Gene
Ppersica Prupe.4G194800
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
|
|---|---|---|---|---|---|---|---|
| Ppersica_Prupe.4G194800 Prupe.4G194800 |
Pp04 | 11842982 | 11849953 | Phytozome | v2.1 | Prunus_persica | 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
|
|---|---|---|---|---|---|
| Ppersica_Prupe.4G194800.1 Prupe.4G194800.1 PAC:32092621 |
High | No | 1147 | Get ORF Coding potential... Type: noncoding Potential: -0.836 Folding energies... MFEI: -20.262 AMFE: -0.525 GC content %: 38.622 | |
| Ppersica_Prupe.4G194800.2 Prupe.4G194800.2 PAC:32092625 |
Low | No | 827 | Get ORF Coding potential... Type: noncoding Potential: -0.923 Folding energies... MFEI: -26.010 AMFE: -0.609 GC content %: 42.684 | |
| Ppersica_Prupe.4G194800.3 Prupe.4G194800.3 PAC:32092626 |
Low | No | 790 | Get ORF Coding potential... Type: noncoding Potential: -0.916 Folding energies... MFEI: -26.658 AMFE: -0.618 GC content %: 43.165 | |
| Ppersica_Prupe.4G194800.4 Prupe.4G194800.4 PAC:32092623 |
Low | No | 1342 | Get ORF Coding potential... Type: noncoding Potential: -1.027 Folding energies... MFEI: -20.462 AMFE: -0.558 GC content %: 36.662 | |
| Ppersica_Prupe.4G194800.5 Prupe.4G194800.5 PAC:32092624 |
Low | No | 1304 | Get ORF Coding potential... Type: noncoding Potential: -1.025 Folding energies... MFEI: -20.759 AMFE: -0.564 GC content %: 36.810 | |
| Ppersica_Prupe.4G194800.6 Prupe.4G194800.6 PAC:32092622 |
High | No | 967 | Get ORF Coding potential... Type: noncoding Potential: -0.989 Folding energies... MFEI: -20.155 AMFE: -0.506 GC content %: 39.814 |
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 |
|---|---|---|---|---|
| Ppersica_Prupe.4G194800.3 | RepBase (RepeatMasker) | 2014-01-31 | DNA-3_FV | |
| Ppersica_Prupe.4G194800.4 | RepBase (RepeatMasker) | 2014-01-31 | MuDRASH3_MT | |
| Ppersica_Prupe.4G194800.5 | RepBase (RepeatMasker) | 2014-01-31 | MuDRASH3_MT | |
| Ppersica_Prupe.4G194800.2 | RepBase (RepeatMasker) | 2014-01-31 | DNA-3_FV |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
