Gene
Ppatens Pp3c23 5270
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
|
|---|---|---|---|---|---|---|---|
| Ppatens_Pp3c23_5270 Pp3c23_5270 |
Chr23 | 3609035 | 3611964 | Phytozome | v3.3 | Physcomitrella_patens | 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
|
|---|---|---|---|---|---|
| Ppatens_Pp3c23_5270V3.1 Pp3c23_5270V3.1 PAC:32949787 |
High | No | 1200 | Get ORF Coding potential... Type: noncoding Potential: -0.918 Folding energies... MFEI: -28.175 AMFE: -0.658 GC content %: 42.833 | |
| Ppatens_Pp3c23_5270V3.2 Pp3c23_5270V3.2 PAC:32949788 |
High | No | 1203 | Get ORF Coding potential... Type: noncoding Potential: -0.919 Folding energies... MFEI: -28.055 AMFE: -0.654 GC content %: 42.893 | |
| Ppatens_Pp3c23_5270V3.3 Pp3c23_5270V3.3 PAC:32949789 |
High | No | 1598 | Get ORF Coding potential... Type: noncoding Potential: -0.944 Folding energies... MFEI: -28.060 AMFE: -0.692 GC content %: 40.551 | |
| Ppatens_Pp3c23_5270V3.4 Pp3c23_5270V3.4 PAC:32949786 |
High | No | 479 | Get ORF Coding potential... Type: noncoding Potential: -0.754 Folding energies... MFEI: -21.106 AMFE: -0.455 GC content %: 46.347 |
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 |
|---|---|---|---|---|
| Ppatens_Pp3c23_5270V3.2 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR | |
| Ppatens_Pp3c23_5270V3.3 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR | |
| Ppatens_Pp3c23_5270V3.1 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
