Gene
Ptrichocarpa Potri.003G044400
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.003G044400 Potri.003G044400 |
Chr03 | 5919475 | 5923945 | 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.003G044400.1 Potri.003G044400.1 PAC:26998565 |
High | No | 1101 | Get ORF Coding potential... Type: noncoding Potential: -0.873 Folding energies... MFEI: -26.176 AMFE: -0.642 GC content %: 40.781 | |
| Ptrichocarpa_Potri.003G044400.2 Potri.003G044400.2 PAC:26998564 |
High | No | 950 | Get ORF Coding potential... Type: noncoding Potential: -0.840 Folding energies... MFEI: -25.221 AMFE: -0.622 GC content %: 40.526 | |
| Ptrichocarpa_Potri.003G044400.3 Potri.003G044400.3 PAC:26998567 |
Low | No | 1659 | Get ORF Coding potential... Type: noncoding Potential: -0.960 Folding energies... MFEI: -25.835 AMFE: -0.662 GC content %: 38.999 | |
| Ptrichocarpa_Potri.003G044400.4 Potri.003G044400.4 PAC:26998568 |
Low | No | 1749 | Get ORF Coding potential... Type: noncoding Potential: -0.967 Folding energies... MFEI: -25.592 AMFE: -0.673 GC content %: 38.022 | |
| Ptrichocarpa_Potri.003G044400.5 Potri.003G044400.5 PAC:26998569 |
Low | No | 1687 | Get ORF Coding potential... Type: noncoding Potential: -0.962 Folding energies... MFEI: -25.649 AMFE: -0.677 GC content %: 37.878 | |
| Ptrichocarpa_Potri.003G044400.6 Potri.003G044400.6 PAC:26998570 |
Low | No | 1547 | Get ORF Coding potential... Type: noncoding Potential: -0.950 Folding energies... MFEI: -25.268 AMFE: -0.664 GC content %: 38.074 | |
| Ptrichocarpa_Potri.003G044400.7 Potri.003G044400.7 PAC:26998566 |
Low | No | 952 | Get ORF Coding potential... Type: noncoding Potential: -0.851 Folding energies... MFEI: -24.149 AMFE: -0.630 GC content %: 38.340 |
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.003G044400.5 | SwissProt | 2015-06-01 | Q8L9S1 | 8.0e-5 |
| Ptrichocarpa_Potri.003G044400.6 | SwissProt | 2015-06-01 | Q8L9S1 | 7.0e-5 |
| Ptrichocarpa_Potri.003G044400.7 | SwissProt | 2015-06-01 | Q8L9S1 | 6.0e-5 |
| Ptrichocarpa_Potri.003G044400.3 | SwissProt | 2015-06-01 | Q8L9S1 | 4.0e-5 |
| Ptrichocarpa_Potri.003G044400.4 | SwissProt | 2015-06-01 | Q8L9S1 | 8.0e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
