Gene
Bdistachyon Bradi1g29106
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_Bradi1g29106 Bradi1g29106 |
Bd1 | 24695512 | 24697309 | 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_Bradi1g29106.1 Bradi1g29106.1 PAC:32792419 |
Low | Yes | 1187 | Get ORF Coding potential... Type: noncoding Potential: -1.248 Folding energies... MFEI: -28.467 AMFE: -0.716 GC content %: 39.764 | |
| Bdistachyon_Bradi1g29106.2 Bradi1g29106.2 PAC:32792420 |
High | No | 874 | Get ORF Coding potential... Type: noncoding Potential: -1.208 Folding energies... MFEI: -25.698 AMFE: -0.634 GC content %: 40.503 | |
| Bdistachyon_Bradi1g29106.3 Bradi1g29106.3 PAC:32792421 |
Low | Yes | 1326 | Get ORF Coding potential... Type: noncoding Potential: -1.260 Folding energies... MFEI: -28.424 AMFE: -0.732 GC content %: 38.839 |
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_Bradi1g29106.3 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy6-VV_I-int | |
| Bdistachyon_Bradi1g29106.1 | Rfam | 11.0 | MIR1122 | 2.2e-11 |
| Bdistachyon_Bradi1g29106.3 | Rfam | 11.0 | MIR1122 | 2.4e-11 |
| Bdistachyon_Bradi1g29106.1 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy6-VV_I-int |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
