Gene
Ptrichocarpa Potri.015G137600
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.015G137600 Potri.015G137600 |
Chr15 | 14660710 | 14664078 | 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.015G137600.1 Potri.015G137600.1 PAC:27017174 |
Low | No | 713 | Get ORF Coding potential... Type: noncoding Potential: -0.318 Folding energies... MFEI: -21.052 AMFE: -0.550 GC content %: 38.289 | |
| Ptrichocarpa_Potri.015G137600.2 Potri.015G137600.2 PAC:27017175 |
Low | No | 724 | Get ORF Coding potential... Type: noncoding Potential: -0.365 Folding energies... MFEI: -22.569 AMFE: -0.594 GC content %: 37.983 | |
| Ptrichocarpa_Potri.015G137600.3 Potri.015G137600.3 PAC:27017176 |
Low | No | 1312 | Get ORF Coding potential... Type: noncoding Potential: -0.486 Folding energies... MFEI: -21.936 AMFE: -0.624 GC content %: 35.137 | |
| Ptrichocarpa_Potri.015G137600.4 Potri.015G137600.4 PAC:27017177 |
Low | No | 814 | Get ORF Coding potential... Type: noncoding Potential: -0.376 Folding energies... MFEI: -21.867 AMFE: -0.608 GC content %: 35.995 | |
| Ptrichocarpa_Potri.015G137600.5 Potri.015G137600.5 PAC:27017178 |
High | No | 701 | Get ORF Coding potential... Type: noncoding Potential: -0.810 Folding energies... MFEI: -21.840 AMFE: -0.643 GC content %: 33.951 |
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.015G137600.3 | SwissProt | 2015-06-01 | Q08747 | 4.0e-8 |
| Ptrichocarpa_Potri.015G137600.4 | SwissProt | 2015-06-01 | Q08747 | 2.0e-8 |
| Ptrichocarpa_Potri.015G137600.1 | SwissProt | 2015-06-01 | Q08747 | 9.0e-9 |
| Ptrichocarpa_Potri.015G137600.2 | SwissProt | 2015-06-01 | Q08747 | 6.0e-9 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
