Gene
Ppatens Pp3c5 19420
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_Pp3c5_19420 Pp3c5_19420 |
Chr05 | 13637791 | 13639377 | 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_Pp3c5_19420V3.1 Pp3c5_19420V3.1 PAC:32955735 |
High | No | 841 | Get ORF Coding potential... Type: noncoding Potential: -1.097 Folding energies... MFEI: -29.512 AMFE: -0.697 GC content %: 42.331 | |
| Ppatens_Pp3c5_19420V3.2 Pp3c5_19420V3.2 PAC:32955736 |
High | No | 838 | Get ORF Coding potential... Type: noncoding Potential: -1.096 Folding energies... MFEI: -29.296 AMFE: -0.697 GC content %: 42.005 | |
| Ppatens_Pp3c5_19420V3.3 Pp3c5_19420V3.3 PAC:32955737 |
High | No | 1399 | Get ORF Coding potential... Type: noncoding Potential: -1.151 Folding energies... MFEI: -29.421 AMFE: -0.669 GC content %: 43.960 |
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_Pp3c5_19420V3.3 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-3_TA | |
| Ppatens_Pp3c5_19420V3.1 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-3_TA | |
| Ppatens_Pp3c5_19420V3.2 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-3_TA |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
