Gene
Stuberosum PGSC0003DMG400019689
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_PGSC0003DMG400019689 PGSC0003DMG400019689 |
chr04 | 52037969 | 52043432 | 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_PGSC0003DMT400050703 PGSC0003DMT400050703 PAC:24384145 |
Low | No | 5464 | Get ORF Coding potential... Type: noncoding Potential: -1.008 Folding energies... MFEI: -24.597 AMFE: -0.683 GC content %: 36.018 | |
| Stuberosum_PGSC0003DMT400050704 PGSC0003DMT400050704 PAC:24384146 |
Low | No | 5464 | Get ORF Coding potential... Type: noncoding Potential: -1.008 Folding energies... MFEI: -24.597 AMFE: -0.683 GC content %: 36.018 | |
| Stuberosum_PGSC0003DMT400050707 PGSC0003DMT400050707 PAC:24384147 |
Low | No | 3522 | Get ORF Coding potential... Type: noncoding Potential: -0.986 Folding energies... MFEI: -24.807 AMFE: -0.689 GC content %: 36.002 |
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_PGSC0003DMT400050704 | RepBase (RepeatMasker) | 2014-01-31 | GYPSODE1_I-int | |
| Stuberosum_PGSC0003DMT400050707 | RepBase (RepeatMasker) | 2014-01-31 | GYPSODE1_I-int | |
| Stuberosum_PGSC0003DMT400050703 | SwissProt | 2015-06-01 | Q5M759 | 9.0e-6 |
| Stuberosum_PGSC0003DMT400050704 | SwissProt | 2015-06-01 | Q5M759 | 9.0e-6 |
| Stuberosum_PGSC0003DMT400050707 | SwissProt | 2015-06-01 | Q5M759 | 6.0e-6 |
| Stuberosum_PGSC0003DMT400050703 | RepBase (RepeatMasker) | 2014-01-31 | GYPSODE1_I-int |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
