ThaleMine: Keyword Search

SO Term

Description:

7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.

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SO Term

SO:0001173 | anticodon_loop

Description:

A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.

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SO Term

SO:0001460 | insulator_binding_site

Description:

A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.

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SO Term

SO:0001461 | enhancer_binding_site

Description:

A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.

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SO Term

SO:0000199 | translocation

Description:

A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.

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SO Term

SO:0000563 | vertebrate_immune_system_gene_recombination_spacer

Description:

A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase.

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SO Term

SO:0001111 | beta_strand

Description:

A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.

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SO Term

SO:0000322 | nuclease_hypersensitive_site

Description:

A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance.

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SO Term

SO:0000561 | heptamer_of_recombination_feature_of_vertebrate_immune_system_gene

Description:

Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.

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SO Term

SO:0000517 | J_spacer

Description:

12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.

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SO Term

SO:0000537 | V_spacer

Description:

12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.

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SO Term

SO:0000150 | read

Description:

A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.

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SO Term

SO:0001058 | promoter_targeting_sequence

Description:

A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.

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SO Term

SO:0001485 | Y_prime_element

Description:

A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.

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SO Term

SO:0001244 | pre_miRNA

Description:

The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.

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SO Term

SO:0001525 | assembly_error_correction

Description:

A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.

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SO Term

SO:0001500 | heritable_phenotypic_marker

Description:

A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.

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SO Term

SO:0000146 | capped

Description:

An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.

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SO Term

SO:0002165 | trinucleotide_repeat_expansion

Description:

A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence.

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SO Term

SO:0000001 | region

Description:

A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.

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SO Term

SO:0001037 | mobile_genetic_element

Description:

A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.

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SO Term

SO:0000498 | five_prime_D_spacer

Description:

12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.

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SO Term

SO:0001526 | base_call_error_correction

Description:

A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.

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SO Term

SO:0001687 | restriction_enzyme_recognition_site

Description:

The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.

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SO Term

SO:0000581 | cap

Description:

A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.

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SO Term

SO:0001520 | translocaton_attribute

Description:

An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.

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SO Term

SO:0000351 | synthetic_sequence

Description:

An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.

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SO Term

SO:0000360 | codon

Description:

A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.

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SO Term

SO:0000453 | chromosomal_transposition

Description:

A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.

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SO Term

SO:0000297 | D_loop

Description:

Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.

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SO Term

SO:0000772 | genomic_island

Description:

A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.

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SO Term

SO:0000276 | miRNA

Description:

Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.

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SO Term

SO:0000727 | CRM

Description:

A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.

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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.

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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'.

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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.

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