Zmays Zm00001d039385
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
|
|---|---|---|---|---|---|---|
| Zmays_Zm00001d039385 [ Zm00001d039385] |
3 | 3092385 | 3107653 | v4 | Zea mays (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
|
|---|---|---|---|---|---|---|
| Zmays_Zm00001d039385_T004 Zm00001d039385_T004 |
Low | No | 4540 | [1] | Get ORF Coding potential... Type: coding Potential: 1.108 Folding energies... MFEI: -26.317 AMFE: -0.660 GC content %: 39.868 | |
| Zmays_Zm00001d039385_T007 Zm00001d039385_T007 |
Low | No | 4435 | [2] | Get ORF Coding potential... Type: coding Potential: 1.723 Folding energies... MFEI: -27.202 AMFE: -0.686 GC content %: 39.662 | |
| Zmays_Zm00001d039385_T024 Zm00001d039385_T024 |
Low | No | 3900 | [3] | Get ORF Coding potential... Type: coding Potential: 3.542 Folding energies... MFEI: -26.179 AMFE: -0.649 GC content %: 40.333 | |
| Zmays_Zm00001d039385_T027 Zm00001d039385_T027 |
Low | No | 3548 | [4] | Get ORF Coding potential... Type: coding Potential: 3.539 Folding energies... MFEI: -24.515 AMFE: -0.646 GC content %: 37.965 | |
| Zmays_Zm00001d039385_T031 Zm00001d039385_T031 |
Low | No | 7336 | [5] | Get ORF Coding potential... Type: coding Potential: 2.961 Folding energies... MFEI: -27.767 AMFE: -0.673 GC content %: 41.249 |
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 |
|---|---|---|---|---|
| Zmays_Zm00001d039385_T031 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Copia | |
| Zmays_Zm00001d039385_T004 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d039385_T007 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d039385_T024 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d039385_T027 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
