Stuberosum PGSC0003DMG402031237
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_PGSC0003DMG402031237 [ PGSC0003DMG402031237] |
ST4.03ch10 | 48908041 | 48919076 | 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_PGSC0003DMT400080249 PGSC0003DMT400080249 |
Low | No | 357 | OG0002722 | Get ORF Coding potential... Type: noncoding Potential: -0.223 Folding energies... MFEI: -33.641 AMFE: -0.667 GC content %: 50.420 | |
| Stuberosum_PGSC0003DMT400080251 PGSC0003DMT400080251 |
Low | No | 345 | OG0002722 | Get ORF Coding potential... Type: noncoding Potential: -0.193 Folding energies... MFEI: -34.899 AMFE: -0.673 GC content %: 51.884 | |
| Stuberosum_PGSC0003DMT400080252 PGSC0003DMT400080252 |
Low | No | 345 | OG0003506 | Get ORF Coding potential... Type: noncoding Potential: -0.091 Folding energies... MFEI: -38.464 AMFE: -0.750 GC content %: 51.304 | |
| Stuberosum_PGSC0003DMT400080253 PGSC0003DMT400080253 |
Low | No | 345 | OG0002722 | Get ORF Coding potential... Type: noncoding Potential: -0.344 Folding energies... MFEI: -36.058 AMFE: -0.687 GC content %: 52.464 |
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_PGSC0003DMT400080251 | SwissProt | 2021-04-01 | Q03461 | 8.0e-51 |
| Stuberosum_PGSC0003DMT400080252 | SwissProt | 2021-04-01 | Q03461 | 1.34e-54 |
| Stuberosum_PGSC0003DMT400080253 | SwissProt | 2021-04-01 | P93224 | 5.04e-42 |
| Stuberosum_PGSC0003DMT400080252 | RepBase (RepeatMasker) | 2014-01-31 | LTR/ERV1 | |
| Stuberosum_PGSC0003DMT400080249 | SwissProt | 2021-04-01 | Q03461 | 2.8e-49 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
