consensus sequences
Splice-site recognition is how the spliceosome locates the short motifs marking where an intron begins and ends; in mammals, consensus sequences are too loose to specify splicing alone.
Spliceosome
Spliceosome: nuclear RNA-protein machine (U1, U2, U4, U5, U6 snRNPs plus ~150 proteins) that removes introns from pre-mRNA via two transesterifications; a parallel minor spliceosome (U11, U12, U4atac, U6atac, shared U5) splices ~0.5% of introns.
Spliceosome assembly pathway
The spliceosome assembly pathway is the ordered sequence of complexes through which the spliceosome forms on pre-mRNA, spanning at least 10 states from E to the intron-lariat spliceosome.
Splicing analysis methods and resources
Splicing analysis methods and resources are the computational tools for detecting and quantifying alternative splicing in RNA-seq, spanning event-level callers like rMATS and long-read isoform tools like IsoQuant.
Splicing factor U2AF
U2AF (U2AF65/U2AF35 heterodimer, U2AF2/U2AF1) is the essential splicing factor that binds the polypyrimidine tract and 3' splice site AG to define 3' splice sites and recruit U2 snRNP.
SRSF1
SRSF1, also called ASF/SF2 or SRp30a, is the founding human SR splicing factor: a 248-aa RRM/RS-domain protein binding exonic splicing enhancers, regulated by SRPK1/CLK1 phosphorylation, with roles in mRNA export, translation, and cancer.
SRSF3
SRSF3 (SRp20, SFRS3), the smallest of the 12 human SR splicing factors, is a 164-aa RNA-binding protein on chromosome 6p21.31 that regulates splicing, export, and translation, is essential for development, and is dysregulated in cancer.
Staufen (protein)
Staufen (Stau1/Stau2) is a family of double-stranded RNA-binding proteins, first found in Drosophila localizing bicoid and oskar mRNAs, that transport and regulate mRNAs in dendrites, control synaptic plasticity, and modify neurodegeneration via mTOR and autophagy.
Staufen proteins
Staufen proteins are a conserved family of double-stranded RNA-binding proteins, first identified in Drosophila, that localize mRNAs and, in mammals, direct bound transcripts into Staufen-mediated decay.
Staufen-mediated decay
Staufen-mediated decay (SMD), or STAU1-mediated mRNA decay, is a mammalian mRNA degradation pathway triggered when Staufen1 or Staufen2 binds double-stranded RNA sites in 3'-UTRs and recruits UPF1, competing with nonsense-mediated mRNA decay and regulating differentiation.
Sup35p
Sup35p (SUP35, eRF3) is the essential yeast translation termination factor whose self-propagating amyloid prion state is the non-Mendelian element [PSI+], causing stop-codon readthrough; domains N, M, C; Hsp104-dependent propagation.
SWI5-dependent HO expression protein 3
She3p (SWI5-dependent HO expression protein 3) is a cytoplasmic adaptor protein in budding yeast. It forms a transport complex to carry transcripts into the growing bud.
T-box leader
T-box leader (Rfam RF00230) is a bacterial riboswitch RNA in 5' leaders of amino acid genes that binds uncharged cognate tRNA at a specifier sequence and antiterminator bulge, senses aminoacylation sterically, and controls transcription or translation, mainly in Firmicutes.
Thiolation of wobble uridine in tRNA
Thiolation of wobble uridine in tRNA is the enzymatic replacement of uridine 34's oxygen with sulfur, forming 2-thiouridine in tRNAs for glutamate, glutamine, and lysine.
Three prime untranslated region
The 3′ UTR (three prime untranslated region) is the noncoding mRNA segment after the stop codon, carrying microRNA and RNA-binding protein sites that control mRNA stability, translation, and localization, and diversified by alternative polyadenylation.
TRAMP complex
TRAMP (Trf4/5-Air1/2-Mtr4 polyadenylation complex) is a yeast nuclear complex of a poly(A) polymerase, zinc-knuckle protein, and Mtr4 helicase that oligoadenylates aberrant RNAs for exosome degradation; homologs exist in humans.
Trans-splicing
Trans-splicing joins exons from separate pre-mRNA molecules into one mature mRNA, unlike cis-splicing. Known as spliced leader trans-splicing in trypanosomes and nematodes, rare in humans, and used therapeutically via SMaRT and split inteins.