Gene
Stuberosum PGSC0003DMG400005068
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_PGSC0003DMG400005068 PGSC0003DMG400005068 |
chr03 | 4877600 | 4878447 | 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_PGSC0003DMT400013006 PGSC0003DMT400013006 PAC:24405613 |
Low | No | 489 | Get ORF Coding potential... Type: noncoding Potential: -1.130 Folding energies... MFEI: -22.147 AMFE: -0.660 GC content %: 33.538 | |
| Stuberosum_PGSC0003DMT400013007 PGSC0003DMT400013007 PAC:24405612 |
Low | No | 564 | Get ORF Coding potential... Type: noncoding Potential: -0.843 Folding energies... MFEI: -21.897 AMFE: -0.686 GC content %: 31.915 |
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_PGSC0003DMT400013007 | SwissProt | 2015-06-01 | P14903 | 6.0e-5 |
| Stuberosum_PGSC0003DMT400013006 | SwissProt | 2015-06-01 | P14903 | 1.0e-4 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
