Gene
Ptrichocarpa Potri.001G400100
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.001G400100 Potri.001G400100 |
Chr01 | 42186605 | 42187952 | Phytozome | v3.0 | Populus_trichocarpa | 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
|
|---|---|---|---|---|---|
| Ptrichocarpa_Potri.001G400100.1 Potri.001G400100.1 PAC:27044569 |
Low | No | 883 | Get ORF Coding potential... Type: noncoding Potential: -0.089 Folding energies... MFEI: -27.531 AMFE: -0.647 GC content %: 42.582 | |
| Ptrichocarpa_Potri.001G400100.2 Potri.001G400100.2 PAC:27044570 |
Low | No | 950 | Get ORF Coding potential... Type: noncoding Potential: -0.102 Folding energies... MFEI: -26.605 AMFE: -0.632 GC content %: 42.105 | |
| Ptrichocarpa_Potri.001G400100.3 Potri.001G400100.3 PAC:27044571 |
Low | No | 944 | Get ORF Coding potential... Type: noncoding Potential: -0.345 Folding energies... MFEI: -26.912 AMFE: -0.640 GC content %: 42.055 | |
| Ptrichocarpa_Potri.001G400100.4 Potri.001G400100.4 PAC:27044572 |
Low | No | 726 | Get ORF Coding potential... Type: noncoding Potential: -0.902 Folding energies... MFEI: -28.127 AMFE: -0.709 GC content %: 39.669 |
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.001G400100.3 | SwissProt | 2015-06-01 | Q96386 | 1.0e-12 |
| Ptrichocarpa_Potri.001G400100.4 | SwissProt | 2015-06-01 | Q96386 | 1.0e-7 |
| Ptrichocarpa_Potri.001G400100.1 | SwissProt | 2015-06-01 | Q96386 | 1.0e-16 |
| Ptrichocarpa_Potri.001G400100.2 | SwissProt | 2015-06-01 | Q96386 | 1.0e-16 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
