Regulatory sequence
A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of ... A regulatory DNA sequence does not regulate unless it is activated. Different regulatory sequences are activated and then ... About 600 regulatory sequences in promoters and about 800 regulatory sequences in enhancers appear to depend on double-strand ... Genomes can be analyzed systematically to identify regulatory regions. Conserved non-coding sequences often contain regulatory ...
List of gene prediction software
Implications for finding sequence motifs in regulatory regions". Nucleic Acids Research. 29 (12): 2607-18. doi:10.1093/nar/ ... regulatory sequence analysis tools 20th anniversary". Nucleic Acids Research. 46 (W1): W209-W214. doi:10.1093/nar/gky317. ISSN ... Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research. ... Rho M, Tang H, Ye Y (November 2010). "FragGeneScan: predicting genes in short and error-prone reads". Nucleic Acids Research. ...
GeneMark
Implications for finding sequence motifs in regulatory regions." Nucleic Acids Research (2001) 29 (12): 2607-2618. doi:10.1093/ ... doi:10.1093/nar/26.4.1107 Besemer J. and Borodovsky M. "Heuristic approach to deriving models for gene finding." Nucleic Acids ... doi:10.1093/nar/gki937 Zhu W., Lomsadze A. and Borodovsky M. "Ab initio gene identification in metagenomic sequences." Nucleic ... Lukashin A. and Borodovsky M. "GeneMark.hmm: new solutions for gene finding." Nucleic Acids Research (1998) 26 (4): 1107-1115. ...
Pan-genome
Implications for finding sequence motifs in regulatory regions". Nucleic Acids Research. 29 (12): 2607-18. doi:10.1093/nar/ ... Ding W, Baumdicker F, Neher RA (January 2018). "panX: pan-genome analysis and exploration". Nucleic Acids Research. 46 (1): e5 ... For species with a closed pan-genome, very few genes are added per sequenced genome (after sequencing many strains), and the ... Nucleic Acids Research. 47 (W1): W52-W58. doi:10.1093/nar/gkz333. PMC 6602458. PMID 31053848. Zhang, Bosen; Huang, Haiyan; ...
Transterm
... a database to aid the analysis of regulatory sequences in mRNAs". Nucleic Acids Research. 37 (Database issue): D72-D76. doi: ... Transterm is a database of mRNA sequences, codon usage, and associated cis-regulatory elements that regulate gene expression. ...
TRANSFAC
... mining cis-regulatory regions in genomes". Nucleic Acids Res. 38 (Web Server issue): W286-92. doi:10.1093/nar/gkq473. PMC ... A tool for searching transcription factor binding sites in DNA sequences". Nucleic Acids Res. 31 (13): 3576-9. doi:10.1093/nar/ ... "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms". Nucleic Acids Res. 27 (1): 318-22 ... Visualisation and analysis of transcription factor binding sites in nucleotide sequences". Nucleic Acids Res. 31 (13): 3572-5. ...
Stein Aerts
... the all-inclusive open source workbench for regulatory sequence analysis". Nucleic Acids Research. 33 (Web Server issue): W393- ... deciphering the cis-regulatory logic of coregulated genes". Nucleic Acids Research. 31 (6): 1753-1764. doi:10.1093/nar/gkg268. ... "TOUCAN - Regulatory Sequence Analysis - Gene Regulation Bioinformatics". toucan.aertslab.org. Retrieved 2022-05-04. Aerts, ... Aerts research interest in regulatory genomics and gene regulatory networks cover a wide range of experimental and ...
RegTransBase
... a database of regulatory sequences and interactions in a wide range of prokaryotic genomes". Nucleic Acids Res. England. 35 ( ... RegTransBase is database of regulatory interactions and transcription factor binding sites in prokaryotes Transcription factors ...
Transposable element
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within ... Mariño-Ramírez L, Lewis KC, Landsman D, Jordan IK (2005). "Transposable elements donate lineage-specific regulatory sequences ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ... Sequence self-comparison programs use databases such as AB-BLAST to conduct an initial sequence alignment. As these programs ...
UTRdb
... a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs". Nucleic Acids Res. 38 (Suppl_ ... UTRdb is a database of 5' and 3' untranslated sequences of eukaryotic mRNAs Five prime untranslated region Three prime ...
PURA
Rather, it is a regulatory nucleic acid sequence to which Pur-alpha binds that is altered. GRCh38: Ensembl release 89: ... in all organisms are united by Pur-alpha's ability to bind nucleic acids coupled to its ability to interact with regulatory and ... There is a documented interaction between Pur-alpha, the HIV-1 protein, Tat, and a Pur-alpha-binding regulatory sequence in JCV ... Bergemann AD, Ma ZW, Johnson EM (December 1992). "Sequence of cDNA comprising the human pur gene and sequence-specific single- ...
E-box
This motif consists of two amphipathic α-helices, separated by a small sequence of amino acids, that form one or more β-turns. ... E-Box+Elements at the U.S. National Library of Medicine Medical Subject Headings (MeSH) (Regulatory sequences, DNA). ... Nucleic Acids Res. 35 (21): 7087-7095. doi:10.1093/nar/gkm746. PMC 2175354. PMID 17942416. Bergstrom, D. A.; Penn, B. H.; ... The consensus sequence of the E-box is usually CANNTG; however, there exist other E-boxes of similar sequences called ...
Complementarity (molecular biology)
These short nucleic acid sequences are commonly found in nature and have regulatory functions such as gene silencing. Antisense ... "The practical and pedagogical advantages of an ambigraphic nucleic acid notation". Nucleosides Nucleotides Nucleic Acids. 25 (7 ... "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences". Retrieved 2008-02-04. Rozak DA (2006). " ... Nucleic acids strands may also form hybrids in which single stranded DNA may readily anneal with complementary DNA or RNA. This ...
Sequence motif
Multiple EM for Motif Elicitation Nucleic acid sequence Protein primary structure Protein I-sites Sequence logo Sequence mining ... there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. Some of these are believed to ... a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ...
Li Zhang (biologist)
Those include the following: Heme binds to a short sequence that serves as a regulatory function in diverse proteins; Heme ... Nucleic Acids Research. 46 (1): 215-228. doi:10.1093/nar/gkx1051. ISSN 0305-1048. PMC 5758875. PMID 29126261. Zhang, L.; ... "Heme binds to a short sequence that serves a regulatory function in diverse proteins". The EMBO Journal. 14 (2): 313-320. doi: ...
LINE1
ORF1 trimers have RNA-binding and nucleic acid chaperone activity that are necessary for retrotransposition. The second ORF of ... "Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable ... International Human Genome Sequencing Consortium) (February 2001). "Initial sequencing and analysis of the human genome". ... Nucleic Acids Research. 32 (13): 3846-55. doi:10.1093/nar/gkh698. PMC 506791. PMID 15272086. Li J, Kannan M, Trivett AL, Liao H ...
Southwestern blot
Nucleic Acids Research. 8 (1): 1-20. doi:10.1093/nar/8.1.1. ISSN 0305-1048. PMC 327239. PMID 6243775. Siu, Francis K Y; Lee, ... of the corresponding selectively bound DNA fragments and may improve protein-mediated cloning of DNA regulatory sequences. ... Moreover, their sequence-specific binding allows the purification ...
List of MeSH codes (G06)
... regulatory sequences, nucleic acid MeSH G06.184.603.080.689.330 - enhancer elements (genetics) MeSH G06.184.603.080.689.330.240 ... amino acid MeSH G06.184.842.200.820 - structural homology, protein MeSH G06.184.842.550 - sequence homology, nucleic acid MeSH ... repetitive sequences, nucleic acid MeSH G06.184.603.080.708.330 - interspersed repetitive sequences MeSH G06.184.603.080. ... regulatory sequences, ribonucleic acid MeSH G06.184.603.080.689.687.249 - rna 3' polyadenylation signals MeSH G06.184.603.080. ...
Mark Borodovsky
Implications for finding sequence motifs in regulatory regions, Nucleic Acids Research Heuristic approach to deriving models ... Nucleic Acids Research GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Nucleic Acids Research ... Nucleic Acids Research GeneMark.hmm: new solutions for gene finding, Nucleic Acids Research GenMark: Parallel Gene recognition ... These algorithms are currently in use in many research labs in the US and abroad as well as at the major sequencing and ...
Cis-regulatory element
Sinha S, Liang Y, Siggia E (2006). "Stubb: a program for discovery and analysis of cis-regulatory modules". Nucleic Acids Res. ... An example of a cis-acting regulatory sequence is the operator in the lac operon. This DNA sequence is bound by the lac ... Sharan R, Ben-Hur A, Loots GG, Ovcharenko I (2004). "CREME: Cis-Regulatory Module Explorer for the human genome". Nucleic Acids ... The design of regulatory modules help in producing feedback, feed forward, and cross-regulatory loops. Cis-regulatory modules ...
OsmY RNA motif
Presumably, the RNAs function as cis-regulatory elements, however the poor sequence conservation makes it difficult to ... Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401. (Orphaned articles from December ... The osmY RNA motif exhibits little conserved sequence in comparison to many known RNAs, although its secondary structure is ... It is generally located nearby to the Shine-Dalgarno sequence of the downstream gene. ...
Pribnow box
Harley, Calvin B.; Reynolds, Robert P. (March 1987). "Analysis of E. coli promoter sequences" (PDF, 0.9 MB). Nucleic Acids ... Regulatory sequences, All stub articles, Genetics stubs). ... It is an idealized or consensus sequence-that is, it shows the ... Nucleic Acids Research. 34 (2): 564-574. doi:10.1093/nar/gkj454. ISSN 0305-1048. PMC 1360284. PMID 16449200. ... It is also commonly called the -10 sequence or element, because it is centered roughly ten base pairs upstream from the site of ...
DNA footprinting
Nucleic Acids Res. 17 (1): 171-183. doi:10.1093/NAR/17.1.171. PMC 331543. PMID 2643080. Becker, M.M.; Wang, Z.; Grossmann, G.; ... regulatory regions predicted using DNA-protein sequence information (encoded in structures such as position weight matrix). ... Nucleic Acids Research. 5 (9): 3157-70. doi:10.1093/nar/5.9.3157. PMC 342238. PMID 212715. Hampshire, A; Rusling, D; Broughton- ... due to a slower reaction and digestion time.Ultraviolet irradiation can be used to excite nucleic acids and create ...
HutP
Nucleic Acids Res suppl. 3 (2003) 199-200. 4. M. Oda, N. Kobayashi, A. Ito, Y. Kurusu, K. Taira, cis-acting regulatory ... the Bacillus subtilis hut operon and histidine-dependent binding of HutP to the transcript containing the regulatory sequences ... Nucleic Acids Res. 33 (2005) 5494-5502. 6. T. S. Kumarevel, S. C. B. Gopinath, S. Nishikawa, H. Mizuno, P. K. R. Kumar, ... Nucleic Acids Res. 32, (2004) 3904-3912. (Articles lacking in-text citations from December 2007, All articles lacking in-text ...
Polypurine reverse-Hoogsteen hairpin
... a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome". Nucleic Acids ... Integrative WEB tools for identification and analysis of the triplex formation target DNA sequences, including PPRH sequences, ... December 2022). "Detection of SARS-CoV-2 Virus by Triplex Enhanced Nucleic Acid Detection Assay (TENADA)". International ... Nucleic Acid Therapeutics. 25 (4): 198-208. doi:10.1089/nat.2015.0531. PMID 26042602. Aubets E, Noé V, Ciudad CJ (May 2020). " ...
NqrA-Marinomonas RNA motif
Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401. Fujiwara-Nagata E, Eguchi Y, ... However, promoter sequences occur upstream of the nqr operon in the distantly related organism Vibrio anguillarum. The fact ... Based on their locations, it is reasonable to hypothesize that nqrA-Marinomonas RNAs function as cis-regulatory elements. ... as nqrA-Marinomonas RNAs raises questions about the putative cis-regulatory function of these RNAs. However, it is possible ...
Interferome
Nucleic Acids Res. England. 37 (Database issue): D852-7. doi:10.1093/nar/gkn732. PMC 2686605. PMID 18996892. "Home". isicr.org ... Regulatory analysis of interferon regulated genes; BLAST (Basic Local Alignment Search Tool) analysis and orthologue sequence ...
MicroDNA
In general, nucleic acid molecules that are found in the bloodstream, termed circulating or cell-free, are a relatively new ... Transcription factors often bind to promoter or regulatory sequences at the 5' end of DNA to initiate transcription. These ... Recent studies have extended the use of cell-free nucleic acids as cancer biomarkers to microDNA. The cfmicroDNA was obtained ... Now with high-throughput sequencing being a more common practice, the complete genomic sequence of mammalian eccDNA has been ...
Thrombomodulin
... nucleic acid sequences of the cDNA and gene predict protein structure and suggest sites of regulatory control". Proceedings of ... Wen DZ, Dittman WA, Ye RD, Deaven LL, Majerus PW, Sadler JE (July 1987). "Human thrombomodulin: complete cDNA sequence and ... Wen DZ, Dittman WA, Ye RD, Deaven LL, Majerus PW, Sadler JE (July 1987). "Human thrombomodulin: complete cDNA sequence and ...
Mu-gpT-DE RNA motif
Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401. (Orphaned articles from December ... Some Mu-gpT-DE RNAs contain a stem that overlaps the Shine-Dalgarno sequence of the downstream gene, which could suggest a cis- ... regulatory function. However, this phenomenon could also arise if Mu-gpT-DE RNAs are part of a tightly packed genome, as is ... The Mu-gpT-DE motif is only found in metagenomic sequences arising from unknown organisms. Mu-gpT-DE RNAs usually occur ...