Gene
Ppatens Pp3c7 14660
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_14660 Pp3c7_14660 |
Chr07 | 9884522 | 9887760 | 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_14660V3.1 Pp3c7_14660V3.1 PAC:32923721 |
High | No | 2384 | Get ORF Coding potential... Type: noncoding Potential: -1.162 Folding energies... MFEI: -27.081 AMFE: -0.667 GC content %: 40.604 | |
| Ppatens_Pp3c7_14660V3.2 Pp3c7_14660V3.2 PAC:32923722 |
High | No | 2394 | Get ORF Coding potential... Type: noncoding Potential: -1.163 Folding energies... MFEI: -26.988 AMFE: -0.666 GC content %: 40.518 | |
| Ppatens_Pp3c7_14660V3.3 Pp3c7_14660V3.3 PAC:32923723 |
High | No | 2312 | Get ORF Coding potential... Type: noncoding Potential: -1.161 Folding energies... MFEI: -26.955 AMFE: -0.669 GC content %: 40.268 | |
| Ppatens_Pp3c7_14660V3.4 Pp3c7_14660V3.4 PAC:32923724 |
High | No | 2322 | Get ORF Coding potential... Type: noncoding Potential: -1.161 Folding energies... MFEI: -26.860 AMFE: -0.668 GC content %: 40.181 | |
| Ppatens_Pp3c7_14660V3.5 Pp3c7_14660V3.5 PAC:32923725 |
High | No | 2538 | Get ORF Coding potential... Type: noncoding Potential: -1.165 Folding energies... MFEI: -26.950 AMFE: -0.664 GC content %: 40.583 | |
| Ppatens_Pp3c7_14660V3.6 Pp3c7_14660V3.6 PAC:32923726 |
High | No | 2431 | Get ORF Coding potential... Type: noncoding Potential: -1.163 Folding energies... MFEI: -27.281 AMFE: -0.635 GC content %: 42.986 | |
| Ppatens_Pp3c7_14660V3.7 Pp3c7_14660V3.7 PAC:32923727 |
High | No | 1444 | Get ORF Coding potential... Type: noncoding Potential: -1.133 Folding energies... MFEI: -28.310 AMFE: -0.618 GC content %: 45.776 |
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_14660V3.5 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR | |
| Ppatens_Pp3c7_14660V3.6 | RepBase (RepeatMasker) | 2014-01-31 | Copia-61_PT-I | |
| Ppatens_Pp3c7_14660V3.1 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR | |
| Ppatens_Pp3c7_14660V3.7 | RepBase (RepeatMasker) | 2014-01-31 | Copia-76_Mad-I | |
| Ppatens_Pp3c7_14660V3.2 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR | |
| Ppatens_Pp3c7_14660V3.3 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-15N_PPa-LTR | |
| Ppatens_Pp3c7_14660V3.4 | 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).
