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16S ribosomal RNA
16S ribosomal RNA, the ~1,500-nucleotide small-subunit rRNA of prokaryotic ribosomes, is the standard molecular marker for bacterial and archaeal identification, phylogeny, and microbiome profiling.
18S ribosomal RNA
18S ribosomal RNA: the small-subunit rRNA of eukaryotic 40S ribosomes, homologous to bacterial 16S rRNA, about 1.8-2.0 kb, central to translation initiation, eukaryotic phylogeny, and metabarcoding.
28S ribosomal RNA
28S rRNA is the large-subunit ribosomal RNA of the eukaryotic 60S ribosome, transcribed from a 45S precursor with 18S and 5.8S rRNA, expanded by eukaryote-specific expansion segments, and widely used as a phylogenetic marker and RNA quality indicator.
3' rapid amplification of cDNA ends
3' rapid amplification of cDNA ends (3' RACE) is a PCR method that maps a transcript's 3' end and polyadenylation site, using one gene-specific primer and the poly(A) tail.
3'-RNA ribose 2'-O-methyltransferase, Hen1
Hen1 (HUA Enhancer 1), InterPro IPR026610, is a conserved SAM-dependent methyltransferase adding a 2'-O-methyl to the 3' terminal ribose of small RNAs, stabilizing plant miRNA/siRNA duplexes and animal piRNAs; loss causes uridylation, decay, and germline defects.
43S preinitiation complex
The 43S preinitiation complex (43S PIC) is the assembly of eukaryotic initiation factors and initiator tRNA that forms on the 40S ribosomal subunit before mRNA binding.
5-(Hydroxymethyl)cytosine
5-(Hydroxymethyl)cytosine (5hmC) is a modified DNA base, often called the "sixth base," produced by TET enzymes and especially abundant in the brain and embryonic stem cells.
5-Methylcytosine
5-Methylcytosine (5mC) is cytosine with a methyl group attached, the principal covalent DNA modification in animals, plants, and bacteria that regulates gene expression and is used in cancer screening tests.
5.8S ribosomal RNA
5.8S ribosomal RNA: ~150-160 nt structural RNA of the eukaryotic 60S large subunit, hydrogen-bonded to 28S rRNA, cleaved from the 47S/35S Pol I pre-rRNA between ITS1 and ITS2; distinct from 5S rRNA and homologous to bacterial 23S rRNA's 5' end.
5' Flanking Region
5' flanking region, also called 5' flanking sequence: DNA upstream of a gene's transcription start site, outside the 5' UTR, holding promoters, enhancers, and transcription factor binding sites that regulate transcription.
5S ribosomal RNA
5S ribosomal RNA (5S rRNA) is a ~120-nt ribosomal RNA of the large ribosomal subunit's central protuberance, binding L5, L18, and L25 in bacteria and only L5 in eukaryotes; its exact function remains unknown.
ABC_AB protein, Emaravirus
The ABC_AB protein, Pfam family PF21707, is an 18 to 27 kDa pathogenicity protein encoded by almost all emaraviruses of clades A, B, and C; some act as RNA silencing suppressors.
AbrB family
AbrB family (InterPro IPR007820): bacterial transition state regulators exemplified by Bacillus subtilis AbrB, a 94-residue dimeric DNA-binding repressor-activator with a novel looped-hinge helix fold; homolog Abh regulates biofilm formation.
ADAR
ADAR (adenosine deaminase acting on RNA) family enzymes catalyze A-to-I editing of double-stranded RNA; mammalian ADAR1 (p150/p110) and ADAR2 are active, ADAR3 is not, and ADAR1 suppresses MDA5 innate immune sensing.
Alternative splicing
Alternative splicing, also called differential splicing, is a process in which a single gene produces multiple proteins by joining its RNA exons in different combinations.
Amanitin
Amanitin is a bicyclic octapeptide toxin from deadly Amanita mushrooms such as the death cap; it blocks RNA polymerase II and causes fatal liver failure.
Amino acid activation
Amino acid activation: ATP-dependent two-step reaction by aminoacyl-tRNA synthetases forming an aminoacyl-adenylate, then charging tRNA's 3' end with a high-energy ester bond for translation.
Aminoacyl tRNA synthetase
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that charge tRNAs with amino acids in a two-step ATP-dependent reaction. Two unrelated classes (I Rossmann fold, II antiparallel beta-sheet) cover the 20 amino acids, with editing domains ensuring fidelity and moonlighting roles in disease.
Aminoacyl-tRNA
Aminoacyl-tRNA (charged tRNA): a transfer RNA ester-linked to its matching amino acid at the 3' end, made by aminoacyl-tRNA synthetases in a two-step ATP reaction, class I charging 2'-OH and class II 3'-OH, with editing for fidelity.
AmiR, N-terminal
AmiR, N-terminal is the pseudo-receiver domain (residues 1–128) of AmiR, whose C-terminal ANTAR domain binds leader RNA to activate the amidase operon of Pseudomonas aeruginosa.
Anaerobic nitric oxide reductase transcription regulator
NorR (anaerobic nitric oxide reductase transcription regulator, gene norR) is a sigma-54-dependent bacterial enhancer-binding protein that senses NO via a non-haem iron center and activates the norVW NO-detoxification operon in E. coli and other proteobacteria.
Anti-sigma factors
Anti-sigma factors are bacterial proteins that bind and inhibit sigma factors, blocking RNA polymerase holoenzyme formation. Classes include cytoplasmic (FlgM, SpoIIAB, DnaK) and membrane-bound ECF anti-σ factors (RseA), released by proteolysis, partner-switching, or direct sensing.
Anticodon-binding
Anticodon-binding: recognition of the tRNA anticodon by protein domains, chiefly the anticodon-binding domains (ABD, IPR004154, HGTP_anticodon, DALR) of aminoacyl-tRNA synthetases, which determine tRNA identity, enhance kcat, and arose about 3 billion years ago.
Antinuclear antibody
Antinuclear antibodies (ANAs) are autoantibodies against nuclear components, detected by HEp-2 indirect immunofluorescence or solid-phase assays; positive in 95-100% of SLE but also in about 5% of healthy adults.
Antisense lncRNAs in neurodegeneration
Antisense lncRNAs in neurodegeneration are regulatory RNAs transcribed opposite coding genes, prominent in the brain, with BACE1-AS elevated up to 6-fold in Alzheimer's brain and linked to tauopathies.
Antisense RNA
Antisense RNA (natural antisense transcript, NAT): RNA transcribed opposite a gene, in cis or trans, regulating sense gene expression via transcriptional interference, epigenetic modification, RNA pairing, and endo-siRNAs; basis of ASO drugs.
Antisynthetase syndrome
Antisynthetase syndrome (ASSD, ASyS) is a rare autoimmune disease defined by anti-aminoacyl-tRNA synthetase antibodies, especially anti-Jo-1, with interstitial lung disease, myositis, arthritis, Raynaud's phenomenon, mechanic's hands, and fever.
AP-1 transcription factor
AP-1 (activator protein 1) is a dimeric transcription factor complex of Jun, Fos, ATF, and MAF bZIP proteins that binds TRE/CRE DNA sites, regulating proliferation, inflammation, memory, and cancer; no direct inhibitor is approved, though T-5224 reached phase II.
AP2/ERF transcription factor family
AP2/ERF transcription factors, also called APETALA2/ethylene responsive factors, are plant-specific regulators with a conserved ~60-70 amino acid AP2 DNA-binding domain, divided into AP2, ERF, DREB, RAV, and Soloist subfamilies that control stress tolerance, hormone signaling, and development.
ARB Project
ARB is a graphical software environment for maintaining, aligning, and phylogenetically analyzing sequence data, developed at the Technical University of Munich and widely used for ribosomal RNA.