Gene
BrapaFPsc Brara.I02960
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
|
|---|---|---|---|---|---|---|---|
| BrapaFPsc_Brara.I02960 Brara.I02960 |
A09 | 28760896 | 28762050 | Phytozome | [[Species:|]]"Species:" cannot be used as a page name in this wiki. | 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
|
|---|---|---|---|---|---|
| BrapaFPsc_Brara.I02960.1 Brara.I02960.1 PAC:30642668 |
Low | Yes | 753 | Get ORF Coding potential... Type: noncoding Potential: -0.678 Folding energies... MFEI: -24.608 AMFE: -0.604 GC content %: 40.770 | |
| BrapaFPsc_Brara.I02960.2 Brara.I02960.2 PAC:30642669 |
Low | Yes | 655 | Get ORF Coding potential... Type: noncoding Potential: -0.639 Folding energies... MFEI: -24.931 AMFE: -0.590 GC content %: 42.290 | |
| BrapaFPsc_Brara.I02960.3 Brara.I02960.3 PAC:30642670 |
Low | Yes | 661 | Get ORF Coding potential... Type: noncoding Potential: -0.641 Folding energies... MFEI: -24.644 AMFE: -0.582 GC content %: 42.360 |
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 |
|---|---|---|---|---|
| BrapaFPsc_Brara.I02960.2 | Rfam | 11.0 | MIR408 | 0.0016 |
| BrapaFPsc_Brara.I02960.3 | Rfam | 11.0 | MIR408 | 0.0016 |
| BrapaFPsc_Brara.I02960.1 | Rfam | 11.0 | MIR408 | 0.0019 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
