Gene
Stuberosum PGSC0003DMG400023979
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_PGSC0003DMG400023979 PGSC0003DMG400023979 |
chr11 | 6745829 | 6747477 | 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_PGSC0003DMT400061601 PGSC0003DMT400061601 PAC:24409805 |
High | No | 294 | Get ORF Coding potential... Type: noncoding Potential: -0.261 Folding energies... MFEI: -25.578 AMFE: -0.549 GC content %: 46.599 | |
| Stuberosum_PGSC0003DMT400061602 PGSC0003DMT400061602 PAC:24409806 |
Low | No | 1311 | Get ORF Coding potential... Type: noncoding Potential: -0.662 Folding energies... MFEI: -25.568 AMFE: -0.721 GC content %: 35.469 | |
| Stuberosum_PGSC0003DMT400061603 PGSC0003DMT400061603 PAC:24409804 |
Low | No | 1442 | Get ORF Coding potential... Type: noncoding Potential: -0.769 Folding energies... MFEI: -25.118 AMFE: -0.710 GC content %: 35.368 |
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_PGSC0003DMT400061602 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-3_STu | |
| Stuberosum_PGSC0003DMT400061603 | RepBase (RepeatMasker) | 2014-01-31 | DNA3-3_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
