Gene
Stuberosum PGSC0003DMG400033140
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_PGSC0003DMG400033140 PGSC0003DMG400033140 |
chr06 | 40146433 | 40149282 | Phytozome | v3.4 | Solanum_tuberosum | Coding? Yes |
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_PGSC0003DMT400083246 PGSC0003DMT400083246 PAC:24394857 |
Low | No | 525 | Get ORF Coding potential... Type: noncoding Potential: -0.876 Folding energies... MFEI: -23.886 AMFE: -0.627 GC content %: 38.095 | |
| Stuberosum_PGSC0003DMT400083247 PGSC0003DMT400083247 PAC:24394858 |
Low | No | 1434 | Get ORF Coding potential... Type: noncoding Potential: -1.081 Folding energies... MFEI: -24.331 AMFE: -0.646 GC content %: 37.657 | |
| Stuberosum_PGSC0003DMT400083249 PGSC0003DMT400083249 PAC:24394856 |
High | No | 1275 | Get ORF Coding potential... Type: noncoding Potential: -0.730 Folding energies... MFEI: -24.643 AMFE: -0.647 GC content %: 38.118 |
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_PGSC0003DMT400083246 | SwissProt | 2015-06-01 | Q3JAI1 | 1.0e-4 |
| Stuberosum_PGSC0003DMT400083247 | SwissProt | 2015-06-01 | Q3JAI1 | 8.0e-4 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
