Gene
Sitalica Seita.3G150900
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
|
|---|---|---|---|---|---|---|---|
| Sitalica_Seita.3G150900 Seita.3G150900 |
scaffold_3 | 10891848 | 10894137 | Phytozome | v2.2 | Setaria_italica | 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
|
|---|---|---|---|---|---|
| Sitalica_Seita.3G150900.1 Seita.3G150900.1 PAC:32713804 |
Low | No | 1103 | Get ORF Coding potential... Type: noncoding Potential: -1.219 Folding energies... MFEI: -29.909 AMFE: -0.672 GC content %: 44.515 | |
| Sitalica_Seita.3G150900.2 Seita.3G150900.2 PAC:32713805 |
Low | No | 1088 | Get ORF Coding potential... Type: noncoding Potential: -1.217 Folding energies... MFEI: -29.706 AMFE: -0.669 GC content %: 44.393 | |
| Sitalica_Seita.3G150900.3 Seita.3G150900.3 PAC:32713806 |
Low | No | 991 | Get ORF Coding potential... Type: noncoding Potential: -1.205 Folding energies... MFEI: -30.061 AMFE: -0.677 GC content %: 44.400 | |
| Sitalica_Seita.3G150900.4 Seita.3G150900.4 PAC:32713807 |
Low | No | 1006 | Get ORF Coding potential... Type: noncoding Potential: -1.207 Folding energies... MFEI: -30.099 AMFE: -0.676 GC content %: 44.533 | |
| Sitalica_Seita.3G150900.5 Seita.3G150900.5 PAC:32713808 |
High | No | 874 | Get ORF Coding potential... Type: noncoding Potential: -1.206 Folding energies... MFEI: -30.927 AMFE: -0.684 GC content %: 45.195 |
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 |
|---|---|---|---|---|
| Sitalica_Seita.3G150900.1 | RepBase (RepeatMasker) | 2014-01-31 | Tourist1g_SB | |
| Sitalica_Seita.3G150900.2 | RepBase (RepeatMasker) | 2014-01-31 | Tourist1g_SB | |
| Sitalica_Seita.3G150900.3 | RepBase (RepeatMasker) | 2014-01-31 | Tourist1g_SB | |
| Sitalica_Seita.3G150900.4 | RepBase (RepeatMasker) | 2014-01-31 | Tourist1g_SB |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
