Deeproot plant base plant information database software. Place is a database of motifs found in plant cisacting regulatory dna elements, all from previously published reports. Plantcare plant cis acting regulatory dna elements db. Plants grow in a dynamic environment that frequently imposes. Nov 18, 2019 by examining chromatin accessibility and modification as well as sequence conservation in plant species, this study characterizes thousands of putative cis regulatory elements and reveals their. Links to the embl, transfac and medline databases are provided when. Plant stilbenes are phytoalexins that accumulate in a small number of plant species, including grapevine vitis vinifera, in response to biotic and abiotic stresses and have been implicated in many beneficial effects on human health. Articles were surveyed reporting identification of cis elements for hormone or drought responses of arabidopsis promoters. Aug 25, 2016 footprintdb is a database and search engine that compiles regulatory sequences from open access libraries of curated dna cis elements and motifs, and their associated transcription factors tfs. Smart database revealed the presence of complete two wds in 11 annotated proteins of cucumber. Cisregulatory dna element data genome annotation omicx.
The data are annotated and the database provides users with information of publications, links to pubmed and ddbjemblgenbank accession numbers. Prediction of transcriptional regulatory elements for. The cis regulatory element annotation for each gene can also be obtained. Search using a variety of parameters, including gene information, domain information, and genome position. Plant transcription factor database an integrative plant transcription factor database that provides a web interface to access large close to complete sets of transcription factors of several plant species, currently. Jan 01, 1999 documents for each motif in the place database contains, in addition to a motif sequence, a brief definition and description of each motif, and relevant literature with pubmed id numbers and genbank accession numbers where available. Phylogram of gh3 homologs from various species and their associated promoter cis element organisations. The database has many useful links to various programs involved in promoter analysis. Place contains some motifs in non plant cis elements in the hope that assist researchers in finding plant homologues. Deeproot plant base plant database software for gardeners. This database is a collection of nucleotide sequence motifs related to the regulations of gene expressions, such as promoters, in higher plants. Cisr14260 construction industry scheme reform manual hmrc.
Nov 26, 2008 therefore, a tool for detecting the coregulation of transcription factors in a group of gene promoters is required. It may also be useful to analyze the promoters to look for known ciselements and to. Services test online regsite database of plant regulatory elements last update. Atcisdb provides a comprehensive resource for the scientific community working with gene regulatory information of arabidopsis thaliana. Plant promoter analysis navigator, for identifying. We note that commercial database transfac annotates also a repertoire of plant dna motifs 39, but a subscription fee is required. Besides the transcription motifs found on a sequence, it also offers. Besides the transcription motifs found on a sequence, it also offers a link to the embl entry that contains the full gene sequence as well as a description of the conditions in which a motif becomes functional.
The prepared rarf tables for various hormone responses enable cis element predictions of hormoneresponsive promoters. The nearest neighbours of the wellcharacterized soybean gh3 gm05g21680 from several plant species were compiled and the corresponding predicted protein sequences were rooted to physcomitrella patens ppgh31 at the bottom to create a neighbourjoining phylogram. Motifs were extracted from previously published reports on genes in vascular plants. Thousands of cisregulatory sequence combinations are shared.
Bioinformatics resources for deciphering the biogenesis and. Based on microarray data from rice flag leaves during early senescence, we identified wbox and gbox cis elements. This study develops a database assisted system, plantpan plant promoter analysis navigator, for recognizing combinatorial cis regulatory elements with a distance constraint in sets of plant genes. Wbox and gbox elements play important roles in early. Athamap athamap provides a genomewide map of potential transcription factor and small rna binding sites in arabidopsis thaliana. Database software well thought out collection of files consists of records row. Arabidopsis thalianagenome sequence and annotation from tair9659 ldsspositive octamer elements identified by our analysis yamamoto et al, bmc genomics 8. Furthermore, a dynamic transcriptional regulatory network under various conditions is first provided in plant resources. Bacterial promoterhunter is part of phisite database which is a collection of phage gene regulatory elements, genes, genomes and other related information, plus tools. Combining the information contained in three public databases of plantspecific cisregulatory elements, agris davuluri et al. Plantcare, a database of plant promoters and their cis. Plantcare a database of plant cisacting elements hsls.
Data about the transcription sites are extracted mainly from the literature, supplemented with an. Plantcare is a database of plant cis acting regulatory elements and a portal to tools for the in silico analysis of promoter sequences. The place database also contains a brief description of each motif and relevant literature with pubmed id numbers. It also allows searching sequences for putative ciselements, but it does not offer access to the entire genome like agris. Database of plant cis acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Plant database software free download plant database. Phagepromoter is a tool for locating promoters in phage genomes, using machine learning. Plant cis elements play important roles in global regulation of gene expression. Plantcare is a database of plant cis acting regulatory elements, enhancers and repressors. Matinspector is a software tool that utilizes a large library of matrix descriptions for transcription factor binding sites to locate matches in dna sequences. Upregulation of over half of these mrnas involves stabilization of five group vii ethylene response factor erfvii. Atcisdb consists of approximately 33,000 upstream regions of annotated arabidopsis genes.
Database of plant cisacting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Our prediction based on the rarf tables was then evaluated with the aid of published results. The identification of cis regulatory modules crms can greatly advance our understanding of gene regulatory mechanisms. Learn vocabulary, terms, and more with flashcards, games, and other study tools. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Arabidopsispbm collections, as well as eeadannot, are valuable resources for plant promoter analysis and cis element discovery. Search for protocols, experimental methods and classroom activities. Please refer to the description page for detailed instructions on how to use the athamap tools. As of 2003, over 380 motifs and their variants were extracted from published reports on genes in vascular and other plants. Plantcare, a database of plant cisacting regulatory elements. In addition to the motifs originally reported, their variations in other genes or in. Welcome to the arabidopsis gene regulatory information server agris the arabidopsis gene regulatory information server agris is a new information resource of arabidopsis promoter sequences, transcription factors and their target genes. In plants, erf genes participate in a variety of regulatory pathways, such as plant growth and biotic andor abiotic stress responses. Search for documented motifs found in plant cisacting regulatory.
Documents for each motif in the place database contains, in addition to a motif sequence, a brief definition and description of each motif, and relevant literature with pubmed id numbers and genbank accession numbers where available. Footprintdb is a database and search engine that compiles regulatory sequences from open access libraries of curated dna cis elements and motifs, and their associated transcription factors tfs. In addition, crm studies in plants are limited to combinations of only a few families of. Find out how element lims software can increase your efficiency, strengthen quality, and expand access to information. A database of plant promoter sequences release 2009. Footprintdb is a database and search engine that compiles regulatory sequences from open access libraries of curated dna ciselements and motifs, and their associated transcription factors tfs. The software p erforms statistical analysis to validate if a given cre has a non randomic pattern in the promoter region of a given gene. It offers functions allowing keyword search, signal scan search, or homology search in fasta format. It systematically annotates the binding interfaces of the tfs by exploiting proteindna complexes deposited in the protein data bank. A database of plant cis acting regulatory elements, enhancers and repressors. Plantcare, a database of plant promoters and their cisacting regulatory elements. Regsite database of plant regulatory elements release 14, may 03, 2014. The red color indicates experimentally validated cis regulatory element present in a specific promoter. The emphasis is to explore useful tools for the analysis of arabidopsis gene promoters.
Plant database software free download plant database top 4 download offers free software downloads for windows, mac, ios and android computers and mobile devices. Thus, accurate models for describing the binding properties of tfs are essential in modeling transcription. Despite the existence of binding sites of more than three transcription factors tfs in a crm, studies in plants often consider only the cooccurrence of binding sites of one or two tfs. A database of nucleotide sequence motifs found in plant cis acting regulatory dna elements cis elements and a tool for homology searches within such a database will be helpful in estimating the mode of gene regulation, regions involved in such regulation, and other pertinent regions in the dna sequence. Although the genome of chinese white pear dangshansuli has been released, knowledge regarding the erf family in pear, such as gene functions, evolutionary history and expression patterns, remains limited. After a search using hmmer and detecting wds by pfam database, it was observed that all cswrkys contain at least one wd and seven cswrks containing nterminal plant zinc cluster domain. The plant in garden database relates the plants to a particular garden. Cis regulatory dna element databases genome annotation transcription factors tfs influence gene expression by binding to specific cis acting elements in a genomic sequence. This database furnishes a brief definition and description of each motif, and. Documents for each motif in the place database contains. Frans plants database free download tucows downloads. The publications in the tair database are derived primarily from pubmed. Data about the transcription sites are extracted mainly from the. Plant base is an a to z encylopedia of plants in the form of a simple software application.
Other valuable plant specific resources such as place and agris were considered. Plant database software free download plant database top. The new construction industry scheme cis post april 2007, showing how payments are taxed from 6 april 2007 cisr14260 construction industry scheme reform manual hmrc internal manual gov. Submitting a sequence to a program which will look for transcription sites known by plantcare. This report summarizes the present status of this database and available tools. Currently contains two databases, atcisdb arabidopsis thaliana cisregulatory database and. Identification of cis regulatory sequence combinations in 1kblong upstream sequences previously, we developed an efficient method cai et al. The germination database covers germination information for a particular plant. Users can search their query sequences for cis elements using the signal scan program at our web site. Plantcare, a plant cisacting regulatory element database. This resource is designed to provide an overview and a brief evaluation of various bioinformatics tools useful for promoter analysis and ciselement searches for beginners like us.
Documents for each motif in the place database contains, in addition to a motif sequence, a brief definition and description of each motif. It is built around a powerful database, but is easy to use and needs no technical skills. Promoter analysis toolstools to find new ciselements. The plant database covers the type of plant, its size and its most suitable environment. The meme suite provides a large number of databases of known motifs that you can use with the motif enrichment and motif comparison tools. Covers motifs found in plant cis acting regulatory dna elements.
Entries with the word arabidopsis in the title, abstract, or mesh headings are downloaded on a. Deeproot plant base software for gardeners, an easily searchable and updatable plant encyclopaedia database for pcs and macs. The content and use of the transfac database is presented in detail. The regulatory elements database provides access to roughly 2. Links to the embl, transfac and medline databases are provided when available. Plantcare, a database of plant promoters and their cisacting. Isolation and analysis of gene regulatory sequences hehl. It originally covered vascular plants only, but we changed the policy in april 2006 see the release note of place 26. A database of plant cisacting regulatory elements, enhancers and repressors. Jan 01, 1998 in addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. It also allows searching sequences for putative cis elements, but it does not offer access to the entire genome like agris. Atcisdb arabidopsis cis regulatory element database.
Besides the transcription motifs found on a sequence, it also offers a link to the embl entry that contains the full gene sequence as well as a description of. Besides the transcription motifs found on a sequence, it also offers a link to the embl entry that. Currently, there are about 150 described cismotifs known in arabidopsis that have been determined and validated in a number of different experiments and by bioinformatic approaches, and various plantspecific ciselement motif databases are available higo et al. Search for documented motifs found in plant cis acting regulatory dna elements. Plantprom db database with annotated, nonredundant collection of proximal promoter sequences for rna polymerase ii with experimentally determined transcription start sites tss from various plant species. Plantcare is a database of plant cisacting regulatory elements, enhancers and repressors. Recent sequencing of many plant genomes makes the task of identifying their regulatory elements very important, yet popular regulatory site databases such as tfd or transfac list very few plant elements. Plantcare, a database of plant cis acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Chinga chow, hanqin zheng, naiyun wu, chiahung chien, hsienda huang, tzongyi lee, yifan chianghsieh, pingfu hou, tienyi yang, and wenchi chang plantpan 2. A database of plant cisacting regulatory dna elements.
Plantcare, a database of plant cisacting regulatory. Place plant cisacting regulatory dna elements hsls. Provides fast access to plant information and the ability to manage custom reference data. Plant cisacting regulatory dna elements place database. Previous databases created for similar purposes such as tfd and transfac 4, 5 contain many cis elements, but only a very small number of those. The garden database lists gardens, their gardeners and the speciality of that garden.
The response of arabidopsis thaliana to lowoxygen stress hypoxia, such as during shoot submergence or root waterlogging, includes increasing the levels of. Users can search their query sequences for ciselements using the signal scan program at the. Plancare is a plant specific database and transfac covers transcription factors of all eukaryotes. A database of plant cis acting regulatory dna elements. In particular, resveratrol, the basic unit of all other complex stilbenes, has received widespread attention because of its cardioprotective, anticarcinogenic. Place is a database of motifs found in plant cisacting regulatory dna elements, which were collected from previously published reports. It is not only efficient to investigate critical cis and transregulatory elements in plant promoters, but also reconstruct highconfidence relationships of tftargets under a specific condition. Place is a database of nucleotide sequence motifs found in plant cisacting regulatory dna elements. Thousands of cisregulatory sequence combinations are. Users can search their query sequences for ciselements using the signal scan program at the web site. A database of plant cisacting regulatory dna elements place is a database of motifs found in plant cisacting regulatory dna elements, which were collected from previously published reports. Characterization and identification of cisregulatory.
Atcisdb consists of a searchable relational database, which includes many different data. Plant cis acting regulatory dna elements place database. Study 33 terms cis 105 midterm chapter 2 flashcards. Comparison of the amino acid sequences of anac019, anac055, and anac072. Place is a database of motifs found in plant cis acting regulatory dna elements, which were collected from previously published reports. Plantcis is a web tool for finding cis regulatory elements cres in plant gene promoters. Search for information on plant cis acting regulatory elements, transcription sites, enhancers and repressors. Database of motifs found in plant cisacting regulatory dna elements, all from previously published reports. The prevalence, evolution and chromatin signatures of plant. Athamap 5 contains 103 transcription factors and nearly 10 million putative tfs binding sites mapping cis regulatory elements in. Purposebuilt our singular focus on the needs of labs that test soil, water, air, food, and cannabis result in a lims that is purposebuilt for the workflow of environmental, waterwastewater, and cannabis laboratories. Pdf plantcare, a database of plant cisacting regulatory.
967 254 1182 320 1069 1496 900 707 359 322 1193 1286 1386 318 171 1309 1476 604 412 774 843 799 527 437 628 920 1069 960 1080 348 781 888 208 277 636 614 62 515 53 1013 80