Gene
Ppatens Pp3c16 4930
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_Pp3c16_4930 Pp3c16_4930 |
Chr16 | 3420153 | 3422177 | 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_Pp3c16_4930V3.2 Pp3c16_4930V3.2 PAC:32984156 |
Low | No | 903 | Get ORF Coding potential... Type: noncoding Potential: -0.459 Folding energies... MFEI: -29.336 AMFE: -0.654 GC content %: 44.850 | |
| Ppatens_Pp3c16_4930V3.3 Pp3c16_4930V3.3 PAC:32984157 |
Low | No | 897 | Get ORF Coding potential... Type: noncoding Potential: -0.300 Folding energies... MFEI: -28.919 AMFE: -0.647 GC content %: 44.705 | |
| Ppatens_Pp3c16_4930V3.5 Pp3c16_4930V3.5 PAC:32984158 |
Low | No | 893 | Get ORF Coding potential... Type: noncoding Potential: -0.300 Folding energies... MFEI: -27.335 AMFE: -0.637 GC content %: 42.889 | |
| Ppatens_Pp3c16_4930V3.7 Pp3c16_4930V3.7 PAC:32984155 |
Low | No | 1120 | Get ORF Coding potential... Type: noncoding Potential: -0.358 Folding energies... MFEI: -28.652 AMFE: -0.650 GC content %: 44.107 | |
| Ppatens_Pp3c16_4930V3.8 Pp3c16_4930V3.8 PAC:32984154 |
Low | No | 958 | Get ORF Coding potential... Type: noncoding Potential: -0.482 Folding energies... MFEI: -29.614 AMFE: -0.657 GC content %: 45.094 |
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_Pp3c16_4930V3.3 | SwissProt | 2015-06-01 | A4K526 | 3.0e-17 |
| Ppatens_Pp3c16_4930V3.5 | SwissProt | 2015-06-01 | A4K526 | 3.0e-12 |
| Ppatens_Pp3c16_4930V3.7 | SwissProt | 2015-06-01 | A4K526 | 6.0e-12 |
| Ppatens_Pp3c16_4930V3.8 | SwissProt | 2015-06-01 | A4K526 | 6.0e-13 |
| Ppatens_Pp3c16_4930V3.2 | SwissProt | 2015-06-01 | A4K526 | 7.0e-16 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
