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Search results 1101 to 1200 out of 2386 for *

Category restricted to SOTerm (x)

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Categories

Category: SOTerm
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Type Details Score
SO Term
SO:0001130 | asx_turn_left_handed_type_two
Description: Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
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SO Term
SO:0001131 | asx_turn_right_handed_type_two
Description: Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
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SO Term
SO:0001132 | asx_turn_right_handed_type_one
Description: Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
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SO Term
SO:0001133 | beta_turn
Description: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
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SO Term
SO:0001134 | beta_turn_left_handed_type_one
Description: Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
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SO Term
SO:0001135 | beta_turn_left_handed_type_two
Description: Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
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SO Term
SO:0001136 | beta_turn_right_handed_type_one
Description: Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
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SO Term
SO:0001137 | beta_turn_right_handed_type_two
Description: Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
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SO Term
SO:0001138 | gamma_turn
Description: Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
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SO Term
SO:0001139 | gamma_turn_classic
Description: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
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SO Term
SO:0001140 | gamma_turn_inverse
Description: Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
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SO Term
SO:0001141 | serine_threonine_turn
Description: A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
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SO Term
SO:0001142 | st_turn_left_handed_type_one
Description: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
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SO Term
SO:0001143 | st_turn_left_handed_type_two
Description: The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
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SO Term
SO:0001144 | st_turn_right_handed_type_one
Description: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
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SO Term
SO:0001145 | st_turn_right_handed_type_two
Description: The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
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SO Term
SO:0001146 | polypeptide_variation_site
Description: A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.
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SO Term
SO:0001147 | natural_variant_site
Description: Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
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SO Term
SO:0001148 | mutated_variant_site
Description: Site which has been experimentally altered.
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SO Term
SO:0001149 | alternate_sequence_site
Description: Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
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SO Term
SO:0001150 | beta_turn_type_six
Description: A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
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SO Term
SO:0001151 | beta_turn_type_six_a
Description: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
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SO Term
SO:0001152 | beta_turn_type_six_a_one
Description: A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees.
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SO Term
SO:0001153 | beta_turn_type_six_a_two
Description: A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees.
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SO Term
SO:0001154 | beta_turn_type_six_b
Description: A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
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SO Term
SO:0001155 | beta_turn_type_eight
Description: A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
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SO Term
SO:0001156 | DRE_motif
Description: A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
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SO Term
SO:0001157 | DMv4_motif
Description: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
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SO Term
SO:0001158 | E_box_motif
Description: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
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SO Term
SO:0001159 | DMv5_motif
Description: A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
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SO Term
SO:0001160 | DMv3_motif
Description: A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
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SO Term
SO:0001161 | DMv2_motif
Description: A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
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SO Term
SO:0001162 | MTE
Description: A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
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SO Term
SO:0001163 | INR1_motif
Description: A promoter motif with consensus sequence TCATTCG.
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SO Term
SO:0001164 | DPE1_motif
Description: A promoter motif with consensus sequence CGGACGT.
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SO Term
SO:0001165 | DMv1_motif
Description: A promoter motif with consensus sequence CARCCCT.
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SO Term
SO:0001166 | GAGA_motif
Description: A non directional promoter motif with consensus sequence GAGAGCG.
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SO Term
SO:0001167 | NDM2_motif
Description: A non directional promoter motif with consensus CGMYGYCR.
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SO Term
SO:0001168 | NDM3_motif
Description: A non directional promoter motif with consensus sequence GAAAGCT.
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SO Term
SO:0001169 | ds_RNA_viral_sequence
Description: A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
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SO Term
SO:0001170 | polinton
Description: A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
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SO Term
SO:0001172 | tRNA_region
Description: A region of a tRNA.
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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:0001174 | anticodon
Description: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
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SO Term
SO:0001175 | CCA_tail
Description: Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
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SO Term
SO:0001176 | DHU_loop
Description: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
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SO Term
SO:0001177 | T_loop
Description: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
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SO Term
SO:0001179 | U3_snoRNA
Description: U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
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SO Term
SO:0001180 | AU_rich_element
Description: A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
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SO Term
SO:0001181 | Bruno_response_element
Description: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
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SO Term
SO:0001182 | iron_responsive_element
Description: A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
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SO Term
SO:0001187 | pseudouridylation_guide_snoRNA
Description: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
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SO Term
SO:0001188 | LNA
Description: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
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SO Term
SO:0001189 | LNA_oligo
Description: An oligo composed of LNA residues.
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SO Term
SO:0001190 | TNA
Description: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
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SO Term
SO:0001191 | TNA_oligo
Description: An oligo composed of TNA residues.
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SO Term
SO:0001192 | GNA
Description: An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
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SO Term
SO:0001193 | GNA_oligo
Description: An oligo composed of GNA residues.
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SO Term
SO:0001194 | R_GNA
Description: An attribute describing a GNA sequence in the (R)-GNA enantiomer.
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SO Term
SO:0001195 | R_GNA_oligo
Description: An oligo composed of (R)-GNA residues.
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SO Term
SO:0001196 | S_GNA
Description: An attribute describing a GNA sequence in the (S)-GNA enantiomer.
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SO Term
SO:0001197 | S_GNA_oligo
Description: An oligo composed of (S)-GNA residues.
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SO Term
SO:0001198 | ds_DNA_viral_sequence
Description: A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
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SO Term
SO:0001199 | ss_RNA_viral_sequence
Description: A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
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SO Term
SO:0001200 | negative_sense_ssRNA_viral_sequence
Description: A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
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SO Term
SO:0001201 | positive_sense_ssRNA_viral_sequence
Description: A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
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SO Term
SO:0001202 | ambisense_ssRNA_viral_sequence
Description: A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
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SO Term
SO:0002311 | viral_promoter
Description: A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses.
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SO Term
SO:0001204 | Phage_RNA_Polymerase_Promoter
Description: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
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SO Term
SO:0001205 | SP6_RNA_Polymerase_Promoter
Description: A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
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SO Term
SO:0001206 | T3_RNA_Polymerase_Promoter
Description: A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
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SO Term
SO:0001207 | T7_RNA_Polymerase_Promoter
Description: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
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SO Term
SO:0001208 | five_prime_EST
Description: An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
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SO Term
SO:0001209 | three_prime_EST
Description: An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
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SO Term
SO:0001210 | translational_frameshift
Description: The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
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SO Term
SO:0001211 | plus_1_translational_frameshift
Description: The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
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SO Term
SO:0001212 | plus_2_translational_frameshift
Description: The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
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SO Term
SO:0001213 | group_III_intron
Description: Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
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SO Term
SO:0001216 | endonuclease_spliced_intron
Description: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
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SO Term
SO:0001218 | transgenic_insertion
Description: An insertion that derives from another organism, via the use of recombinant DNA technology.
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SO Term
SO:0001219 | retrogene
Description: A gene that has been produced as the product of a reverse transcriptase mediated event.
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SO Term
SO:0001220 | silenced_by_RNA_interference
Description: An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
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SO Term
SO:0001221 | silenced_by_histone_modification
Description: An attribute describing an epigenetic process where a gene is inactivated by histone modification.
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SO Term
SO:0001222 | silenced_by_histone_methylation
Description: An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
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SO Term
SO:0001223 | silenced_by_histone_deacetylation
Description: An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
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SO Term
SO:0001224 | gene_silenced_by_RNA_interference
Description: A gene that is silenced by RNA interference.
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SO Term
SO:0001225 | gene_silenced_by_histone_modification
Description: A gene that is silenced by histone modification.
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SO Term
SO:0001226 | gene_silenced_by_histone_methylation
Description: A gene that is silenced by histone methylation.
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SO Term
SO:0001227 | gene_silenced_by_histone_deacetylation
Description: A gene that is silenced by histone deacetylation.
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SO Term
SO:0001277 | modified_uridine
Description: A uridine base that has been modified.
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SO Term
SO:0001228 | dihydrouridine
Description: A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
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SO Term
SO:0001229 | pseudouridine
Description: A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
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SO Term
SO:0001230 | inosine
Description: A modified RNA base in which hypoxanthine is bound to the ribose ring.
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SO Term
SO:0001231 | seven_methylguanine
Description: A modified RNA base in which guanine is methylated at the 7- position.
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SO Term
SO:0001232 | ribothymidine
Description: A modified RNA base in which thymine is bound to the ribose ring.
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SO Term
SO:0001274 | modified_inosine
Description: A modified inosine is an inosine base feature that has been altered.
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SO Term
SO:0001233 | methylinosine
Description: A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
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SO Term
SO:0001238 | major_TSS
Description: The tanscription start site that is most frequently used for transcription of a gene.
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SO Term
SO:0001239 | minor_TSS
Description: A tanscription start site that is not the most frequently used for transcription of a gene.
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SO Term
SO:0001241 | encodes_alternate_transcription_start_sites
Description: A gene that has multiple possible transcription start sites.
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