Sbicolor Sobic.008G005700
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
|
|---|---|---|---|---|---|---|
| Sbicolor_Sobic.008G005700 [ Sobic.008G005700] |
Chr08 | 489090 | 501266 | v3.1.1 | Sorghum bicolor (Phytozome 13) | Coding? Yes |
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
|
|---|---|---|---|---|---|---|
| Sbicolor_Sobic.008G005700.3 Sobic.008G005700.3 |
Low | No | 1819 | OG0014555 | Get ORF Coding potential... Type: noncoding Potential: -1.039 Folding energies... MFEI: -32.661 AMFE: -0.715 GC content %: 45.684 | |
| Sbicolor_Sobic.008G005700.4 Sobic.008G005700.4 |
Low | No | 747 | OG0014555 | Get ORF Coding potential... Type: noncoding Potential: -0.881 Folding energies... MFEI: -34.110 AMFE: -0.662 GC content %: 51.539 | |
| Sbicolor_Sobic.008G005700.5 Sobic.008G005700.5 |
Low | No | 2302 | OG0014555 | Get ORF Coding potential... Type: noncoding Potential: -0.233 Folding energies... MFEI: -34.088 AMFE: -0.730 GC content %: 46.699 | |
| Sbicolor_Sobic.008G005700.6 Sobic.008G005700.6 |
Low | No | 1230 | OG0014555 | Get ORF Coding potential... Type: noncoding Potential: -0.122 Folding energies... MFEI: -36.390 AMFE: -0.712 GC content %: 51.138 |
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 |
|---|---|---|---|---|
| Sbicolor_Sobic.008G005700.3 | RepBase (RepeatMasker) | 2014-01-31 | LTR/Gypsy | |
| Sbicolor_Sobic.008G005700.4 | RepBase (RepeatMasker) | 2014-01-31 | LINE/L1; LTR/Gypsy | |
| Sbicolor_Sobic.008G005700.5 | RepBase (RepeatMasker) | 2014-01-31 | LTR/Gypsy | |
| Sbicolor_Sobic.008G005700.6 | RepBase (RepeatMasker) | 2014-01-31 | LINE/L1; LTR/Gypsy |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
