Gene
Stuberosum PGSC0003DMG400003862
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_PGSC0003DMG400003862 PGSC0003DMG400003862 |
chr09 | 4433882 | 4441967 | 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_PGSC0003DMT400009846 PGSC0003DMT400009846 PAC:24400805 |
Low | No | 908 | Get ORF Coding potential... Type: noncoding Potential: -1.270 Folding energies... MFEI: -24.196 AMFE: -0.631 GC content %: 38.326 | |
| Stuberosum_PGSC0003DMT400009847 PGSC0003DMT400009847 PAC:24400804 |
Low | No | 432 | Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -25.532 AMFE: -0.649 GC content %: 39.352 |
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_PGSC0003DMT400009846 | RepBase (RepeatMasker) | 2014-01-31 | RTE-1_STu | |
| Stuberosum_PGSC0003DMT400009847 | RepBase (RepeatMasker) | 2014-01-31 | SINE2-1_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
