Gene
Bdistachyon Bradi2g59836
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_Bradi2g59836 Bradi2g59836 |
Bd2 | 57192993 | 57204174 | 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_Bradi2g59836.3 Bradi2g59836.3 PAC:32778399 |
Low | Yes | 6494 | Get ORF Coding potential... Type: noncoding Potential: -1.170 Folding energies... MFEI: -32.099 AMFE: -0.745 GC content %: 43.101 | |
| Bdistachyon_Bradi2g59836.4 Bradi2g59836.4 PAC:32778400 |
Low | Yes | 9325 | Get ORF Coding potential... Type: noncoding Potential: -1.180 Folding energies... MFEI: -30.902 AMFE: -0.754 GC content %: 40.965 | |
| Bdistachyon_Bradi2g59836.5 Bradi2g59836.5 PAC:32778401 |
Low | Yes | 9302 | Get ORF Coding potential... Type: noncoding Potential: -1.180 Folding energies... MFEI: -30.732 AMFE: -0.751 GC content %: 40.916 | |
| Bdistachyon_Bradi2g59836.6 Bradi2g59836.6 PAC:32778402 |
Low | Yes | 9403 | Get ORF Coding potential... Type: noncoding Potential: -1.180 Folding energies... MFEI: -30.792 AMFE: -0.752 GC content %: 40.934 | |
| Bdistachyon_Bradi2g59836.7 Bradi2g59836.7 PAC:32778403 |
Low | Yes | 6595 | Get ORF Coding potential... Type: noncoding Potential: -1.170 Folding energies... MFEI: -32.255 AMFE: -0.748 GC content %: 43.093 | |
| Bdistachyon_Bradi2g59836.8 Bradi2g59836.8 PAC:32778404 |
Low | Yes | 9218 | Get ORF Coding potential... Type: noncoding Potential: -1.180 Folding energies... MFEI: -30.776 AMFE: -0.751 GC content %: 40.963 |
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_Bradi2g59836.8 | RepBase (RepeatMasker) | 2014-01-31 | TREP216 | |
| Bdistachyon_Bradi2g59836.7 | miRBase | 21.0 | tae-miR1128 | 0.022 |
| Bdistachyon_Bradi2g59836.3 | RepBase (RepeatMasker) | 2014-01-31 | TREP216 | |
| Bdistachyon_Bradi2g59836.7 | miRBase | 21.0 | bdi-miR5181c-5p | 0.006 |
| Bdistachyon_Bradi2g59836.4 | Rfam | 11.0 | MIR1122 | 2.3e-13 |
| Bdistachyon_Bradi2g59836.3 | miRBase | 21.0 | mtr-miR5205b | 0.022 |
| Bdistachyon_Bradi2g59836.3 | miRBase | 21.0 | tae-miR5049-3p | 0.002 |
| Bdistachyon_Bradi2g59836.4 | RepBase (RepeatMasker) | 2014-01-31 | TREP216 | |
| Bdistachyon_Bradi2g59836.7 | miRBase | 21.0 | bdi-miR5181b | 0.006 |
| Bdistachyon_Bradi2g59836.5 | Rfam | 11.0 | MIR1122 | 2.3e-13 |
... further results
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
