Gene
Stuberosum PGSC0003DMG400001428
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_PGSC0003DMG400001428 PGSC0003DMG400001428 |
chr02 | 67293567 | 67296488 | 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_PGSC0003DMT400003612 PGSC0003DMT400003612 PAC:24426331 |
Low | No | 2794 | Get ORF Coding potential... Type: noncoding Potential: -1.021 Folding energies... MFEI: -23.769 AMFE: -0.666 GC content %: 35.684 | |
| Stuberosum_PGSC0003DMT400003613 PGSC0003DMT400003613 PAC:24426330 |
Low | No | 2797 | Get ORF Coding potential... Type: noncoding Potential: -1.022 Folding energies... MFEI: -23.790 AMFE: -0.666 GC content %: 35.717 | |
| Stuberosum_PGSC0003DMT400003614 PGSC0003DMT400003614 PAC:24426329 |
Low | No | 2467 | Get ORF Coding potential... Type: noncoding Potential: -1.010 Folding energies... MFEI: -23.956 AMFE: -0.666 GC content %: 35.995 |
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_PGSC0003DMT400003614 | SwissProt | 2015-06-01 | Q9D8Z1 | 4.0e-5 |
| Stuberosum_PGSC0003DMT400003612 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-6_STu | |
| Stuberosum_PGSC0003DMT400003613 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-6_STu | |
| Stuberosum_PGSC0003DMT400003614 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-6_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
