Gene
Stuberosum PGSC0003DMG400003511
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_PGSC0003DMG400003511 PGSC0003DMG400003511 |
chr02 | 62413307 | 62418945 | Phytozome | v3.4 | Solanum_tuberosum | 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
|
|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMT400009034 PGSC0003DMT400009034 PAC:24426269 |
Low | No | 4832 | Get ORF Coding potential... Type: noncoding Potential: -1.293 Folding energies... MFEI: -20.346 AMFE: -0.646 GC content %: 31.478 | |
| Stuberosum_PGSC0003DMT400009035 PGSC0003DMT400009035 PAC:24426267 |
Low | No | 3887 | Get ORF Coding potential... Type: noncoding Potential: -1.282 Folding energies... MFEI: -20.846 AMFE: -0.640 GC content %: 32.596 | |
| Stuberosum_PGSC0003DMT400009036 PGSC0003DMT400009036 PAC:24426270 |
Low | No | 3049 | Get ORF Coding potential... Type: noncoding Potential: -1.304 Folding energies... MFEI: -19.475 AMFE: -0.622 GC content %: 31.322 | |
| Stuberosum_PGSC0003DMT400009037 PGSC0003DMT400009037 PAC:24426268 |
Low | No | 2454 | Get ORF Coding potential... Type: noncoding Potential: -1.249 Folding energies... MFEI: -22.115 AMFE: -0.654 GC content %: 33.822 | |
| Stuberosum_PGSC0003DMT400009038 PGSC0003DMT400009038 PAC:24426271 |
High | No | 1155 | Get ORF Coding potential... Type: noncoding Potential: -1.230 Folding energies... MFEI: -24.320 AMFE: -0.670 GC content %: 36.277 |
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_PGSC0003DMT400009035 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-6_STu | |
| Stuberosum_PGSC0003DMT400009036 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-6_STu | |
| Stuberosum_PGSC0003DMT400009037 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-6_STu | |
| Stuberosum_PGSC0003DMT400009034 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-6_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
