Stuberosum PGSC0003DMG400000397
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 | Assembly | Species | Details
|
|---|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMG400000397 [ PGSC0003DMG400000397] |
ST4.03ch11 | 38663468 | 38666293 | v4.03 | Solanum tuberosum (Phytozome 13) | 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 | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Stuberosum_PGSC0003DMT400001052 PGSC0003DMT400001052 |
Low | No | 204 | OG0014490 | Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -23.873 AMFE: -0.594 GC content %: 40.196 | |
| Stuberosum_PGSC0003DMT400001053 PGSC0003DMT400001053 |
High | No | 318 | OG0332517 | Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -25.409 AMFE: -0.599 GC content %: 42.453 | |
| Stuberosum_PGSC0003DMT400001054 PGSC0003DMT400001054 |
Low | No | 204 | OG0014490 | Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -23.873 AMFE: -0.594 GC content %: 40.196 | |
| Stuberosum_PGSC0003DMT400001055 PGSC0003DMT400001055 |
Low | No | 210 | OG0014490 | Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -22.333 AMFE: -0.527 GC content %: 42.381 | |
| Stuberosum_PGSC0003DMT400001056 PGSC0003DMT400001056 |
Low | No | 204 | OG0014490 | Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -23.873 AMFE: -0.594 GC content %: 40.196 |
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_PGSC0003DMT400001056 | SwissProt | 2021-04-01 | Q8L7W2 | 6.76e-4 |
| Stuberosum_PGSC0003DMT400001052 | SwissProt | 2021-04-01 | Q8L7W2 | 6.76e-4 |
| Stuberosum_PGSC0003DMT400001054 | SwissProt | 2021-04-01 | Q8L7W2 | 6.76e-4 |
| Stuberosum_PGSC0003DMT400001055 | SwissProt | 2021-04-01 | Q8L7W2 | 1.38e-6 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
