Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Genome Biol
2009 Jan 01;108:R86. doi: 10.1186/gb-2009-10-8-r86.
Show Gene links
Show Anatomy links
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes.
Dong X
,
Fredman D
,
Lenhard B
.
???displayArticle.abstract???
Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.
Figure 1. Species available for comparison in Synorth and their associated species tree. (a) Phylogenetic tree based on data from [14,50,70-72]. The red dots indicate the second-round (2R) and third-round (3R) WGD events [72]. The blue dot indicates the genome compaction in the pufferfish lineage beginning 20 to 30 Myr ago [70]. The species shown in the tree are: bichir (Polypterus senegalus), zebrafish (Danio rerio), fugu (Takifugu rubripes), Tetraodon (Tetraodon nigroviridis), stickleback (Gasterosteus aculeatus), medaka (Oryzias latipes), frog (Xenopus tropicalis), chicken (Gallus gallus), mouse (Mus musculus), and human (Homo sapiens). Sources of fish images: Byrappa Venkatesh (fugu), Manfred Schartl (medaka), Wikipedia (zebrafish, tetraodon), Kraft CE et al. [73] (stickleback). (b) Reference and comparison species available in Synorth. Shaded boxes correspond to the reference genomes in Synorth. Connecting lines indicate genome pairs between which GRBs are available to check in the browser. Dashed lines indicate the genome comparison to be offered in the near future. The following genome assemblies underlie the current data sets: human NCBI 36, zebrafish Zv7 (The Wellcome Trust Sanger Institute), fugu v4.0 [74], tetraodon V7 [75], stickleback v1.0 (The Broad Institute), medaka v1.0 [51].
Figure 2. Synorth pipeline and three data views. (a) The Synorth data/analysis pipeline. (b) The Synorth genome locus browser: (A) navigation bar; (B) search field; (C) external link to other browsers (Ancora, UCSC Genome Browser, Ensembl and Vista) for the same region; (D) GRB genomic coordinates - the coordinates are the union of all synteny regions overlapping with the query gene - if no overlapping synteny region is found, no region will be shown; (E) reference species track; (F) track(s) of compared species - in each track, the species name and the sub-tracks for all synteny regions are shown; (G) browser legend; (H) chromosome color key for the compared species. For more details, see the description in the Help page of the Synorth website [20]. (c) Synorth table browser (d) Synorth tree browser.
Figure 3. Scenario code illustration and statistics. (a) Definition of scenario code. (b) Descriptive statistics of scenario codes for all bystander-target pairs in 215 curated GRBs.
Figure 4. Using Synorth to show GRB duplication, maintenance and breakage. (a) FOXD3 locus, (b) TBX2 locus and (c) LHX1 locus. See the text for description.
Figure 5. PAX2 example. Using Synorth to trace the GRB changes between teleost fish and to detect possible errors in genome assembly or missed annotation. See detailed interpretation in the text.
Akalin,
Transcriptional features of genomic regulatory blocks.
2009, Pubmed
Akalin,
Transcriptional features of genomic regulatory blocks.
2009,
Pubmed
Aparicio,
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.
2002,
Pubmed
Ashery-Padan,
Conditional inactivation of Pax6 in the pancreas causes early onset of diabetes.
2004,
Pubmed
Bailey,
Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci.
1978,
Pubmed
Becker,
The random versus fragile breakage models of chromosome evolution: a matter of resolution.
2007,
Pubmed
Berglund,
InParanoid 6: eukaryotic ortholog clusters with inparalogs.
2008,
Pubmed
Burton,
The role of Pax2 in mouse inner ear development.
2004,
Pubmed
,
Xenbase
Chen,
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.
2006,
Pubmed
Dheen,
Zebrafish tbx-c functions during formation of midline structures.
1999,
Pubmed
Dressler,
Pax2, a new murine paired-box-containing gene and its expression in the developing excretory system.
1990,
Pubmed
Engström,
Genomic regulatory blocks underlie extensive microsynteny conservation in insects.
2007,
Pubmed
Engström,
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes.
2008,
Pubmed
Force,
Preservation of duplicate genes by complementary, degenerative mutations.
1999,
Pubmed
Fredman,
Web-based tools and approaches to study long-range gene regulation in Metazoa.
2009,
Pubmed
Fu,
MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.
2007,
Pubmed
Gray,
Mouse brain organization revealed through direct genome-scale TF expression analysis.
2004,
Pubmed
Gross,
Tbx2b is essential for neuronal differentiation along the dorsal/ventral axis of the zebrafish retina.
2005,
Pubmed
Hanna,
Requirement for Foxd3 in maintaining pluripotent cells of the early mouse embryo.
2002,
Pubmed
Hubbard,
Ensembl 2007.
2007,
Pubmed
Hunter,
LIM-homeodomain genes in mammalian development and human disease.
2005,
Pubmed
International Chicken Genome Sequencing Consortium,
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
2004,
Pubmed
Jaillon,
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
2004,
Pubmed
Jamieson,
Domain disruption and mutation of the bZIP transcription factor, MAF, associated with cataract, ocular anterior segment dysgenesis and coloboma.
2002,
Pubmed
Kasahara,
The medaka draft genome and insights into vertebrate genome evolution.
2007,
Pubmed
Kikuta,
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.
2007,
Pubmed
Kimura-Yoshida,
Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification.
2004,
Pubmed
Kleinjan,
Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence.
2008,
Pubmed
Kuhn,
The UCSC Genome Browser Database: update 2009.
2009,
Pubmed
Kuhn,
The UCSC genome browser database: update 2007.
2007,
Pubmed
Law,
Identification, characterization, and localization to chromosome 17q21-22 of the human TBX2 homolog, member of a conserved developmental gene family.
1995,
Pubmed
Lehmann,
SynBlast: assisting the analysis of conserved synteny information.
2008,
Pubmed
Lenhard,
Identification of conserved regulatory elements by comparative genome analysis.
2003,
Pubmed
Li,
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
2003,
Pubmed
Li,
TreeFam: a curated database of phylogenetic trees of animal gene families.
2006,
Pubmed
Matsumoto,
[Role of Pax6 in the developing central nervous system].
2008,
Pubmed
Matsuya,
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
2008,
Pubmed
Meyer,
From 2R to 3R: evidence for a fish-specific genome duplication (FSGD).
2005,
Pubmed
Mungpakdee,
Differential evolution of the 13 Atlantic salmon Hox clusters.
2008,
Pubmed
Navratilova,
Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes.
2009,
Pubmed
Nobrega,
Scanning human gene deserts for long-range enhancers.
2003,
Pubmed
,
Xenbase
Nornes,
Spatially and temporally restricted expression of Pax2 during murine neurogenesis.
1990,
Pubmed
Nornes,
Zebrafish contains two pax6 genes involved in eye development.
1998,
Pubmed
O'Brien,
Inparanoid: a comprehensive database of eukaryotic orthologs.
2005,
Pubmed
Ovcharenko,
Evolution and functional classification of vertebrate gene deserts.
2005,
Pubmed
Panopoulou,
Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis.
2005,
Pubmed
Pennacchio,
In vivo enhancer analysis of human conserved non-coding sequences.
2006,
Pubmed
Pfeffer,
The activation and maintenance of Pax2 expression at the mid-hindbrain boundary is controlled by separate enhancers.
2002,
Pubmed
Prince,
Tbx2 directly represses the expression of the p21(WAF1) cyclin-dependent kinase inhibitor.
2004,
Pubmed
Putnam,
The amphioxus genome and the evolution of the chordate karyotype.
2008,
Pubmed
Remm,
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
2001,
Pubmed
Ribeiro,
Tbx2 and Tbx3 regulate the dynamics of cell proliferation during heart remodeling.
2007,
Pubmed
Ruan,
TreeFam: 2008 Update.
2008,
Pubmed
Sandelin,
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.
2004,
Pubmed
Schneider,
OMA Browser--exploring orthologous relations across 352 complete genomes.
2007,
Pubmed
Shanmugalingam,
Ace/Fgf8 is required for forebrain commissure formation and patterning of the telencephalon.
2000,
Pubmed
Sonnhammer,
Orthology, paralogy and proposed classification for paralog subtypes.
2002,
Pubmed
Sprague,
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.
2008,
Pubmed
,
Xenbase
Sémon,
Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor.
2007,
Pubmed
Tatusov,
The COG database: an updated version includes eukaryotes.
2003,
Pubmed
Teng,
A role for Tbx2 in the regulation of the alpha2(1) collagen gene in human fibroblasts.
2007,
Pubmed
Toyama,
lim6, a novel LIM homeobox gene in the zebrafish: comparison of its expression pattern with lim1.
1997,
Pubmed
Vilella,
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
2009,
Pubmed
Visel,
VISTA Enhancer Browser--a database of tissue-specific human enhancers.
2007,
Pubmed
Volff,
Genome evolution and biodiversity in teleost fish.
2005,
Pubmed
Wagner,
Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.
2005,
Pubmed
Wittbrodt,
Medaka--a model organism from the far East.
2002,
Pubmed
Woolfe,
Highly conserved non-coding sequences are associated with vertebrate development.
2005,
Pubmed
Zeng,
Identification of a novel human doublecortin-domain-containing gene (DCDC1) expressed mainly in testis.
2003,
Pubmed
Zheng,
Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs.
2005,
Pubmed
de la Calle-Mustienes,
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.
2005,
Pubmed
,
Xenbase