Zmays Zm00001d027752
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_Zm00001d027752 [ Zm00001d027752] |
1 | 12628889 | 12640144 | 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_Zm00001d027752_T016 Zm00001d027752_T016 |
Low | No | 2586 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.054 Folding energies... MFEI: -28.550 AMFE: -0.652 GC content %: 43.813 | |
| Zmays_Zm00001d027752_T018 Zm00001d027752_T018 |
Low | No | 901 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.921 Folding energies... MFEI: -30.799 AMFE: -0.651 GC content %: 47.281 | |
| Zmays_Zm00001d027752_T019 Zm00001d027752_T019 |
Low | No | 1419 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.206 Folding energies... MFEI: -27.576 AMFE: -0.630 GC content %: 43.763 | |
| Zmays_Zm00001d027752_T022 Zm00001d027752_T022 |
Low | No | 1519 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.234 Folding energies... MFEI: -27.986 AMFE: -0.633 GC content %: 44.240 | |
| Zmays_Zm00001d027752_T023 Zm00001d027752_T023 |
Low | No | 2238 | [5] | Get ORF Coding potential... Type: noncoding Potential: -1.035 Folding energies... MFEI: -27.980 AMFE: -0.638 GC content %: 43.834 |
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_Zm00001d027752_T022 | SwissProt | 2021-04-01 | P73161 | 2.03e-11 |
| Zmays_Zm00001d027752_T023 | SwissProt | 2021-04-01 | B0JUK5 | 8.29e-7 |
| Zmays_Zm00001d027752_T016 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d027752_T016 | SwissProt | 2021-04-01 | B0JUK5 | 2.66e-7 |
| Zmays_Zm00001d027752_T019 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d027752_T018 | SwissProt | 2021-04-01 | B0JUK5 | 7.29e-8 |
| Zmays_Zm00001d027752_T022 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d027752_T019 | SwissProt | 2021-04-01 | P73161 | 3.81e-9 |
| Zmays_Zm00001d027752_T023 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
