Zmays Zm00001d006861
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_Zm00001d006861 [ Zm00001d006861] |
2 | 218041355 | 218048937 | 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_Zm00001d006861_T001 Zm00001d006861_T001 |
Low | No | 5092 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.187 Folding energies... MFEI: -27.590 AMFE: -0.656 GC content %: 42.066 | |
| Zmays_Zm00001d006861_T008 Zm00001d006861_T008 |
Low | No | 5746 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.192 Folding energies... MFEI: -28.474 AMFE: -0.636 GC content %: 44.779 | |
| Zmays_Zm00001d006861_T009 Zm00001d006861_T009 |
Low | No | 4442 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.182 Folding energies... MFEI: -26.727 AMFE: -0.662 GC content %: 40.342 | |
| Zmays_Zm00001d006861_T010 Zm00001d006861_T010 |
Low | No | 5210 | [4] | Get ORF Coding potential... Type: noncoding Potential: -1.188 Folding energies... MFEI: -28.263 AMFE: -0.652 GC content %: 43.321 | |
| Zmays_Zm00001d006861_T019 Zm00001d006861_T019 |
Low | No | 3864 | [5] | Get ORF Coding potential... Type: noncoding Potential: -1.229 Folding energies... MFEI: -26.907 AMFE: -0.647 GC content %: 41.563 | |
| Zmays_Zm00001d006861_T024 Zm00001d006861_T024 |
Low | No | 4460 | [6] | Get ORF Coding potential... Type: noncoding Potential: -1.235 Folding energies... MFEI: -27.753 AMFE: -0.645 GC content %: 43.049 | |
| Zmays_Zm00001d006861_T028 Zm00001d006861_T028 |
Low | No | 3841 | [7] | Get ORF Coding potential... Type: noncoding Potential: -1.229 Folding energies... MFEI: -28.946 AMFE: -0.644 GC content %: 44.962 | |
| Zmays_Zm00001d006861_T030 Zm00001d006861_T030 |
Low | No | 4167 | [8] | Get ORF Coding potential... Type: noncoding Potential: -1.232 Folding energies... MFEI: -27.996 AMFE: -0.648 GC content %: 43.221 | |
| Zmays_Zm00001d006861_T034 Zm00001d006861_T034 |
Low | No | 3988 | [9] | Get ORF Coding potential... Type: noncoding Potential: -1.088 Folding energies... MFEI: -28.282 AMFE: -0.649 GC content %: 43.581 | |
| Zmays_Zm00001d006861_T037 Zm00001d006861_T037 |
Low | No | 4224 | [10] | Get ORF Coding potential... Type: noncoding Potential: -1.118 Folding energies... MFEI: -28.063 AMFE: -0.646 GC content %: 43.466 | |
| Zmays_Zm00001d006861_T045 Zm00001d006861_T045 |
Low | No | 3037 | [11] | Get ORF Coding potential... Type: noncoding Potential: -1.235 Folding energies... MFEI: -25.775 AMFE: -0.637 GC content %: 40.468 |
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_Zm00001d006861_T030 | SwissProt | 2021-04-01 | Q0D5P3 | 1.31e-4 |
| Zmays_Zm00001d006861_T009 | SwissProt | 2021-04-01 | Q0D5P3 | 1.4e-4 |
| Zmays_Zm00001d006861_T034 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d006861_T010 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d006861_T034 | SwissProt | 2021-04-01 | Q0D5P3 | 1.25e-4 |
| Zmays_Zm00001d006861_T010 | SwissProt | 2021-04-01 | Q0D5P3 | 2.01e-4 |
| Zmays_Zm00001d006861_T037 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d006861_T019 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d006861_T037 | SwissProt | 2021-04-01 | Q0D5P3 | 2.11e-4 |
| Zmays_Zm00001d006861_T019 | SwissProt | 2021-04-01 | Q2R2P7 | 3.21e-5 |
... further results
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
