Pvirgatum Pavir.4KG233800
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.4KG233800 [ Pavir.4KG233800] |
Chr04K | 24176839 | 24179757 | 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.4KG233800.1 Pavir.4KG233800.1 |
High | No | 566 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -1.099 Folding energies... MFEI: -29.823 AMFE: -0.532 GC content %: 56.007 | |
| Pvirgatum_Pavir.4KG233800.10 Pavir.4KG233800.10 |
Low | No | 625 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -1.126 Folding energies... MFEI: -29.440 AMFE: -0.558 GC content %: 52.800 | |
| Pvirgatum_Pavir.4KG233800.11 Pavir.4KG233800.11 |
High | No | 731 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -0.929 Folding energies... MFEI: -32.585 AMFE: -0.588 GC content %: 55.404 | |
| Pvirgatum_Pavir.4KG233800.12 Pavir.4KG233800.12 |
Low | No | 880 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -0.887 Folding energies... MFEI: -30.477 AMFE: -0.576 GC content %: 52.955 | |
| Pvirgatum_Pavir.4KG233800.13 Pavir.4KG233800.13 |
High | No | 724 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -0.894 Folding energies... MFEI: -32.500 AMFE: -0.590 GC content %: 55.110 | |
| Pvirgatum_Pavir.4KG233800.14 Pavir.4KG233800.14 |
High | No | 686 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -0.882 Folding energies... MFEI: -33.790 AMFE: -0.602 GC content %: 56.122 | |
| Pvirgatum_Pavir.4KG233800.15 Pavir.4KG233800.15 |
Low | No | 1008 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -0.961 Folding energies... MFEI: -29.623 AMFE: -0.597 GC content %: 49.603 | |
| Pvirgatum_Pavir.4KG233800.8 Pavir.4KG233800.8 |
High | No | 698 | OG0003481 | Get ORF Coding potential... Type: noncoding Potential: -0.919 Folding energies... MFEI: -33.223 AMFE: -0.598 GC content %: 55.587 |
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.4KG233800.10 | RepBase (RepeatMasker) | 2014-01-31 | RC/Helitron | |
| Pvirgatum_Pavir.4KG233800.12 | RepBase (RepeatMasker) | 2014-01-31 | RC/Helitron | |
| Pvirgatum_Pavir.4KG233800.15 | 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).
