Gene
Stuberosum PGSC0003DMG400019084
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
|
|---|---|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMG400019084 PGSC0003DMG400019084 |
chr06 | 31762809 | 31771983 | Phytozome | v3.4 | Solanum_tuberosum | Coding? Yes |
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
|
|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMT400049099 PGSC0003DMT400049099 PAC:24394694 |
Low | No | 1141 | Get ORF Coding potential... Type: noncoding Potential: -1.101 Folding energies... MFEI: -19.711 AMFE: -0.592 GC content %: 33.304 | |
| Stuberosum_PGSC0003DMT400049102 PGSC0003DMT400049102 PAC:24394692 |
Low | No | 3803 | Get ORF Coding potential... Type: noncoding Potential: -1.195 Folding energies... MFEI: -21.636 AMFE: -0.669 GC content %: 32.343 | |
| Stuberosum_PGSC0003DMT400049105 PGSC0003DMT400049105 PAC:24394693 |
Low | No | 898 | Get ORF Coding potential... Type: noncoding Potential: -0.970 Folding energies... MFEI: -23.452 AMFE: -0.642 GC content %: 36.526 | |
| Stuberosum_PGSC0003DMT400049106 PGSC0003DMT400049106 PAC:24394691 |
Low | No | 2921 | Get ORF Coding potential... Type: noncoding Potential: -1.165 Folding energies... MFEI: -23.352 AMFE: -0.674 GC content %: 34.646 |
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 |
|---|---|---|---|---|
| Stuberosum_PGSC0003DMT400049099 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_STu | |
| Stuberosum_PGSC0003DMT400049102 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_STu | |
| Stuberosum_PGSC0003DMT400049105 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_STu | |
| Stuberosum_PGSC0003DMT400049106 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
