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The Genome of the Purple Sea Urchin, Strongylocentrotus purpuratus

This page acts as a direct entryway to Sea Urchin annotation content browsable via Genboree. This project was originally in support of the annotation efforts by the Sea Urchin Genome Sequencing Consortium, but is now publicly accessible with the publication of 'The Genome of the Sea Urchin Strongylocentrotus purpuratus'. Please note there is also public annotation database hosted by HGSC at Baylor College of Medicine, which is navigable via the web and also integrated with Genboree.

Sea Urchin Browser Entry: Longest Scaffolds: To jump into the Genboree browser view of the Sea Urchin genome, you could pick one of 10 longest scaffolds listed below. (Please note that the best place to look for gene-related annotations is via the HGSC urchin annotation database, which has curated gene data.) Longest 10 Scaffolds: Scaffold Name Length Contigs tRNAs Repeat Satellites CpG Islands Low Complexity Repeats Simple Repeats TRFs Scaffold1 962155 52 5 0 0 155 148 191 Scaffold2 864004 64 15 0 0 0 0 0 Scaffold9 842709 0 4 0 0 0 0 0 Scaffold4 821411 40 2 0 0 0 0 0 Scaffold3 777215 82 6 2 0 0 0 0 Scaffold16 724811 44 7 0 0 150 150 0 Scaffold12 713009 71 9 0 0 124 179 189 Scaffold7 709258 0 8 0 0 0 0 0 Scaffold27 703368 28 1 0 2 0 0 0 Scaffold18 662339 41 2 0 0 149 0 0 Keyword Search You could also try a keyword search, if you know some of the annotation ID's that may be present. To find a scaffold or annotation to view, try entering its name in the search box below. If you only know the start of the name, that should also work but will be slower if many names match. Enter a scaffold name, gene id, annotation name, contig name, or other keyword (see examples below)

  Example Search Terms:

Below are some examples of search terms for different types of annotation data.

Annotation Type Search example Notes Assembly:Contig AAGJ01213243 accession number Angerer:Genscan Supertig100487_1 lab-specific ID scheme BCM:CDS 20193 transcript ID BCM:Gene 40415 gene ID GLEAN3:Prediction GLEAN3_14881 GLEAN gene ID Exon:FirstEF CX694625 urchin cDNA clone GC:CpG Islands cpg.15262 arbitrary ID Repeat:Low Complex Low_complexity.111 arbitrary ID Repeat:Satellite Satellite.166841 arbitrary ID Repeat:Simple Simple_repeat.355 arbitrary ID Repeat:TRF trf.1114587 arbitrary ID Scaffold Scaffold124 urchin scaffold name tRNA:tRNAscan Pseudo.1854 or Ser.1871 arbitrary tRNA IDs