Table 1.
Examples of transcriptome annotations available on the public QuantPrime server
Annotated features included in QuantPrime | |||||
Species | Genomic sequences | Splice variants | Keyword search | Annotation source | Reference |
254 different species or crosses | No | No | Yes | TIGR plant transcript assemblies | [22] |
91 different species or crosses | No | No | Yes | UniGene | [23] |
Arabidopsis thaliana | Yes | Yes | Yes | TAIR release 7 | [24] |
Aspergillus niger | Yes | No | No* | JGI assembly v1.0 | Non-published data |
Bos taurus | Yes | No | Yes | NCBI RefSeq | [25] |
Chlamydomonas reinhardtii | Yes | No | No* | JGI assembly v3.1 | [26] |
Danio rerio | Yes | No | Yes | NCBI RefSeq | [25] |
Drosophila melanogaster | Yes | Yes | Yes | FlyBase release 5.4 | [27] |
Homo sapiens | Yes | No | Yes | NCBI RefSeq | [25] |
Homo sapiens | Yes | Yes | Yes | H-Invitational Database 5.0 | [28] |
Mus musculus | Yes | No | Yes | NCBI RefSeq | [25] |
Oryza sativa ssp japonica | Yes | Yes | Yes | TIGR release 5 | [29] |
Ostreococcus lucimarinus | Yes | No | No* | JGI assembly v2.0 | Non-published data |
Physcomitrella patens ssp patens | Yes | No | No* | JGI assembly v1.1 | [30] |
Populus trichocarpa | Yes | No | No* | JGI assembly v1.1 | [31] |
Rattus norvegicus | Yes | No | Yes | NCBI RefSeq | [25] |
Saccharomyces cerevisiae | Yes | No | Yes | Saccharomyces Genome Database | [32] |
Selaginella moellendorffii | Yes | No | No* | JGI assembly v1.0 | Non-published data |
Vitis vinifera | Yes | No | No | Genoscope assembly | [33] |
Xenopus tropicalis | Yes | No | Yes | NCBI RefSeq | [25] |
The latest versions of the annotations were added, and are updated regularly as updates become available.
* Protein IDs are searchable.