Gene
Ppatens Pp3c7 24660
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_Pp3c7_24660 Pp3c7_24660 |
Chr07 | 16590371 | 16592768 | 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_Pp3c7_24660V3.1 Pp3c7_24660V3.1 PAC:32925204 |
Low | No | 922 | Get ORF Coding potential... Type: noncoding Potential: -0.515 Folding energies... MFEI: -28.427 AMFE: -0.649 GC content %: 43.818 | |
| Ppatens_Pp3c7_24660V3.2 Pp3c7_24660V3.2 PAC:32925205 |
Low | No | 1024 | Get ORF Coding potential... Type: noncoding Potential: -0.540 Folding energies... MFEI: -27.246 AMFE: -0.638 GC content %: 42.676 | |
| Ppatens_Pp3c7_24660V3.3 Pp3c7_24660V3.3 PAC:32925206 |
Low | No | 1054 | Get ORF Coding potential... Type: noncoding Potential: -0.547 Folding energies... MFEI: -27.960 AMFE: -0.656 GC content %: 42.600 | |
| Ppatens_Pp3c7_24660V3.4 Pp3c7_24660V3.4 PAC:32925211 |
Low | No | 991 | Get ORF Coding potential... Type: noncoding Potential: -0.620 Folding energies... MFEI: -27.598 AMFE: -0.644 GC content %: 42.886 | |
| Ppatens_Pp3c7_24660V3.5 Pp3c7_24660V3.5 PAC:32925208 |
High | No | 899 | Get ORF Coding potential... Type: noncoding Potential: -0.588 Folding energies... MFEI: -28.276 AMFE: -0.650 GC content %: 43.493 | |
| Ppatens_Pp3c7_24660V3.6 Pp3c7_24660V3.6 PAC:32925209 |
High | No | 1001 | Get ORF Coding potential... Type: noncoding Potential: -0.612 Folding energies... MFEI: -26.923 AMFE: -0.636 GC content %: 42.358 | |
| Ppatens_Pp3c7_24660V3.7 Pp3c7_24660V3.7 PAC:32925210 |
High | No | 1031 | Get ORF Coding potential... Type: noncoding Potential: -0.618 Folding energies... MFEI: -27.682 AMFE: -0.655 GC content %: 42.289 | |
| Ppatens_Pp3c7_24660V3.8 Pp3c7_24660V3.8 PAC:32925207 |
Low | No | 862 | Get ORF Coding potential... Type: noncoding Potential: -0.498 Folding energies... MFEI: -27.111 AMFE: -0.640 GC content %: 42.343 |
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_Pp3c7_24660V3.3 | SwissProt | 2015-06-01 | O65154 | 5.0e-10 |
| Ppatens_Pp3c7_24660V3.4 | SwissProt | 2015-06-01 | O65154 | 2.0e-6 |
| Ppatens_Pp3c7_24660V3.8 | SwissProt | 2015-06-01 | O65154 | 2.0e-10 |
| Ppatens_Pp3c7_24660V3.1 | SwissProt | 2015-06-01 | O65154 | 3.0e-10 |
| Ppatens_Pp3c7_24660V3.2 | SwissProt | 2015-06-01 | O65154 | 5.0e-10 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
