Gene
Stuberosum PGSC0003DMG400003507
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_PGSC0003DMG400003507 PGSC0003DMG400003507 |
chr02 | 62513229 | 62521477 | 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_PGSC0003DMT400009022 PGSC0003DMT400009022 PAC:24425172 |
High | No | 3527 | Get ORF Coding potential... Type: noncoding Potential: -1.110 Folding energies... MFEI: -20.743 AMFE: -0.619 GC content %: 33.513 | |
| Stuberosum_PGSC0003DMT400009024 PGSC0003DMT400009024 PAC:24425169 |
Low | No | 4279 | Get ORF Coding potential... Type: noncoding Potential: -0.635 Folding energies... MFEI: -21.028 AMFE: -0.648 GC content %: 32.437 | |
| Stuberosum_PGSC0003DMT400009025 PGSC0003DMT400009025 PAC:24425170 |
Low | No | 5607 | Get ORF Coding potential... Type: noncoding Potential: -0.648 Folding energies... MFEI: -22.096 AMFE: -0.654 GC content %: 33.761 | |
| Stuberosum_PGSC0003DMT400009026 PGSC0003DMT400009026 PAC:24425168 |
High | No | 4412 | Get ORF Coding potential... Type: noncoding Potential: -0.637 Folding energies... MFEI: -21.074 AMFE: -0.645 GC content %: 32.661 | |
| Stuberosum_PGSC0003DMT400009027 PGSC0003DMT400009027 PAC:24425167 |
Low | No | 5006 | Get ORF Coding potential... Type: noncoding Potential: -0.643 Folding energies... MFEI: -22.299 AMFE: -0.651 GC content %: 34.239 | |
| Stuberosum_PGSC0003DMT400009029 PGSC0003DMT400009029 PAC:24425173 |
Low | No | 1573 | Get ORF Coding potential... Type: noncoding Potential: -0.935 Folding energies... MFEI: -24.107 AMFE: -0.656 GC content %: 36.745 |
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_PGSC0003DMT400009029 | SwissProt | 2015-06-01 | P26577 | 3.0e-83 |
| Stuberosum_PGSC0003DMT400009024 | RepBase (RepeatMasker) | 2014-01-31 | Copia-1_ST-LTR | |
| Stuberosum_PGSC0003DMT400009025 | SwissProt | 2015-06-01 | P26577 | 1.0e-82 |
| Stuberosum_PGSC0003DMT400009027 | SwissProt | 2015-06-01 | P26577 | 1.0e-82 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
