Gene
Stuberosum PGSC0003DMG400011010
From GreeNC
This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.
| Gene alias / name | Chrom. | Start | End | Source | Assembly | Species | Details
|
|---|---|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMG400011010 PGSC0003DMG400011010 |
chr10 | 47052896 | 47058503 | Phytozome | v3.4 | Solanum_tuberosum | Coding? No |
This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.
| Transcript alias / name | Confidence | Pre-miRNA | Length | Sequence | Details
|
|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMT400028604 PGSC0003DMT400028604 PAC:24411859 |
High | No | 330 | Get ORF Coding potential... Type: noncoding Potential: -0.328 Folding energies... MFEI: -26.485 AMFE: -0.629 GC content %: 42.121 | |
| Stuberosum_PGSC0003DMT400028606 PGSC0003DMT400028606 PAC:24411860 |
Low | No | 4851 | Get ORF Coding potential... Type: noncoding Potential: -1.009 Folding energies... MFEI: -23.395 AMFE: -0.694 GC content %: 33.704 | |
| Stuberosum_PGSC0003DMT400028608 PGSC0003DMT400028608 PAC:24411861 |
Low | No | 5234 | Get ORF Coding potential... Type: noncoding Potential: -1.017 Folding energies... MFEI: -23.489 AMFE: -0.698 GC content %: 33.645 |
The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.
| Transcript alias | Database | Version | Hit | Evalue |
|---|---|---|---|---|
| Stuberosum_PGSC0003DMT400028606 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-5_STu | |
| Stuberosum_PGSC0003DMT400028608 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-5_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
