Gtomentosum Gotom.A01G270000
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
|
|---|---|---|---|---|---|---|
| Gtomentosum_Gotom.A01G270000 [ Gotom.A01G270000] |
A01 | 113960623 | 113961802 | v1.1 | Gossypium tomentosum (Phytozome 13) | 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 | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Gtomentosum_Gotom.A01G270000.1 Gotom.A01G270000.1 |
Low | Yes | 1013 | OG0034729 | Get ORF Coding potential... Type: noncoding Potential: -1.111 Folding energies... MFEI: -26.456 AMFE: -0.730 GC content %: 36.229 | |
| Gtomentosum_Gotom.A01G270000.2 Gotom.A01G270000.2 |
Low | Yes | 751 | OG0034729 | Get ORF Coding potential... Type: noncoding Potential: -1.050 Folding energies... MFEI: -25.752 AMFE: -0.722 GC content %: 35.686 | |
| Gtomentosum_Gotom.A01G270000.3 Gotom.A01G270000.3 |
High | No | 216 | OG0180421 | Get ORF Coding potential... Type: noncoding Potential: -0.742 Folding energies... MFEI: -21.204 AMFE: -0.645 GC content %: 32.870 |
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 |
|---|---|---|---|---|
| Gtomentosum_Gotom.A01G270000.2 | Rfam | 14.6 | MIR390 | 2.4e-25 |
| Gtomentosum_Gotom.A01G270000.1 | RepBase (RepeatMasker) | 2014-01-31 | DNA/PIF-Harbinger | |
| Gtomentosum_Gotom.A01G270000.2 | RepBase (RepeatMasker) | 2014-01-31 | DNA/PIF-Harbinger | |
| Gtomentosum_Gotom.A01G270000.1 | Rfam | 14.6 | MIR390 | 3.2e-25 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
