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The Genome of the Purple Sea Urchin, Strongylocentrotus purpuratus
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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.
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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:
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962155 | 52 | 5 | 0 | 0 | 155 | 148 | 191 |
864004 | 64 | 15 | 0 | 0 | 0 | 0 | 0 |
842709 | 0 | 4 | 0 | 0 | 0 | 0 | 0 |
821411 | 40 | 2 | 0 | 0 | 0 | 0 | 0 |
777215 | 82 | 6 | 2 | 0 | 0 | 0 | 0 |
724811 | 44 | 7 | 0 | 0 | 150 | 150 | 0 |
713009 | 71 | 9 | 0 | 0 | 124 | 179 | 189 |
709258 | 0 | 8 | 0 | 0 | 0 | 0 | 0 |
703368 | 28 | 1 | 0 | 2 | 0 | 0 | 0 |
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)
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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 |
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