GlycineMine: Keyword Search

SO Term

Description:

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.

•

SO Term

SO:0000234 | mRNA

Description:

Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.

•

SO Term

SO:0000340 | chromosome

Description:

Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.

•

SO Term

SO:0000851 | CDS_region

Description:

A region of a CDS.

•

SO Term

SO:0000147 | exon

Description:

A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.

•

SO Term

SO:0000316 | CDS

Description:

A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.

•

SO Term

SO:0000148 | supercontig

Description:

One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.

•

SO Term

SO:0000204 | five_prime_UTR

Description:

A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.

•

SO Term

SO:0000205 | three_prime_UTR

Description:

A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.

•

SO Term

SO:0000253 | tRNA

Description:

Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.

•

SO Term

SO:0000336 | pseudogene

Description:

A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).

•

SO Term

SO:0000252 | rRNA

Description:

rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.

•

SO Term

SO:0000275 | snoRNA

Description:

A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.

•

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:0001244) 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.

•

SO Term

SO:0000274 | snRNA

Description:

A small nuclear RNA molecule involved in pre-mRNA splicing and processing.

•

SO Term

SO:0000110 | sequence_feature

Description:

Any extent of continuous biological sequence.

•

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.

•

SO Term

SO:0001411 | biological_region

Description:

A region defined by its disposition to be involved in a biological process.

•

SO Term

SO:0000002 | sequence_secondary_structure

Description:

A folded sequence.

•

SO Term

SO:0000003 | G_quartet

Description:

G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.

•

SO Term

SO:0000195 | coding_exon

Description:

An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).

•

SO Term

SO:0000004 | interior_coding_exon

Description:

A coding exon that is not the most 3-prime or the most 5-prime in a given transcript.

•

SO Term

SO:0000673 | transcript

Description:

An RNA synthesized on a DNA or RNA template by an RNA polymerase.

•

SO Term

SO:0000833 | transcript_region

Description:

A region of a transcript.

•

SO Term

SO:0005855 | gene_group

Description:

A collection of related genes.

•

SO Term

SO:0000831 | gene_member_region

Description:

A region of a gene.

•

SO Term

SO:0000705 | tandem_repeat

Description:

Two or more adjacent copies of a region (of length greater than 1).

•

SO Term

SO:0000005 | satellite_DNA

Description:

The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.

•

SO Term

SO:0000726 | repeat_unit

Description:

The simplest repeated component of a repeat region. A single repeat.

•

SO Term

SO:0000657 | repeat_region

Description:

A region of sequence containing one or more repeat units.

•

SO Term

SO:0000695 | reagent

Description:

A sequence used in experiment.

•

SO Term

SO:0000006 | PCR_product

Description:

A region amplified by a PCR reaction.

•

SO Term

SO:0001409 | biomaterial_region

Description:

A region which is intended for use in an experiment.

•

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.

•

SO Term

SO:0000007 | read_pair

Description:

One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.

•

SO Term

SO:0000149 | contig

Description:

A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.

•

SO Term

SO:0001790 | paired_end_fragment

Description:

An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).

•

SO Term

SO:0000143 | assembly_component

Description:

A region of known length which may be used to manufacture a longer region.

•

SO Term

SO:0000719 | ultracontig

Description:

An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.

•

SO Term

SO:0001410 | experimental_feature

Description:

A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.

•

SO Term

SO:0001876 | partial_genomic_sequence_assembly

Description:

A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's.

•

SO Term

SO:0001248 | assembly

Description:

A region of the genome of known length that is composed by ordering and aligning two or more different regions.

•

SO Term

SO:0000353 | sequence_assembly

Description:

A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.

•

SO Term

SO:0000401 | gene_attribute

Description:

An attribute describing a gene.

•

SO Term

SO:0000010 | protein_coding

Description:

A gene which, when transcribed, can be translated into a protein.

•

SO Term

SO:0000733 | feature_attribute

Description:

An attribute describing a located_sequence_feature.

•

SO Term

SO:0000400 | sequence_attribute

Description:

An attribute describes a quality of sequence.

•

SO Term

SO:0000011 | non_protein_coding

Description:

A gene which can be transcribed, but will not be translated into a protein.

•

SO Term

SO:0000483 | nc_primary_transcript

Description:

A primary transcript that is never translated into a protein.

•

SO Term

SO:0000012 | scRNA_primary_transcript

Description:

The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.

•

SO Term

SO:0002300 | unit_of_gene_expression

Description:

Transcription units or transcribed coding sequences.

•

SO Term

SO:0000185 | primary_transcript

Description:

A transcript that in its initial state requires modification to be functional.

•

SO Term

SO:0000655 | ncRNA

Description:

An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

•

SO Term

SO:0000013 | scRNA

Description:

A small non coding RNA sequence, present in the cytoplasm.

•

SO Term

SO:0000233 | mature_transcript

Description:

A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.

•

SO Term

SO:0001669 | RNApol_II_core_promoter

Description:

The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.

•

SO Term

SO:0000014 | INR_motif

Description:

A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.

•

SO Term

SO:0001660 | core_eukaryotic_promoter_element

Description:

An element that only exists within the promoter region of a eukaryotic gene.

•

SO Term

SO:0001654 | nucleotide_to_protein_binding_site

Description:

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

•

SO Term

SO:0005836 | regulatory_region

Description:

A region of sequence that is involved in the control of a biological process.

•

SO Term

SO:0001055 | transcriptional_cis_regulatory_region

Description:

A regulatory_region that modulates the transcription of a gene or genes.

•

SO Term

SO:0001683 | sequence_motif

Description:

A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.

•

SO Term

SO:0000842 | gene_component_region

Description:

A region of a gene that has a specific function.

•

SO Term

SO:0000167 | promoter

Description:

A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.

•

SO Term

SO:0002221 | eukaryotic_promoter

Description:

A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions.

•

SO Term

SO:0002309 | core_promoter_element

Description:

An element that always exists within the promoter region of a gene. When multiple transcripts exist for a gene, the separate transcripts may have separate core_promoter_elements.

•

SO Term

SO:0001659 | promoter_element

Description:

An element that can exist within the promoter region of a gene.

•

SO Term

SO:0000235 | TF_binding_site

Description:

A DNA site where a transcription factor binds.

•

SO Term

SO:0000410 | protein_binding_site

Description:

A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.

•

SO Term

SO:0000409 | binding_site

Description:

A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.

•

SO Term

SO:0000170 | RNApol_II_promoter

Description:

A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.

•

SO Term

SO:0000713 | DNA_motif

Description:

A motif that is active in the DNA form of the sequence.

•

SO Term

SO:0000714 | nucleotide_motif

Description:

A region of nucleotide sequence corresponding to a known motif.

•

SO Term

SO:0000015 | DPE_motif

Description:

A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).

•

SO Term

SO:0000016 | BREu_motif

Description:

A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.

•

SO Term

SO:0000017 | PSE_motif

Description:

A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes.

•

SO Term

SO:0000018 | linkage_group

Description:

A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.

•

SO Term

SO:0000715 | RNA_motif

Description:

A motif that is active in RNA sequence.

•

SO Term

SO:0000020 | RNA_internal_loop

Description:

A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.

•

SO Term

SO:0000021 | asymmetric_RNA_internal_loop

Description:

An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.

•

SO Term

SO:0000022 | A_minor_RNA_motif

Description:

A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.

•

SO Term

SO:0000023 | K_turn_RNA_motif

Description:

The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.

•

SO Term

SO:0000024 | sarcin_like_RNA_motif

Description:

A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.

•

SO Term

SO:0000025 | symmetric_RNA_internal_loop

Description:

An internal RNA loop where the extent of the loop on both stands is the same size.

•

SO Term

SO:0000026 | RNA_junction_loop

•

SO Term

SO:0000027 | RNA_hook_turn

•

SO Term

SO:0000028 | base_pair

Description:

Two bases paired opposite each other by hydrogen bonds creating a secondary structure.

•

SO Term

SO:0000029 | WC_base_pair

Description:

The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.

•

SO Term

SO:0000030 | sugar_edge_base_pair

Description:

A type of non-canonical base-pairing.

•

SO Term

SO:0000696 | oligo

Description:

A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.

•

SO Term

SO:0000031 | aptamer

Description:

DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.

•

SO Term

SO:0000032 | DNA_aptamer

Description:

DNA molecules that have been selected from random pools based on their ability to bind other molecules.

•

SO Term

SO:0000033 | RNA_aptamer

Description:

RNA molecules that have been selected from random pools based on their ability to bind other molecules.

•

SO Term

SO:0001247 | synthetic_oligo

Description:

An oligo composed of synthetic nucleotides.

•

SO Term

SO:0000034 | morpholino_oligo

Description:

Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.

•

SO Term

SO:0001183 | morpholino_backbone

Description:

An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.

•

SO Term

SO:0000348 | nucleic_acid

Description:

An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.

•

SO Term

SO:0000443 | polymer_attribute

Description:

An attribute to describe the kind of biological sequence.

•

SO Term

SO:0000035 | riboswitch

Description:

A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.

•

SO Term

SO:0000836 | mRNA_region

Description:

A region of an mRNA.

•

Your name:
Your email address:
Subject:
Message:	---- Current page: ---- /glycinemine/keywordSearchResults.do;jsessionid=35FE62C740E73EFEAAF0742F38987F1E?facet_Category=SOTerm&searchTerm=%2A

GlycineMine

Search our database by keyword

Examples

Search results 1 to 100 out of 2386 for *

Category restricted to SOTerm

Categories