Zmays Zm00001d040051
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_Zm00001d040051 [ Zm00001d040051] |
3 | 24858774 | 24877660 | 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_Zm00001d040051_T039 Zm00001d040051_T039 |
Low | Yes | 686 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.719 Folding energies... MFEI: -32.230 AMFE: -0.716 GC content %: 45.044 | |
| Zmays_Zm00001d040051_T145 Zm00001d040051_T145 |
Low | No | 1298 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.341 Folding energies... MFEI: -27.126 AMFE: -0.576 GC content %: 47.072 |
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_Zm00001d040051_T039 | Rfam | 14.6 | MIR2118 | 0.0055 |
| Zmays_Zm00001d040051_T039 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger | |
| Zmays_Zm00001d040051_T145 | SwissProt | 2021-04-01 | Q10MI0 | 1.43e-8 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
