Pvirgatum Pavir.9KG218557
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 | Assembly | Species | Details
|
|---|---|---|---|---|---|---|
| Pvirgatum_Pavir.9KG218557 [ Pavir.9KG218557] |
Chr09K | 47883119 | 47889346 | v5.1 | Panicum virgatum (Phytozome 13) | 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 | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Pvirgatum_Pavir.9KG218557.1 Pavir.9KG218557.1 |
Low | No | 1155 | OG0014289 | Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -27.654 AMFE: -0.645 GC content %: 42.857 | |
| Pvirgatum_Pavir.9KG218557.2 Pavir.9KG218557.2 |
High | No | 231 | OG0056230 | Get ORF Coding potential... Type: noncoding Potential: -0.662 Folding energies... MFEI: -29.091 AMFE: -0.521 GC content %: 55.844 | |
| Pvirgatum_Pavir.9KG218557.3 Pavir.9KG218557.3 |
Low | No | 941 | OG0014289 | Get ORF Coding potential... Type: noncoding Potential: -1.002 Folding energies... MFEI: -28.108 AMFE: -0.636 GC content %: 44.208 | |
| Pvirgatum_Pavir.9KG218557.4 Pavir.9KG218557.4 |
Low | No | 837 | OG0014289 | Get ORF Coding potential... Type: noncoding Potential: -0.977 Folding energies... MFEI: -28.781 AMFE: -0.636 GC content %: 45.281 | |
| Pvirgatum_Pavir.9KG218557.5 Pavir.9KG218557.5 |
High | No | 213 | OG0056230 | Get ORF Coding potential... Type: noncoding Potential: -0.843 Folding energies... MFEI: -31.549 AMFE: -0.542 GC content %: 58.216 | |
| Pvirgatum_Pavir.9KG218557.6 Pavir.9KG218557.6 |
Low | No | 840 | OG0014289 | Get ORF Coding potential... Type: noncoding Potential: -1.176 Folding energies... MFEI: -28.024 AMFE: -0.628 GC content %: 44.643 |
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 |
|---|---|---|---|---|
| Pvirgatum_Pavir.9KG218557.1 | RepBase (RepeatMasker) | 2014-01-31 | RC/Helitron | |
| Pvirgatum_Pavir.9KG218557.3 | RepBase (RepeatMasker) | 2014-01-31 | RC/Helitron | |
| Pvirgatum_Pavir.9KG218557.4 | RepBase (RepeatMasker) | 2014-01-31 | RC/Helitron | |
| Pvirgatum_Pavir.9KG218557.6 | RepBase (RepeatMasker) | 2014-01-31 | RC/Helitron |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
