Ciona robusta genome portal
JBrowse – Query page – Genome content overview – Gene content overview – Download section
A Genome Browser access point is available and it includes:
- 3 different JBrowses built based on the genome assembly sequences from: 1) RefSeq, 2) Ensembl and 3) Aniseed;
- all the gene annotations versions from RefSeq, Ensembl and Aniseed (predicted and re-mapped);
- all the available 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:
- GCF_000224145.3 from RefSeq;
- GCF_000224145.1 from ENSEMBL;
- KHGene.2012 from Aniseed.
Notes from BIOINforMA:
All the assemblies consist of 14 chromosomes plus the mitochondrion and 1257 unplaced scaffolds, having in total 1272 sequences. We compared the sequences of the assemblies, checking how many sequences are completely identical. The number of genomic elements in common (identical sequence) among the assemblies is reported in the following table:
| RefSeq | Ensembl | Aniseed | |
| RefSeq | 1272 | 1129 | 1266 |
| Ensembl | 1129 | 1272 | 1128 |
| Aniseed | 1166 | 1128 | 1272 |
Gene content overview:
the following gene annotations are available in the platform:
- version 104 from RefSeq;
- version 95 from Ensembl;
- KH.Gene.2012 from Aniseed.
Notes from BIOINforMA:
we re-mapped the transcripts sequences predicted by a source on the assembly of another one.
The results are three extended annotation files:
1) based on the RefSeq assembly,
2) based on the Ensembl assembly,
3) based on the Aniseed 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 | GCF_000224145.3 | v. 104 | download | download | download |
| Ensembl | GCF_000224145.1 | KH.95 | download | download | download |
| Aniseed | KHGene.2012 | KHGene.2012 | 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.