Gene
Stuberosum PGSC0003DMG401005707
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_PGSC0003DMG401005707 PGSC0003DMG401005707 |
chr03 | 44787952 | 44791257 | 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_PGSC0003DMT400014584 PGSC0003DMT400014584 PAC:24404470 |
Low | No | 2061 | Get ORF Coding potential... Type: noncoding Potential: -0.184 Folding energies... MFEI: -23.081 AMFE: -0.688 GC content %: 33.527 | |
| Stuberosum_PGSC0003DMT400014586 PGSC0003DMT400014586 PAC:24404471 |
Low | No | 2061 | Get ORF Coding potential... Type: noncoding Potential: -0.184 Folding energies... MFEI: -23.081 AMFE: -0.688 GC content %: 33.527 | |
| Stuberosum_PGSC0003DMT400014587 PGSC0003DMT400014587 PAC:24404472 |
Low | No | 3306 | Get ORF Coding potential... Type: noncoding Potential: -0.233 Folding energies... MFEI: -22.519 AMFE: -0.664 GC content %: 33.938 | |
| Stuberosum_PGSC0003DMT400014588 PGSC0003DMT400014588 PAC:24404473 |
Low | No | 3306 | Get ORF Coding potential... Type: noncoding Potential: -0.233 Folding energies... MFEI: -22.519 AMFE: -0.664 GC content %: 33.938 |
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_PGSC0003DMT400014588 | RepBase (RepeatMasker) | 2014-01-31 | DNA-TA-1_STu | |
| Stuberosum_PGSC0003DMT400014587 | SwissProt | 2015-06-01 | Q8GXE2 | 4.0e-10 |
| Stuberosum_PGSC0003DMT400014588 | SwissProt | 2015-06-01 | Q8GXE2 | 4.0e-10 |
| Stuberosum_PGSC0003DMT400014584 | RepBase (RepeatMasker) | 2014-01-31 | DNA-TA-1_STu | |
| Stuberosum_PGSC0003DMT400014586 | RepBase (RepeatMasker) | 2014-01-31 | DNA-TA-1_STu | |
| Stuberosum_PGSC0003DMT400014584 | SwissProt | 2015-06-01 | Q8GXE2 | 2.0e-10 |
| Stuberosum_PGSC0003DMT400014587 | RepBase (RepeatMasker) | 2014-01-31 | DNA-TA-1_STu | |
| Stuberosum_PGSC0003DMT400014586 | SwissProt | 2015-06-01 | Q8GXE2 | 2.0e-10 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
