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Search results 2101 to 2200 out of 2386 for *

Category restricted to SOTerm (x)

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Categories

Category: SOTerm
Type Details Score
SO Term
Description: A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.
SO Term
Description: The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.
SO Term
Description: The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.
SO Term
Description: The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.
SO Term
Description: A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.
SO Term
Description: A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat.
SO Term
Description: A repeat region that is prone to expansions and/or contractions.
SO Term
Description: A nucleotide site from which replication initiates.
SO Term
Description: A regulatory element that acts in response to a stimulus, usually via transcription factor binding.
SO Term
Description: Identifies the biological source of the specified span of the sequence
SO Term
Description: A hexameric RNA motif consisting of nucleotides UNAAAC (where N can be any nucleotide) that targets the RNA for degradation.
SO Term
Description: An RNA that is transcribed from a long terminal repeat.
SO Term
Description: A contig composed of genomic DNA derived sequences.
SO Term
Description: A variation qualifying the presence of a sequence in a genome which is entirely missing in another genome.
SO Term
Description: A self replicating circular nucleic acid molecule that is distinct from a chromosome in the organism.
SO Term
Description: A self replicating linear nucleic acid molecule that is distinct from a chromosome in the organism. They are capped by terminal proteins covalently bound to the 5' ends of the DNA.
SO Term
Description: Termination signal preferentially observed downstream of polyadenylation signal
SO Term
Description: A sequence variant whereby at least one base of a codon is changed, resulting in a stop codon inserted next to an existing stop codon. This leads to a polypeptide of the same length.
SO Term
Description: A DNA motif to which the S. pombe Zas1 protein binds. The consensus sequence is 5'-(Y)CCCCAY-3'.
SO Term
Description: A promoter element with consensus sequence [5'-TCG(G/C)(A/T)xxTTxAA], bound by the transcription factor Pho7.
SO Term
Description: A sequence alteration which includes an insertion or a deletion. This describes a sequence length change when the direction of the change is unspecified or when such changes are pooled into one category.
SO Term
Description: A sequence variant in which the function of a gene product is retained with respect to a reference.
SO Term
Description: A sequence variant in which the function of a gene product is unknown with respect to a reference.
SO Term
Description: Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes.
SO Term
Description: A region that codes for a 2A self-cleaving polypeptide region, which is a region that can result in a break in the peptide sequence at its terminal G-P junction.
SO Term
Description: A conserved sequence (5'-CGNMGATCNTY-3') transcription repressor binding site required for gene repression in the presence of high zinc.
SO Term
Description: A group II intron that recognizes IBS1/EBS1 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon and may also recognize a stem-loop in the RNA.
SO Term
Description: A C-terminus protein motif (CAAX) serving as a post-translational prenylation site modified by the attachment of either a farnesyl or a geranyl-geranyl group to a cysteine residue. Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, whereas Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E.
SO Term
Description: An RNA that catalyzes its own cleavage.
SO Term
Description: A genetic feature that encodes a trait used for artificial selection of a subpopulation.
SO Term
Description: A chromosomal locus where complementary lncRNA and associated proteins accumulate at the corresponding lncRNA gene loci to tether homologous chromosome during chromosome pairing at meiosis I.
SO Term
Description: A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA).
SO Term
Description: A polypeptide region that mediates binding to SUMO. The motif contains a hydrophobic core sequence consisting of three or four Ile, Leu, or Val residues plus one acidic or polar residue at position 2 or 3.
SO Term
Description: A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes.
SO Term
Description: A gene that codes for cytosolic SSU rRNA.
SO Term
Description: A gene that codes for cytosolic rRNA.
SO Term
Description: A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes.
SO Term
Description: A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes.
SO Term
Description: A gene that codes for cytosolic LSU rRNA.
SO Term
Description: A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes.
SO Term
Description: A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes.
SO Term
Description: A gene which codes for 21S_rRNA, which functions as a component of the large subunit of the ribosome in mitochondria.
SO Term
Description: A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes.
SO Term
Description: A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes.
SO Term
Description: A transcript which is partially duplicated due to duplication of DNA, leading to a new transcript that is only partial and likely nonfunctional.
SO Term
Description: A partially_duplicated_transcript where the 5' end of the transcript is duplicated.
SO Term
Description: A partially_duplicated_transcript where the 3' end of the transcript is duplicated.
SO Term
Description: A region of DNA that is predicted to be translated and transcribed into a protein by a protein detection algorithm that does not get transcribed in nature.
SO Term
Description: A portion of a stem loop secondary structure in RNA.
SO Term
Description: The loop portion of a stem loop, which is not folded back upon itself.
SO Term
Description: The portion of a stem loop where the RNA is folded back upon itself.
SO Term
Description: A region of a stem in a stem loop structure where the sequences are non-complimentary.
SO Term
Description: Cytologically observable heterochromatic regions of chromosomes away from centromeres that contain predominatly large tandem repeats and retrotransposons.
SO Term
Description: A binding motif with the consensus sequence TTAGGG to which Teb1 binds.
SO Term
Description: A region defined by a cluster of experimentally determined polyadenylation sites, typically less than 25 bp in length and associated with a single polyadenylation signal.
SO Term
Description: Large Retrotransposon Derivative elements are long-terminal repeats that contain reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins . The LARDs identified in barley and other Triticeae have LTRs ~5.5 kb and an interal domain of ~3.5 kb. LARDs lack coding domains and thus do not encode proteins.
SO Term
Description: TRIM elements have terminal direct repeat sequences of 100-250 bp in length that flank an internal domain of 100–300 bp. TRIMs lack coding domains and thus do not encode proteins.
SO Term
Description: An absolute reference to the strand. When a chromosome has p and q arms, the Watson strand is the strand whose 5'-end is on the short arm of the chromosome. Of note, the term 'plus strand' is typically based on a reference sequence where it's preferred for the plus strand to be the Watson strand, but might not be and 'plus strand' is therefore not an exact synonym.
SO Term
Description: An absolute reference to the strand. When a chromosome has p and q arms, the Crick strand is the strand whose 5'-end is on the long arm of the chromosome. Of note, the term 'minus strand' is typically based on a reference sequence where it's preferred for the minus strand to be the Crick strand, but might not be and 'minus strand' is therefore not an exact synonym.
SO Term
Description: LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO Term
Description: LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO Term
Description: LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO Term
Description: LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein.
SO Term
Description: R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes.
SO Term
Description: RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain.
SO Term
Description: Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT).
SO Term
Description: Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain.
SO Term
Description: Short interspersed elements that originated from tRNAs.
SO Term
Description: Short interspersed elements that originated from 7SL RNAs.
SO Term
Description: Short interspersed elements that originated from 5S rRNAs.
SO Term
Description: Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules.
SO Term
Description: Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp.
SO Term
Description: The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb.
SO Term
Description: Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent, either sharing only terminal G…C nucleotides, or with the G…C nucleotides absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification.
SO Term
Description: Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD).
SO Term
Description: Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination.
SO Term
Description: Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA.
SO Term
Description: Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly 'TAA' or 'TTA'. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are 'GGG/CCC…GGC/GCC' or 'GA/GGCA…TGCC/TC'.
SO Term
Description: This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are 'CACTA/G…C/TAGTG'.
SO Term
Description: Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs).
SO Term
Description: Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase.
SO Term
Description: Ngaro retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs.
SO Term
Description: VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes.
SO Term
Description: Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease.
SO Term
Description: A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.
SO Term
Description: An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.
SO Term
Description: The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis.
SO Term
Description: Mitochondrial 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.
SO Term
Description: A TF_binding_site that is involved in regulation of expression.
SO Term
Description: The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter.
SO Term
Description: The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter.
SO Term
Description: An operon whose transcription is coordinated on a single transcription unit.
SO Term
Description: An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.
SO Term
Description: DNA regions delimited by different nonspurious TSS-TTS pairs.
SO Term
Description: A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products.
SO Term
Description: A regulon defined by considering one regulatory gene product.
SO Term
Description: A regulon defined by considering the units of expression regulated by a specified set of regulatory gene products.
SO Term
Description: An instance of a self-interacting DNA region flanked by left and right TAD boundaries.
SO Term
Description: A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance.
SO Term
Description: A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications.
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