Gene
Csinensis orange1.1g034171m.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_orange1.1g034171m.g orange1.1g034171m.g |
scaffold00690 | 929 | 3205 | Phytozome | v1.1 | Citrus_sinensis | 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
|
|---|---|---|---|---|---|
| Csinensis_orange1.1g034171m orange1.1g034171m PAC:18110726 |
High | No | 411 | Get ORF Coding potential... Type: noncoding Potential: -0.768 Folding energies... MFEI: -24.696 AMFE: -0.495 GC content %: 49.878 | |
| Csinensis_orange1.1g034473m orange1.1g034473m PAC:18110727 |
Low | No | 387 | Get ORF Coding potential... Type: noncoding Potential: -0.602 Folding energies... MFEI: -22.739 AMFE: -0.421 GC content %: 54.005 | |
| Csinensis_orange1.1g034682m orange1.1g034682m PAC:18110728 |
High | No | 344 | Get ORF Coding potential... Type: noncoding Potential: -0.798 Folding energies... MFEI: -22.936 AMFE: -0.453 GC content %: 50.581 | |
| Csinensis_orange1.1g034803m orange1.1g034803m PAC:18110729 |
Low | No | 320 | Get ORF Coding potential... Type: noncoding Potential: -1.042 Folding energies... MFEI: -19.094 AMFE: -0.343 GC content %: 55.625 | |
| Csinensis_orange1.1g035001m orange1.1g035001m PAC:18110730 |
High | No | 538 | Get ORF Coding potential... Type: noncoding Potential: -1.003 Folding energies... MFEI: -25.242 AMFE: -0.543 GC content %: 46.468 | |
| Csinensis_orange1.1g035004m orange1.1g035004m PAC:18110732 |
Low | No | 597 | Get ORF Coding potential... Type: noncoding Potential: -1.151 Folding energies... MFEI: -23.719 AMFE: -0.509 GC content %: 46.566 | |
| Csinensis_orange1.1g035007m orange1.1g035007m PAC:18110731 |
High | No | 470 | Get ORF Coding potential... Type: noncoding Potential: -0.965 Folding energies... MFEI: -25.043 AMFE: -0.525 GC content %: 47.660 |
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_orange1.1g034473m | SwissProt | 2015-06-01 | Q8RU95 | 2.0e-4 |
| Csinensis_orange1.1g034803m | SwissProt | 2015-06-01 | Q8RU95 | 1.0e-4 |
| Csinensis_orange1.1g035004m | SwissProt | 2015-06-01 | Q8RU95 | 5.0e-12 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
