Gene
Ptrichocarpa Potri.003G038400
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.003G038400 Potri.003G038400 |
Chr03 | 5053587 | 5059322 | 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.003G038400.10 Potri.003G038400.10 PAC:26997488 |
High | No | 685 | Get ORF Coding potential... Type: noncoding Potential: -0.525 Folding energies... MFEI: -24.599 AMFE: -0.674 GC content %: 36.496 | |
| Ptrichocarpa_Potri.003G038400.2 Potri.003G038400.2 PAC:26997482 |
High | No | 624 | Get ORF Coding potential... Type: noncoding Potential: -0.390 Folding energies... MFEI: -26.330 AMFE: -0.682 GC content %: 38.622 | |
| Ptrichocarpa_Potri.003G038400.3 Potri.003G038400.3 PAC:26997486 |
Low | No | 1091 | Get ORF Coding potential... Type: noncoding Potential: -0.535 Folding energies... MFEI: -27.965 AMFE: -0.675 GC content %: 41.430 | |
| Ptrichocarpa_Potri.003G038400.4 Potri.003G038400.4 PAC:26997483 |
Low | No | 561 | Get ORF Coding potential... Type: noncoding Potential: -0.359 Folding energies... MFEI: -28.039 AMFE: -0.690 GC content %: 40.642 | |
| Ptrichocarpa_Potri.003G038400.5 Potri.003G038400.5 PAC:26997484 |
Low | No | 1188 | Get ORF Coding potential... Type: noncoding Potential: -0.554 Folding energies... MFEI: -27.955 AMFE: -0.678 GC content %: 41.246 | |
| Ptrichocarpa_Potri.003G038400.6 Potri.003G038400.6 PAC:26997485 |
High | No | 761 | Get ORF Coding potential... Type: noncoding Potential: -0.446 Folding energies... MFEI: -26.938 AMFE: -0.666 GC content %: 40.473 | |
| Ptrichocarpa_Potri.003G038400.8 Potri.003G038400.8 PAC:26997487 |
High | No | 468 | Get ORF Coding potential... Type: noncoding Potential: -0.356 Folding energies... MFEI: -24.167 AMFE: -0.628 GC content %: 38.462 | |
| Ptrichocarpa_Potri.003G038400.9 Potri.003G038400.9 PAC:26997489 |
High | No | 1217 | Get ORF Coding potential... Type: noncoding Potential: -0.793 Folding energies... MFEI: -24.429 AMFE: -0.711 GC content %: 34.347 |
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.003G038400.5 | SwissProt | 2015-06-01 | Q8DLQ0 | 1.0e-5 |
| Ptrichocarpa_Potri.003G038400.3 | SwissProt | 2015-06-01 | Q8DLQ0 | 8.0e-6 |
| Ptrichocarpa_Potri.003G038400.4 | SwissProt | 2015-06-01 | Q8DLQ0 | 2.0e-6 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
