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Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and Fugu genomes. It is freely accessible at http://ecrbase.dcode.org
ECRbase was supported in part by grants from the Lawrence Livermore National Laboratory
G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1):122-4 (2007)
Genomic information on chicken and other avian species
GEISHA (Gallus Expression In Situ Hybridization Analysis) is a centralized and comprehensive repository of precise spatial and temporal information on chicken embryonic gene expression created through in situ hybridization. Annotations include probe sequence, stage, anatomical location of expressing tissues, citation for published images and source for unpublished curated photos. Images and annotation can improve researchersí hypotheses about gene function and genetic networks, which for a significant fraction of genes remain to be explored. As in situ hybridization information is accumulated, the GEISHA database becomes an increasingly valuable resource for the chicken biomedical and agricultural research communities.
Recent develoments :
The database has recently been redesigned to incorporate gene information from Ensembl (UK), NCBI (USA) and miRBase (USA). A comprehensive screen of the microRNA genes has been posted (Darnell et al., 2006) and we are currently conducting a comprehensive transcription factor expression screen. We are also incorporating BioMart into GEISHA to augment search and retrieval of sequence and gene annotation information.
GEISHA is supported by grant no. R01HD044767 from the National Institutes of Health
1. Darnell, D.K., Kaur S., Stanislaw S., Davey S.,. Konieczka JH, Yatskievych TA., and Antin PB. (2007) GEISHA: An In Situ Hybridization Gene Expression Resource for the Chicken Embryo. In Avian Genomics in Evolution, Agriculture and Health. Cytogenet. Genome Res. 117:30-35.
2. Antin, P.B., Kaur S., Stanislaw S., Davey S.,. Konieczka J.H., Yatskievych T.A., and Darnell D.K. (2007). Gallus Expression In Situ Hybridization Analysis (GEISHA): A chicken Embryo Gene Expression Database. Poult Sci. 86(7): 1472-1477.
3. 3. Darnell, D.K., Kaur, S, Stanislaw S., Konieczka J.H., Yatskievych T.A., and Antin P.B. (2006) MicroRNA Expression During Chick Embryo Development. Dev. Dyn. 235:3156-3165.
The SNPSTR database contains the SNP-STR/microsatellite compound markers in the five model species, where sufficient SNP information exists in both of the NCBI and Ensembl databases. These species are human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), dog (Canis familiaris) and chicken (Gallus gallus).
The authors gratefully acknowledge financial support from the Wellcome Trust.
The Exon-Intron Database (EID), publicly available since 2000, is a flat-file, Fasta-formated collection of sequences and annotations for all exons and introns obtained from GenBank. The primary goal of EID is to offer a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. New innovations in EID have been implemented in 2005. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. Currently, these species-specific sets of all introns and all exons are available for human, mouse, rat, dog, chicken, zebrafish, fruit fly, worm (C. elegans), and mouse-ear cress (A. thaliana). This list will be extended on a monthly basis in accordance with GenBank updates. EID is freely available at http://www.meduohio.edu/bioinfo/eid/.
Recent develoments :
All recent improvements in EID are described in http://www.meduohio.edu/bioinfo/eid/word/README_Sept05.DOC
Support for this work was provided by the Medical University of Ohio Foundation and the Stranahan Foundation, through the Program in Bioinformatics and Proteomics/Genomics. We would like to thank Robert Blumenthal and Peter Bazeley, Medical University of Ohio, for discussion and suggestions on our database.
1. Saxonov, S., Daizadeh, I., Fedorov, A. and Gilbert, W. (2000) EID: The Exon-Intron Database: An exhaustive database of protein-containing genes. Nucl. Acids Res., 28, 185-190.
2. Fedorov, A., Stombaugh, J., Harr, M.W., Yu, S., Nasalean, L. and Shepelev, V. (2005) Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucl. Acids Res., 33, 4578-4583.
Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the .Chicken Variation Database. (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci (QTL) using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches.
This project was funded by the Chinese Academy of Sciences, Commission for Economy Planning, Ministry of Science and Technology (2002AA104250, 2002AA234011, 2001AA231061, 2001AA231011, 2001AA231101 and 2004AA231050), Danish National Research Foundation (Danish Platform for Integrative Biology) and the China National Grid (2002AA104250).
Wang J, He X, Ruan J, Dai M, Chen J, Zhang Y, Hu Y, Ye C, Li S, Cong L, Fang L, Liu B, Li S, Wang J, Burt DW, Wong GK, Yu J, Yang H, Wang J. ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res. 2005, 33: D438-D441.
This web site contains information about segmental duplications in the genomes of mouse, dog chicken and rat. Information about segmental duplication in the human genome is presented at http://projects.tcag.ca/humandup. Analyses based on previous genome assemblies can be found in the Previous Analyses section.
The criteria used to identify regions of segmental duplication are as follows:
- Sequence identity of at least 90%
-Sequence length of at least 5 kb
-Not be entirely composed of repetitive elements
The segmental duplication data and summary statistics are available for download in the Data section. Publications and their supplementary materials can be accessed in the Publications section. The segmental duplication data can be visualized in a genome browser in the GBrowse section. Selected annotation tracks (except the segmental duplication track) have also been obtained from UCSC and loaded into the genome browser. Detailed information (e.g. overlapping genes, overlapping clones, detailed alignment) can be obtained by clicking on a duplication cluster in GBrowse. Both keyword search and BLAT search are available from the Home page.
Recent develoments :
The Non-Human Genome Segmental Duplication Database is continually updated, including the archived copies of the analysis of all previous genome assemblies, and will include all new species as they become available.
We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada, the Howard Hughes Medical Institute International Scholar Program (to S.W.S.) and the HSC Foundation.
1. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 2003;4(4):R25. Epub 2003 Mar 17.
2. Armengol L, Pujana MA, Cheung J, Scherer SW, Estivill X. Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum Mol Genet. 2003 Sep 1;12(17):2201-8. Epub 2003 Jul 08.
3. Scherer SW, Cheung J, MacDonald JR, et al. Human chromosome 7: DNA sequence and biology. Science. 2003 May 2;300(5620):767-72. Epub 2003 Apr 10.
4. Gimelli G, Pujana MA, Patricelli MG, Russo S, Giardino D, Larizza L, Cheung J, Armengol L, Schinzel A, Estivill X, Zuffardi O. Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet. 2003 Apr 15;12(8):849-58.
5. Estivill X, Cheung J, Pujana MA, Nakabayashi K, Scherer SW, Tsui LC. Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum Mol Genet. 2002 Aug 15;11(17):1987-95.
6: Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, Heng HH, Koop BF, Scherer SW. Recent segmental and gene duplications in the mouse genome. Genome Biol. 2003;4(8):R47. Epub 2003 Jul 09.