Gene
Csinensis orange1.1g032267m.g
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
|
|---|---|---|---|---|---|---|---|
| Csinensis_orange1.1g032267m.g orange1.1g032267m.g |
scaffold00011 | 2202207 | 2203140 | Phytozome | v1.1 | Citrus_sinensis | Coding? Yes |
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
|
|---|---|---|---|---|---|
| Csinensis_orange1.1g034162m orange1.1g034162m PAC:18105777 |
Low | No | 500 | Get ORF Coding potential... Type: noncoding Potential: -0.373 Folding energies... MFEI: -26.660 AMFE: -0.629 GC content %: 42.400 | |
| Csinensis_orange1.1g034166m orange1.1g034166m PAC:18105776 |
Low | No | 829 | Get ORF Coding potential... Type: noncoding Potential: -0.477 Folding energies... MFEI: -27.045 AMFE: -0.692 GC content %: 39.083 | |
| Csinensis_orange1.1g034198m orange1.1g034198m PAC:18105778 |
Low | No | 497 | Get ORF Coding potential... Type: noncoding Potential: -0.362 Folding energies... MFEI: -26.398 AMFE: -0.622 GC content %: 42.455 | |
| Csinensis_orange1.1g034211m orange1.1g034211m PAC:18105779 |
Low | No | 826 | Get ORF Coding potential... Type: noncoding Potential: -0.466 Folding energies... MFEI: -27.143 AMFE: -0.694 GC content %: 39.104 |
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 |
|---|---|---|---|---|
| Csinensis_orange1.1g034162m | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_HV | |
| Csinensis_orange1.1g034166m | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_HV | |
| Csinensis_orange1.1g034198m | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_HV | |
| Csinensis_orange1.1g034211m | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-1_HV |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
