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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
Scaffold196215552500155148191
Scaffold2864004641500000
Scaffold98427090400000
Scaffold482141140200000
Scaffold377721582620000
Scaffold16724811447001501500
Scaffold1271300971900124179189
Scaffold77092580800000
Scaffold2770336828102000
Scaffold186623394120014900


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 TypeSearch exampleNotes
Assembly:ContigAAGJ01213243accession number
Angerer:GenscanSupertig100487_1lab-specific ID scheme
BCM:CDS20193transcript ID
BCM:Gene40415gene ID
GLEAN3:PredictionGLEAN3_14881GLEAN gene ID
Exon:FirstEFCX694625urchin cDNA clone
GC:CpG Islandscpg.15262arbitrary ID
Repeat:Low ComplexLow_complexity.111arbitrary ID
Repeat:SatelliteSatellite.166841arbitrary ID
Repeat:SimpleSimple_repeat.355arbitrary ID
Repeat:TRFtrf.1114587arbitrary ID
ScaffoldScaffold124urchin scaffold name
tRNA:tRNAscanPseudo.1854 or Ser.1871arbitrary tRNA IDs



 

 


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