Strongylocentrotus purpuratus genome portal
JBrowse – Query page – Genome content overview – Gene content overview – Download section
A Genome Browser access point is available and it includes:
- genome sequences from REFSEQ and ENSEMBL;
- all gene annotations versions from REFSEQ, ENSEMBL and ECHINOBASE;
- ESTs downloaded from dbEST.
Search for specific elements through the dedicated Query page
Genome content overview:
the following genome assemblies are available in the platform:
- v. 4.2 from REFSEQ;
- v. 3.1 from ENSEMBL.
Gene content overview:
the following gene annotations are available in the platform:
- version 101 from RefSeq;
- version 37 from Ensembl;
- Build 8 from Echinobase.
Notes from BIOINforMA:
we re-mapped the transcripts sequences predicted by a source on the assembly of another one.
The results are two extended annotation files:
1) based on the RefSeq assembly,
2) based on the Ensembl assembly.
Clicking on the links above, you will redirect to dedicated pages with an interactive table, where there are reported the annotated and remapped transcripts (Transcript ID) per available resource (Annotated by), their location (Region, Start, End, Strand) and their functional annotation (when available). Search by keyword in the “Search” box, plus Sorting and Filtering can be applied. Direct links of the selected genes to the JBrowse is also available.
| Source | Genome Assembly (FASTA-big file) | Gene Annotation (GFF3) | Gene Sequences (FASTA) | mRNA Sequences (FASTA) | Protein Sequences (FASTA) |
| REFSEQ | 4.2 | v. 101 | download | download | download |
| ENSEMBL | 3.1 | v. 37 | download | download | download |
| ECHINOBASE | 3.1 | build 8 | download | download | download |
Genome Assembly: FASTA file of all the chromosome/scaffolds/contigs;
Gene Annotation: GFF file containing information about all the annotated genes, mRNAs, UTRs, CDSs;
Gene Sequences: FASTA file of all the gene sequences;
mRNA Sequences: FASTA file of all the mRNA sequences;
Protein Sequences: FASTA file of all the protein sequences.