Gene
Stuberosum PGSC0003DMG400020979
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_PGSC0003DMG400020979 PGSC0003DMG400020979 |
chr01 | 73522852 | 73525411 | 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_PGSC0003DMT400054095 PGSC0003DMT400054095 PAC:24421642 |
High | No | 462 | Get ORF Coding potential... Type: noncoding Potential: -0.958 Folding energies... MFEI: -22.338 AMFE: -0.558 GC content %: 40.043 | |
| Stuberosum_PGSC0003DMT400054096 PGSC0003DMT400054096 PAC:24421641 |
High | No | 364 | Get ORF Coding potential... Type: noncoding Potential: -0.810 Folding energies... MFEI: -21.593 AMFE: -0.514 GC content %: 42.033 | |
| Stuberosum_PGSC0003DMT400054097 PGSC0003DMT400054097 PAC:24421640 |
Low | No | 1847 | Get ORF Coding potential... Type: noncoding Potential: -0.622 Folding energies... MFEI: -24.970 AMFE: -0.681 GC content %: 36.654 |
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_PGSC0003DMT400054097 | SwissProt | 2015-06-01 | Q9LHY9 | 1.0e-10 |
| Stuberosum_PGSC0003DMT400054097 | RepBase (RepeatMasker) | 2014-01-31 | HARB-1_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
