Gene
Stuberosum PGSC0003DMG402018530
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_PGSC0003DMG402018530 PGSC0003DMG402018530 |
chr03 | 17023196 | 17025355 | 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_PGSC0003DMT400047678 PGSC0003DMT400047678 PAC:24403613 |
Low | No | 587 | Get ORF Coding potential... Type: noncoding Potential: -0.360 Folding energies... MFEI: -25.468 AMFE: -0.680 GC content %: 37.479 | |
| Stuberosum_PGSC0003DMT400047679 PGSC0003DMT400047679 PAC:24403614 |
Low | No | 1116 | Get ORF Coding potential... Type: noncoding Potential: -0.681 Folding energies... MFEI: -25.412 AMFE: -0.697 GC content %: 36.470 | |
| Stuberosum_PGSC0003DMT400047680 PGSC0003DMT400047680 PAC:24403615 |
High | No | 606 | Get ORF Coding potential... Type: noncoding Potential: -0.729 Folding energies... MFEI: -24.340 AMFE: -0.699 GC content %: 34.818 |
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_PGSC0003DMT400047678 | SwissProt | 2015-06-01 | Q14657 | 1.0e-5 |
| Stuberosum_PGSC0003DMT400047679 | SwissProt | 2015-06-01 | Q14657 | 4.0e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
