Gene
Stuberosum PGSC0003DMG402008965
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_PGSC0003DMG402008965 PGSC0003DMG402008965 |
chr09 | 7288986 | 7295904 | 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_PGSC0003DMT400023163 PGSC0003DMT400023163 PAC:24398861 |
Low | No | 3385 | Get ORF Coding potential... Type: noncoding Potential: -0.255 Folding energies... MFEI: -23.232 AMFE: -0.697 GC content %: 33.323 | |
| Stuberosum_PGSC0003DMT400023164 PGSC0003DMT400023164 PAC:24398862 |
Low | No | 6802 | Get ORF Coding potential... Type: noncoding Potential: -0.290 Folding energies... MFEI: -21.808 AMFE: -0.684 GC content %: 31.873 | |
| Stuberosum_PGSC0003DMT400023165 PGSC0003DMT400023165 PAC:24398863 |
Low | No | 6802 | Get ORF Coding potential... Type: noncoding Potential: -0.290 Folding energies... MFEI: -21.808 AMFE: -0.684 GC content %: 31.873 | |
| Stuberosum_PGSC0003DMT400023167 PGSC0003DMT400023167 PAC:24398864 |
Low | No | 2981 | Get ORF Coding potential... Type: noncoding Potential: -0.303 Folding energies... MFEI: -22.298 AMFE: -0.680 GC content %: 32.808 | |
| Stuberosum_PGSC0003DMT400023169 PGSC0003DMT400023169 PAC:24398865 |
Low | No | 4075 | Get ORF Coding potential... Type: noncoding Potential: -1.101 Folding energies... MFEI: -20.744 AMFE: -0.654 GC content %: 31.706 |
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_PGSC0003DMT400023163 | SwissProt | 2015-06-01 | Q6NQB7 | 3.0e-10 |
| Stuberosum_PGSC0003DMT400023165 | RepBase (RepeatMasker) | 2014-01-31 | SONATA2 | |
| Stuberosum_PGSC0003DMT400023164 | SwissProt | 2015-06-01 | Q6NQB7 | 7.0e-10 |
| Stuberosum_PGSC0003DMT400023169 | RepBase (RepeatMasker) | 2014-01-31 | SONATA2 | |
| Stuberosum_PGSC0003DMT400023165 | SwissProt | 2015-06-01 | Q6NQB7 | 7.0e-10 |
| Stuberosum_PGSC0003DMT400023167 | SwissProt | 2015-06-01 | Q6NQB7 | 3.0e-10 |
| Stuberosum_PGSC0003DMT400023169 | SwissProt | 2015-06-01 | Q9SAA4 | 4.0e-6 |
| Stuberosum_PGSC0003DMT400023164 | RepBase (RepeatMasker) | 2014-01-31 | SONATA2 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
