Brapa Brara.F03543
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 | Assembly | Species | Details
|
|---|---|---|---|---|---|---|
| Brapa_Brara.F03543 [ Brara.F03543] |
A06 | 27346660 | 27348064 | v1.3 | Brassica rapa (Phytozome 13) | 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 | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Brapa_Brara.F03543.1 Brara.F03543.1 |
Low | No | 532 | OG0000389 | Get ORF Coding potential... Type: noncoding Potential: -1.027 Folding energies... MFEI: -27.820 AMFE: -0.565 GC content %: 49.248 | |
| Brapa_Brara.F03543.2 Brara.F03543.2 |
Low | No | 584 | OG0000389 | Get ORF Coding potential... Type: noncoding Potential: -1.080 Folding energies... MFEI: -27.723 AMFE: -0.572 GC content %: 48.459 | |
| Brapa_Brara.F03543.3 Brara.F03543.3 |
Low | No | 629 | OG0000389 | Get ORF Coding potential... Type: noncoding Potential: -1.155 Folding energies... MFEI: -26.455 AMFE: -0.555 GC content %: 47.695 |
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 |
|---|---|---|---|---|
| Brapa_Brara.F03543.2 | RepBase (RepeatMasker) | 2014-01-31 | LTR/Gypsy | |
| Brapa_Brara.F03543.3 | RepBase (RepeatMasker) | 2014-01-31 | LTR/Gypsy | |
| Brapa_Brara.F03543.1 | SwissProt | 2021-04-01 | Q6NNL9 | 3.44e-9 |
| Brapa_Brara.F03543.2 | SwissProt | 2021-04-01 | Q6NNL9 | 4.3e-9 |
| Brapa_Brara.F03543.3 | SwissProt | 2021-04-01 | Q6NNL9 | 5.46e-9 |
| Brapa_Brara.F03543.1 | RepBase (RepeatMasker) | 2014-01-31 | LTR/Gypsy |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
