Gene
Stuberosum PGSC0003DMG400014763
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_PGSC0003DMG400014763 PGSC0003DMG400014763 |
chr08 | 32179476 | 32182377 | 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_PGSC0003DMT400038263 PGSC0003DMT400038263 PAC:24392495 |
Low | No | 1431 | Get ORF Coding potential... Type: noncoding Potential: -0.686 Folding energies... MFEI: -22.131 AMFE: -0.644 GC content %: 34.382 | |
| Stuberosum_PGSC0003DMT400038264 PGSC0003DMT400038264 PAC:24392494 |
Low | No | 2569 | Get ORF Coding potential... Type: noncoding Potential: -1.151 Folding energies... MFEI: -22.818 AMFE: -0.675 GC content %: 33.787 | |
| Stuberosum_PGSC0003DMT400038265 PGSC0003DMT400038265 PAC:24392496 |
Low | No | 1936 | Get ORF Coding potential... Type: noncoding Potential: -0.711 Folding energies... MFEI: -23.249 AMFE: -0.669 GC content %: 34.762 | |
| Stuberosum_PGSC0003DMT400038266 PGSC0003DMT400038266 PAC:24392497 |
Low | No | 2818 | Get ORF Coding potential... Type: noncoding Potential: -0.734 Folding energies... MFEI: -23.034 AMFE: -0.678 GC content %: 33.960 | |
| Stuberosum_PGSC0003DMT400038267 PGSC0003DMT400038267 PAC:24392493 |
High | No | 475 | Get ORF Coding potential... Type: noncoding Potential: -1.435 Folding energies... MFEI: -18.884 AMFE: -0.619 GC content %: 30.526 |
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_PGSC0003DMT400038264 | RepBase (RepeatMasker) | 2014-01-31 | MuDR-1_STu | |
| Stuberosum_PGSC0003DMT400038265 | RepBase (RepeatMasker) | 2014-01-31 | MuDR-1_STu | |
| Stuberosum_PGSC0003DMT400038264 | SwissProt | 2015-06-01 | Q0JD42 | 5.0e-6 |
| Stuberosum_PGSC0003DMT400038266 | RepBase (RepeatMasker) | 2014-01-31 | MuDR-1_STu | |
| Stuberosum_PGSC0003DMT400038265 | SwissProt | 2015-06-01 | Q0JD42 | 4.0e-6 |
| Stuberosum_PGSC0003DMT400038266 | SwissProt | 2015-06-01 | Q0JD42 | 6.0e-6 |
| Stuberosum_PGSC0003DMT400038263 | RepBase (RepeatMasker) | 2014-01-31 | MuDR-1_STu |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
