Search our database by keyword

- or -

Examples

  • Search this entire website. Enter identifiers, names or keywords for genes, pathways, authors, ontology terms, etc. (e.g. eve, embryo, zen, allele)
  • Use OR to search for either of two terms (e.g. fly OR drosophila) or quotation marks to search for phrases (e.g. "dna binding").
  • Boolean search syntax is supported: e.g. dros* for partial matches or fly AND NOT embryo to exclude a term

Search results 501 to 600 out of 2386 for *

Category restricted to SOTerm (x)

<< First    < Previous  |  Next >    Last >>
0.009s

Categories

Category: SOTerm
« show all
Type Details Score
SO Term
SO:0000378 | DsrA_RNA
Description: DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
•
•
•
•
•
SO Term
SO:0000379 | GcvB_RNA
Description: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
•
•
•
•
•
SO Term
SO:0000380 | hammerhead_ribozyme
Description: A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
•
•
•
•
•
SO Term
SO:0000603 | group_II_intron
Description: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
•
•
•
•
•
SO Term
SO:0000381 | group_IIA_intron
Description: A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon.
•
•
•
•
•
SO Term
SO:0000588 | autocatalytically_spliced_intron
Description: A self spliced intron.
•
•
•
•
•
SO Term
SO:0000382 | group_IIB_intron
Description: A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon.
•
•
•
•
•
SO Term
SO:0000644 | antisense_RNA
Description: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
•
•
•
•
•
SO Term
SO:0000383 | MicF_RNA
Description: A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
•
•
•
•
•
SO Term
SO:0000645 | antisense_primary_transcript
Description: The reverse complement of the primary transcript.
•
•
•
•
•
SO Term
SO:0000384 | OxyS_RNA
Description: A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
•
•
•
•
•
SO Term
SO:0000385 | RNase_MRP_RNA
Description: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
•
•
•
•
•
SO Term
SO:0000386 | RNase_P_RNA
Description: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
•
•
•
•
•
SO Term
SO:0000387 | RprA_RNA
Description: Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
•
•
•
•
•
SO Term
SO:0000388 | RRE_RNA
Description: The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
•
•
•
•
•
SO Term
SO:0000389 | spot_42_RNA
Description: A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
•
•
•
•
•
SO Term
SO:0000390 | telomerase_RNA
Description: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
•
•
•
•
•
SO Term
SO:0000391 | U1_snRNA
Description: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
•
•
•
•
•
SO Term
SO:0000392 | U2_snRNA
Description: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
•
•
•
•
•
SO Term
SO:0000393 | U4_snRNA
Description: 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.
•
•
•
•
•
SO Term
SO:0000394 | U4atac_snRNA
Description: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
•
•
•
•
•
SO Term
SO:0000395 | U5_snRNA
Description: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
•
•
•
•
•
SO Term
SO:0000396 | U6_snRNA
Description: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
•
•
•
•
•
SO Term
SO:0000397 | U6atac_snRNA
Description: U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
•
•
•
•
•
SO Term
SO:0000398 | U11_snRNA
Description: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
•
•
•
•
•
SO Term
SO:0000399 | U12_snRNA
Description: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
•
•
•
•
•
SO Term
SO:0005837 | U14_snoRNA_primary_transcript
Description: The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
•
•
•
•
•
SO Term
SO:0000403 | U14_snoRNA
Description: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
•
•
•
•
•
SO Term
SO:0000593 | C_D_box_snoRNA
Description: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
•
•
•
•
•
SO Term
SO:0000595 | C_D_box_snoRNA_primary_transcript
Description: A primary transcript encoding a small nucleolar RNA of the box C/D family.
•
•
•
•
•
SO Term
SO:0000404 | vault_RNA
Description: A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
•
•
•
•
•
SO Term
SO:0000405 | Y_RNA
Description: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
•
•
•
•
•
SO Term
SO:0000406 | twintron
Description: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
•
•
•
•
•
SO Term
SO:0000650 | cytosolic_SSU_rRNA
Description: Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.
•
•
•
•
•
SO Term
SO:0000407 | cytosolic_18S_rRNA
Description: Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.
•
•
•
•
•
SO Term
SO:0000411 | rescue_region
Description: A region that rescues.
•
•
•
•
•
SO Term
SO:0000814 | rescue
Description: An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
•
•
•
•
•
SO Term
SO:0000700 | remark
Description: A comment about the sequence.
•
•
•
•
•
SO Term
SO:0000413 | sequence_difference
Description: A region where the sequence differs from that of a specified sequence.
•
•
•
•
•
SO Term
SO:0000414 | invalidated_by_genomic_contamination
Description: An attribute to describe a feature that is invalidated due to genomic contamination.
•
•
•
•
•
SO Term
SO:0000415 | invalidated_by_genomic_polyA_primed_cDNA
Description: An attribute to describe a feature that is invalidated due to polyA priming.
•
•
•
•
•
SO Term
SO:0000416 | invalidated_by_partial_processing
Description: An attribute to describe a feature that is invalidated due to partial processing.
•
•
•
•
•
SO Term
SO:0001070 | polypeptide_structural_region
Description: Region of polypeptide with a given structural property.
•
•
•
•
•
SO Term
SO:0000417 | polypeptide_domain
Description: A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
•
•
•
•
•
SO Term
SO:0100021 | polypeptide_conserved_region
Description: A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
•
•
•
•
•
SO Term
SO:0000839 | polypeptide_region
Description: Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
•
•
•
•
•
SO Term
SO:0001062 | propeptide
Description: Part of a peptide chain which is cleaved off during the formation of the mature protein.
•
•
•
•
•
SO Term
SO:0000418 | signal_peptide
Description: The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
•
•
•
•
•
SO Term
SO:0002251 | signal_peptide_region_of_CDS
Description: A CDS region corresponding to a signal peptide of a polypeptide.
•
•
•
•
•
SO Term
SO:0001527 | peptide_localization_signal
Description: A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
•
•
•
•
•
SO Term
SO:0100011 | cleaved_peptide_region
Description: The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
•
•
•
•
•
SO Term
SO:0001063 | immature_peptide_region
Description: An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
•
•
•
•
•
SO Term
SO:0002249 | mature_protein_region_of_CDS
Description: A CDS region corresponding to a mature protein region of a polypeptide.
•
•
•
•
•
SO Term
SO:0000419 | mature_protein_region
Description: The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
•
•
•
•
•
SO Term
SO:0000481 | terminal_inverted_repeat
Description: An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
•
•
•
•
•
SO Term
SO:0000420 | five_prime_terminal_inverted_repeat
Description: An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon.
•
•
•
•
•
SO Term
SO:0000421 | three_prime_terminal_inverted_repeat
Description: An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon.
•
•
•
•
•
SO Term
SO:0000848 | LTR_component
Description: The long terminal repeat found at the ends of the sequence to be inserted into the host genome.
•
•
•
•
•
SO Term
SO:0000422 | U5_LTR_region
Description: The U5 segment of the long terminal repeats.
•
•
•
•
•
SO Term
SO:0000840 | repeat_component
Description: A region of a repeated sequence.
•
•
•
•
•
SO Term
SO:0000423 | R_LTR_region
Description: The R segment of the long terminal repeats.
•
•
•
•
•
SO Term
SO:0000424 | U3_LTR_region
Description: The U3 segment of the long terminal repeats.
•
•
•
•
•
SO Term
SO:0000425 | five_prime_LTR
Description: The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome.
•
•
•
•
•
SO Term
SO:0000426 | three_prime_LTR
Description: The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome.
•
•
•
•
•
SO Term
SO:0000850 | five_prime_LTR_component
Description: A component of the five-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000427 | R_five_prime_LTR_region
Description: The R segment of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000428 | U5_five_prime_LTR_region
Description: The U5 segment of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000429 | U3_five_prime_LTR_region
Description: The U3 segment of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000849 | three_prime_LTR_component
Description: A component of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000430 | R_three_prime_LTR_region
Description: The R segment of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000431 | U3_three_prime_LTR_region
Description: The U3 segment of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000432 | U5_three_prime_LTR_region
Description: The U5 segment of the three-prime long terminal repeat.
•
•
•
•
•
SO Term
SO:0000433 | non_LTR_retrotransposon_polymeric_tract
Description: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
•
•
•
•
•
SO Term
SO:0000434 | target_site_duplication
Description: A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
•
•
•
•
•
SO Term
SO:0000435 | RR_tract
Description: A polypurine tract within an LTR_retrotransposon.
•
•
•
•
•
SO Term
SO:0000436 | ARS
Description: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
•
•
•
•
•
SO Term
SO:1000045 | ring_chromosome
Description: A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.
•
•
•
•
•
SO Term
SO:0000439 | inverted_ring_chromosome
Description: A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome.
•
•
•
•
•
SO Term
SO:1000030 | chromosomal_inversion
Description: An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.
•
•
•
•
•
SO Term
SO:0000988 | circular
Description: A quality of a nucleotide polymer that has no terminal nucleotide residues.
•
•
•
•
•
SO Term
SO:0000986 | topology_attribute
Description: The attribute of whether a nucleotide polymer is linear or circular.
•
•
•
•
•
SO Term
SO:0000444 | three_prime_noncoding_exon
Description: Non-coding exon in the 3' UTR.
•
•
•
•
•
SO Term
SO:0000445 | five_prime_noncoding_exon
Description: Non-coding exon in the 5' UTR.
•
•
•
•
•
SO Term
SO:0000446 | UTR_intron
Description: Intron located in the untranslated region.
•
•
•
•
•
SO Term
SO:0000447 | five_prime_UTR_intron
Description: An intron located in the 5' UTR.
•
•
•
•
•
SO Term
SO:0000448 | three_prime_UTR_intron
Description: An intron located in the 3' UTR.
•
•
•
•
•
SO Term
SO:0000449 | random_sequence
Description: A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.
•
•
•
•
•
SO Term
SO:0000450 | interband
Description: A light region between two darkly staining bands in a polytene chromosome.
•
•
•
•
•
SO Term
SO:0001217 | protein_coding_gene
Description: A gene that codes for an RNA that can be translated into a protein.
•
•
•
•
•
SO Term
SO:0000451 | gene_with_polyadenylated_mRNA
Description: A gene that encodes a polyadenylated mRNA.
•
•
•
•
•
SO Term
SO:0000871 | polyadenylated_mRNA
Description: An mRNA that is polyadenylated.
•
•
•
•
•
SO Term
SO:0000454 | rasiRNA
Description: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
•
•
•
•
•
SO Term
SO:0000455 | gene_with_mRNA_with_frameshift
Description: A gene that encodes an mRNA with a frameshift.
•
•
•
•
•
SO Term
SO:0000457 | interchromosomal_duplication
Description: A chromosome duplication involving an insertion from another chromosome.
•
•
•
•
•
SO Term
SO:0000460 | vertebrate_immunoglobulin_T_cell_receptor_segment
Description: Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor.
•
•
•
•
•
SO Term
SO:0000458 | D_gene_segment
Description: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
•
•
•
•
•
SO Term
SO:0000479 | trans_spliced_transcript
Description: A transcript that is trans-spliced.
•
•
•
•
•
SO Term
SO:0000459 | gene_with_trans_spliced_transcript
Description: A gene with a transcript that is trans-spliced.
•
•
•
•
•
SO Term
SO:0000461 | inversion_derived_bipartite_deficiency
Description: A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
•
•
•
•
•
SO Term
SO:0000462 | pseudogenic_region
Description: A non-functional descendant of a functional entity.
•
•
•
•
•
USDA
InterMine logo
The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
LegumeMine || ArachisMine | CicerMine | GlycineMine | LensMine | LupinusMine | PhaseolusMine | VignaMine | MedicagoMine
InterMine © 2002 - 2022 Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom