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Synteny Database specifications

Information


Unique identifier OMICS_32619
Name Synteny Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline John Postlethwait

Publication for Synteny Database

Synteny Database citations

 (20)
library_books

Loss of function of the ciliopathy protein Cc2d2a disorganizes the vesicle fusion machinery at the periciliary membrane and indirectly affects Rab8 trafficking in zebrafish photoreceptors

2017
PLoS Genet
PMCID: 5760100
PMID: 29281629
DOI: 10.1371/journal.pgen.1007150

[…] Synteny analysis was done using the synteny database (http://syntenydb.uoregon.edu/synteny_db/) []. Parameters were adjusted to a sliding window size of 50, and several genes in the vicinity of rab8b were used for additional syntenic co […]

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Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions

2017
Front Physiol
PMCID: 5526904
PMID: 28798696
DOI: 10.3389/fphys.2017.00539
call_split See protocol

[…] The Ohnologs database is a repository of paralogous genes retained from WGDs (i.e., ohnologs) in the vertebrate genomes (Singh et al., ) (http://ohnologs.curie.fr/). The Synteny Database (Catchen et al., ) (http://syntenydb.uoregon.edu/synteny_db/) is an automated system to identify conserved syntenic regions produced from WGD. NIX and BNIP3 were housed in the Ohnolog […]

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Evolutionary divergence of the vertebrate TNFAIP8 gene family: Applying the spotted gar orthology bridge to understand ohnolog loss in teleosts

2017
PLoS One
PMCID: 5489176
PMID: 28658311
DOI: 10.1371/journal.pone.0179517
call_split See protocol

[…] Conserved synteny analyses were performed using the Synteny Database []. Amino acid sequence alignments were generated using standard procedures in Clustal Omega [] available at http://www.ebi.ac.uk/Tools/msa/clustalo/. Molecular phylogenetic analyses […]

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Lipid droplet biology and evolution illuminated by the characterization of a novel perilipin in teleost fish

2017
eLife
PMCID: 5342826
PMID: 28244868
DOI: 10.7554/eLife.21771.025
call_split See protocol

[…] le at Ensembl under accession ENSGT00500000044795. The tree in presents data after the collapse of large clades while retaining rayfin fish genes shown in detail. Conserved Synteny analysis used the Synteny Database (, ). […]

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Down regulation of coasy, the gene associated with NBIA VI, reduces Bmp signaling, perturbs dorso ventral patterning and alters neuronal development in zebrafish

2016
Sci Rep
PMCID: 5124858
PMID: 27892483
DOI: 10.1038/srep37660
call_split See protocol

[…] http://genome.ucsc.edu/) on the Zv10 (Sept 2014) Danio rerio assembly and the Ensembl zebrafish genome database (http://www.ensembl.org/Danio_rerio/Info/Index).Synteny analysis was achieved using the Synteny Database. Nucleotide and amino acid sequences were compared to the non-redundant sequences present at the NCBI (National Center for Biotechnology Information) using the Basic Local Alignment S […]

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Evolutionary and developmental analysis reveals KANK genes were co opted for vertebrate vascular development

2016
Sci Rep
PMCID: 4904190
PMID: 27292017
DOI: 10.1038/srep27816
call_split See protocol

[…] ://tree.bio.ed.ac.uk/software/figtree). Gene intron-exon structures were analyzed using the longest transcripts in Ensembl. The synteny of KANK genes were analyzed using Ensembl, UCSC genome browser, Synteny Database and Genomicus browser. Protein domain analysis was carried out using the SMART online tool. […]

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Synteny Database institution(s)
Department of Computer and Information Science, University of Oregon, Eugene, OR, USA; Institute of Neuroscience, University of Oregon, Eugene, OR, USA
Synteny Database funding source(s)
Supported in part by an IGERT grant from NSF in Evolution, Development, and Genomics (DGE 9972830); by grant 5R01RR020833 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health.

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