Gene
Stuberosum PGSC0003DMG403001341
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_PGSC0003DMG403001341 PGSC0003DMG403001341 |
chr02 | 67220033 | 67223604 | 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_PGSC0003DMT400003392 PGSC0003DMT400003392 PAC:24426897 |
Low | No | 3242 | Get ORF Coding potential... Type: noncoding Potential: -0.730 Folding energies... MFEI: -24.479 AMFE: -0.653 GC content %: 37.477 | |
| Stuberosum_PGSC0003DMT400003393 PGSC0003DMT400003393 PAC:24426898 |
Low | No | 3376 | Get ORF Coding potential... Type: noncoding Potential: -0.855 Folding energies... MFEI: -24.843 AMFE: -0.661 GC content %: 37.589 |
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_PGSC0003DMT400003392 | RepBase (RepeatMasker) | 2014-01-31 | TS | |
| Stuberosum_PGSC0003DMT400003393 | RepBase (RepeatMasker) | 2014-01-31 | TS |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
