Gene
Bdistachyon Bradi5g01976
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_Bradi5g01976 Bradi5g01976 |
Bd5 | 2078360 | 2085412 | 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_Bradi5g01976.1 Bradi5g01976.1 PAC:32810530 |
Low | No | 4542 | Get ORF Coding potential... Type: noncoding Potential: -1.251 Folding energies... MFEI: -28.520 AMFE: -0.665 GC content %: 42.867 | |
| Bdistachyon_Bradi5g01976.2 Bradi5g01976.2 PAC:32810531 |
Low | No | 2309 | Get ORF Coding potential... Type: noncoding Potential: -0.953 Folding energies... MFEI: -28.242 AMFE: -0.659 GC content %: 42.876 | |
| Bdistachyon_Bradi5g01976.3 Bradi5g01976.3 PAC:32810532 |
Low | No | 4141 | Get ORF Coding potential... Type: noncoding Potential: -1.247 Folding energies... MFEI: -26.945 AMFE: -0.641 GC content %: 42.043 | |
| Bdistachyon_Bradi5g01976.4 Bradi5g01976.4 PAC:32810533 |
Low | No | 2122 | Get ORF Coding potential... Type: noncoding Potential: -1.214 Folding energies... MFEI: -27.879 AMFE: -0.617 GC content %: 45.193 | |
| Bdistachyon_Bradi5g01976.5 Bradi5g01976.5 PAC:32810534 |
Low | No | 1722 | Get ORF Coding potential... Type: noncoding Potential: -1.198 Folding energies... MFEI: -29.129 AMFE: -0.615 GC content %: 47.387 |
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_Bradi5g01976.5 | RepBase (RepeatMasker) | 2014-01-31 | RIRE8C_I-int | |
| Bdistachyon_Bradi5g01976.1 | RepBase (RepeatMasker) | 2014-01-31 | RETROSAT4_LTR | |
| Bdistachyon_Bradi5g01976.2 | RepBase (RepeatMasker) | 2014-01-31 | RIRE8C_I-int | |
| Bdistachyon_Bradi5g01976.3 | RepBase (RepeatMasker) | 2014-01-31 | RIRE8C_I-int | |
| Bdistachyon_Bradi5g01976.4 | RepBase (RepeatMasker) | 2014-01-31 | RIRE8C_I-int |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
