Gene
Sbicolor Sobic.004G181800
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
|
|---|---|---|---|---|---|---|---|
| Sbicolor_Sobic.004G181800 Sobic.004G181800 |
Chr04 | 53500071 | 53504700 | Phytozome | v3.1 | Sorghum_bicolor | 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
|
|---|---|---|---|---|---|
| Sbicolor_Sobic.004G181800.1 Sobic.004G181800.1 PAC:32745743 |
Low | Yes | 747 | Get ORF Coding potential... Type: noncoding Potential: -0.713 Folding energies... MFEI: -42.784 AMFE: -0.664 GC content %: 64.391 | |
| Sbicolor_Sobic.004G181800.10 Sobic.004G181800.10 PAC:32745739 |
Low | No | 2448 | Get ORF Coding potential... Type: noncoding Potential: -0.834 Folding energies... MFEI: -30.911 AMFE: -0.671 GC content %: 46.078 | |
| Sbicolor_Sobic.004G181800.11 Sobic.004G181800.11 PAC:32745740 |
Low | No | 2376 | Get ORF Coding potential... Type: noncoding Potential: -0.832 Folding energies... MFEI: -31.103 AMFE: -0.674 GC content %: 46.128 | |
| Sbicolor_Sobic.004G181800.12 Sobic.004G181800.12 PAC:32745741 |
Low | Yes | 1404 | Get ORF Coding potential... Type: noncoding Potential: -0.788 Folding energies... MFEI: -33.034 AMFE: -0.645 GC content %: 51.211 | |
| Sbicolor_Sobic.004G181800.4 Sobic.004G181800.4 PAC:32745735 |
Low | No | 3462 | Get ORF Coding potential... Type: noncoding Potential: -0.853 Folding energies... MFEI: -29.697 AMFE: -0.684 GC content %: 43.414 | |
| Sbicolor_Sobic.004G181800.5 Sobic.004G181800.5 PAC:32745744 |
Low | Yes | 1395 | Get ORF Coding potential... Type: noncoding Potential: -0.787 Folding energies... MFEI: -33.326 AMFE: -0.650 GC content %: 51.254 | |
| Sbicolor_Sobic.004G181800.6 Sobic.004G181800.6 PAC:32745742 |
Low | Yes | 1312 | Get ORF Coding potential... Type: noncoding Potential: -0.781 Folding energies... MFEI: -34.009 AMFE: -0.658 GC content %: 51.677 | |
| Sbicolor_Sobic.004G181800.7 Sobic.004G181800.7 PAC:32745736 |
Low | No | 2468 | Get ORF Coding potential... Type: noncoding Potential: -0.834 Folding energies... MFEI: -30.831 AMFE: -0.669 GC content %: 46.070 | |
| Sbicolor_Sobic.004G181800.8 Sobic.004G181800.8 PAC:32745737 |
Low | Yes | 862 | Get ORF Coding potential... Type: noncoding Potential: -0.732 Folding energies... MFEI: -39.606 AMFE: -0.641 GC content %: 61.833 | |
| Sbicolor_Sobic.004G181800.9 Sobic.004G181800.9 PAC:32745738 |
Low | Yes | 1415 | Get ORF Coding potential... Type: noncoding Potential: -0.789 Folding energies... MFEI: -33.018 AMFE: -0.645 GC content %: 51.166 |
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.004G181800.9 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi | |
| Sbicolor_Sobic.004G181800.12 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi | |
| Sbicolor_Sobic.004G181800.4 | RepBase (RepeatMasker) | 2014-01-31 | TSB1 | |
| Sbicolor_Sobic.004G181800.5 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi | |
| Sbicolor_Sobic.004G181800.6 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi | |
| Sbicolor_Sobic.004G181800.10 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi | |
| Sbicolor_Sobic.004G181800.7 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi | |
| Sbicolor_Sobic.004G181800.11 | RepBase (RepeatMasker) | 2014-01-31 | EnSpm-N20_SBi |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
