Gene
Ptrichocarpa Potri.013G131200
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.013G131200 Potri.013G131200 |
Chr13 | 14263846 | 14265139 | 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.013G131200.1 Potri.013G131200.1 PAC:26994480 |
Low | No | 841 | Get ORF Coding potential... Type: noncoding Potential: -0.004 Folding energies... MFEI: -25.945 AMFE: -0.667 GC content %: 38.882 | |
| Ptrichocarpa_Potri.013G131200.2 Potri.013G131200.2 PAC:26994481 |
Low | No | 923 | Get ORF Coding potential... Type: noncoding Potential: -0.028 Folding energies... MFEI: -25.991 AMFE: -0.661 GC content %: 39.328 | |
| Ptrichocarpa_Potri.013G131200.3 Potri.013G131200.3 PAC:26994482 |
Low | No | 872 | Get ORF Coding potential... Type: noncoding Potential: -0.038 Folding energies... MFEI: -25.837 AMFE: -0.659 GC content %: 39.220 |
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.013G131200.2 | SwissProt | 2015-06-01 | P43390 | 5.0e-17 |
| Ptrichocarpa_Potri.013G131200.3 | SwissProt | 2015-06-01 | P43390 | 9.0e-18 |
| Ptrichocarpa_Potri.013G131200.1 | SwissProt | 2015-06-01 | P43390 | 3.0e-17 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
