Gene
Ptrichocarpa Potri.011G057300
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
|
|---|---|---|---|---|---|---|---|
| Ptrichocarpa_Potri.011G057300 Potri.011G057300 |
Chr11 | 5054662 | 5057043 | Phytozome | v3.0 | Populus_trichocarpa | 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
|
|---|---|---|---|---|---|
| Ptrichocarpa_Potri.011G057300.2 Potri.011G057300.2 PAC:27002913 |
Low | No | 753 | Get ORF Coding potential... Type: noncoding Potential: -0.897 Folding energies... MFEI: -24.236 AMFE: -0.538 GC content %: 45.020 | |
| Ptrichocarpa_Potri.011G057300.3 Potri.011G057300.3 PAC:27002917 |
Low | No | 684 | Get ORF Coding potential... Type: noncoding Potential: -0.877 Folding energies... MFEI: -24.327 AMFE: -0.533 GC content %: 45.614 | |
| Ptrichocarpa_Potri.011G057300.4 Potri.011G057300.4 PAC:27002914 |
Low | No | 884 | Get ORF Coding potential... Type: noncoding Potential: -0.939 Folding energies... MFEI: -22.738 AMFE: -0.529 GC content %: 42.986 | |
| Ptrichocarpa_Potri.011G057300.5 Potri.011G057300.5 PAC:27002918 |
Low | No | 947 | Get ORF Coding potential... Type: noncoding Potential: -0.979 Folding energies... MFEI: -27.064 AMFE: -0.631 GC content %: 42.872 | |
| Ptrichocarpa_Potri.011G057300.6 Potri.011G057300.6 PAC:27002915 |
Low | No | 692 | Get ORF Coding potential... Type: noncoding Potential: -0.883 Folding energies... MFEI: -25.087 AMFE: -0.565 GC content %: 44.364 | |
| Ptrichocarpa_Potri.011G057300.7 Potri.011G057300.7 PAC:27002916 |
Low | No | 687 | Get ORF Coding potential... Type: noncoding Potential: -0.928 Folding energies... MFEI: -24.600 AMFE: -0.558 GC content %: 44.105 |
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 |
|---|---|---|---|---|
| Ptrichocarpa_Potri.011G057300.2 | SwissProt | 2015-06-01 | Q93ZJ3 | 3.0e-12 |
| Ptrichocarpa_Potri.011G057300.3 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-8 |
| Ptrichocarpa_Potri.011G057300.4 | SwissProt | 2015-06-01 | Q93ZJ3 | 5.0e-12 |
| Ptrichocarpa_Potri.011G057300.5 | SwissProt | 2015-06-01 | Q93ZJ3 | 4.0e-8 |
| Ptrichocarpa_Potri.011G057300.6 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-8 |
| Ptrichocarpa_Potri.011G057300.7 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-8 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
