Gene
Ppatens Pp3c27 440
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_Pp3c27_440 Pp3c27_440 |
Chr27 | 268067 | 271575 | 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_Pp3c27_440V3.1 Pp3c27_440V3.1 PAC:32952307 |
High | No | 1842 | Get ORF Coding potential... Type: noncoding Potential: -1.193 Folding energies... MFEI: -26.037 AMFE: -0.638 GC content %: 40.825 | |
| Ppatens_Pp3c27_440V3.10 Pp3c27_440V3.10 PAC:32952317 |
High | No | 2216 | Get ORF Coding potential... Type: noncoding Potential: -1.210 Folding energies... MFEI: -27.572 AMFE: -0.652 GC content %: 42.283 | |
| Ppatens_Pp3c27_440V3.11 Pp3c27_440V3.11 PAC:32952318 |
High | No | 2403 | Get ORF Coding potential... Type: noncoding Potential: -1.216 Folding energies... MFEI: -27.495 AMFE: -0.652 GC content %: 42.197 | |
| Ppatens_Pp3c27_440V3.12 Pp3c27_440V3.12 PAC:32952319 |
High | No | 2503 | Get ORF Coding potential... Type: noncoding Potential: -1.219 Folding energies... MFEI: -27.024 AMFE: -0.645 GC content %: 41.870 | |
| Ppatens_Pp3c27_440V3.13 Pp3c27_440V3.13 PAC:32952320 |
High | No | 2690 | Get ORF Coding potential... Type: noncoding Potential: -1.224 Folding energies... MFEI: -26.993 AMFE: -0.645 GC content %: 41.822 | |
| Ppatens_Pp3c27_440V3.14 Pp3c27_440V3.14 PAC:32952309 |
High | No | 1755 | Get ORF Coding potential... Type: noncoding Potential: -1.093 Folding energies... MFEI: -25.100 AMFE: -0.632 GC content %: 39.715 | |
| Ppatens_Pp3c27_440V3.2 Pp3c27_440V3.2 PAC:32952308 |
High | No | 2029 | Get ORF Coding potential... Type: noncoding Potential: -1.202 Folding energies... MFEI: -26.111 AMFE: -0.639 GC content %: 40.858 | |
| Ppatens_Pp3c27_440V3.3 Pp3c27_440V3.3 PAC:32952310 |
High | No | 1555 | Get ORF Coding potential... Type: noncoding Potential: -1.175 Folding energies... MFEI: -26.701 AMFE: -0.648 GC content %: 41.222 | |
| Ppatens_Pp3c27_440V3.4 Pp3c27_440V3.4 PAC:32952311 |
High | No | 1742 | Get ORF Coding potential... Type: noncoding Potential: -1.187 Folding energies... MFEI: -26.734 AMFE: -0.649 GC content %: 41.217 | |
| Ppatens_Pp3c27_440V3.5 Pp3c27_440V3.5 PAC:32952312 |
High | No | 3206 | Get ORF Coding potential... Type: noncoding Potential: -1.235 Folding energies... MFEI: -27.261 AMFE: -0.645 GC content %: 42.265 | |
| Ppatens_Pp3c27_440V3.6 Pp3c27_440V3.6 PAC:32952313 |
High | No | 2014 | Get ORF Coding potential... Type: noncoding Potential: -1.201 Folding energies... MFEI: -27.105 AMFE: -0.641 GC content %: 42.304 | |
| Ppatens_Pp3c27_440V3.7 Pp3c27_440V3.7 PAC:32952314 |
High | No | 2201 | Get ORF Coding potential... Type: noncoding Potential: -1.209 Folding energies... MFEI: -26.901 AMFE: -0.637 GC content %: 42.208 | |
| Ppatens_Pp3c27_440V3.8 Pp3c27_440V3.8 PAC:32952315 |
High | No | 2301 | Get ORF Coding potential... Type: noncoding Potential: -1.213 Folding energies... MFEI: -26.601 AMFE: -0.636 GC content %: 41.851 | |
| Ppatens_Pp3c27_440V3.9 Pp3c27_440V3.9 PAC:32952316 |
High | No | 2488 | Get ORF Coding potential... Type: noncoding Potential: -1.219 Folding energies... MFEI: -26.483 AMFE: -0.634 GC content %: 41.801 |
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_Pp3c27_440V3.10 | RepBase (RepeatMasker) | 2014-01-31 | Copia-9_TA-I | |
| Ppatens_Pp3c27_440V3.11 | RepBase (RepeatMasker) | 2014-01-31 | Copia-9_TA-I | |
| Ppatens_Pp3c27_440V3.12 | RepBase (RepeatMasker) | 2014-01-31 | Copia-9_TA-I | |
| Ppatens_Pp3c27_440V3.13 | RepBase (RepeatMasker) | 2014-01-31 | Copia-9_TA-I |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
