Gene
Csinensis orange1.1g033799m.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_orange1.1g033799m.g orange1.1g033799m.g |
scaffold00096 | 410929 | 412829 | 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_orange1.1g033799m orange1.1g033799m PAC:18120797 |
Low | No | 1011 | Get ORF Coding potential... Type: noncoding Potential: -0.084 Folding energies... MFEI: -24.975 AMFE: -0.625 GC content %: 39.960 | |
| Csinensis_orange1.1g034779m orange1.1g034779m PAC:18120799 |
Low | No | 892 | Get ORF Coding potential... Type: noncoding Potential: -0.271 Folding energies... MFEI: -25.065 AMFE: -0.613 GC content %: 40.919 | |
| Csinensis_orange1.1g035391m orange1.1g035391m PAC:18120801 |
Low | No | 1605 | Get ORF Coding potential... Type: noncoding Potential: -1.117 Folding energies... MFEI: -24.704 AMFE: -0.669 GC content %: 36.947 |
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_orange1.1g033799m | SwissProt | 2015-06-01 | Q6CS47 | 1.0e-9 |
| Csinensis_orange1.1g034779m | SwissProt | 2015-06-01 | P0CM86 | 1.0e-9 |
| Csinensis_orange1.1g035391m | SwissProt | 2015-06-01 | Q6CS47 | 1.0e-8 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
