Gene
Bdistachyon Bradi2g55292
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
|
|---|---|---|---|---|---|---|---|
| Bdistachyon_Bradi2g55292 Bradi2g55292 |
Bd2 | 53727467 | 53731294 | Phytozome | v3.1 | Brachypodium_distachyon | 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
|
|---|---|---|---|---|---|
| Bdistachyon_Bradi2g55292.1 Bradi2g55292.1 PAC:32773776 |
Low | Yes | 2289 | Get ORF Coding potential... Type: noncoding Potential: -1.392 Folding energies... MFEI: -27.864 AMFE: -0.704 GC content %: 39.581 | |
| Bdistachyon_Bradi2g55292.2 Bradi2g55292.2 PAC:32773774 |
Low | Yes | 2559 | Get ORF Coding potential... Type: noncoding Potential: -1.397 Folding energies... MFEI: -26.720 AMFE: -0.676 GC content %: 39.508 | |
| Bdistachyon_Bradi2g55292.3 Bradi2g55292.3 PAC:32773775 |
Low | Yes | 1991 | Get ORF Coding potential... Type: noncoding Potential: -1.386 Folding energies... MFEI: -28.980 AMFE: -0.723 GC content %: 40.080 |
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 |
|---|---|---|---|---|
| Bdistachyon_Bradi2g55292.1 | RepBase (RepeatMasker) | 2014-01-31 | TREP216 | |
| Bdistachyon_Bradi2g55292.3 | RepBase (RepeatMasker) | 2014-01-31 | TREP216 | |
| Bdistachyon_Bradi2g55292.1 | Rfam | 11.0 | MIR1122 | 1.5e-12 |
| Bdistachyon_Bradi2g55292.2 | Rfam | 11.0 | MIR1122 | 1.7e-12 |
| Bdistachyon_Bradi2g55292.3 | Rfam | 11.0 | MIR1122 | 1.3e-12 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
