Zmays Zm00001d027240
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_Zm00001d027240 [ Zm00001d027240] |
1 | 199345 | 205715 | 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_Zm00001d027240_T009 Zm00001d027240_T009 |
Low | No | 1277 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.108 Folding energies... MFEI: -31.143 AMFE: -0.653 GC content %: 47.690 | |
| Zmays_Zm00001d027240_T013 Zm00001d027240_T013 |
Low | No | 4362 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.153 Folding energies... MFEI: -26.309 AMFE: -0.667 GC content %: 39.454 | |
| Zmays_Zm00001d027240_T014 Zm00001d027240_T014 |
Low | No | 4201 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.149 Folding energies... MFEI: -26.625 AMFE: -0.666 GC content %: 39.967 | |
| Zmays_Zm00001d027240_T015 Zm00001d027240_T015 |
Low | No | 4072 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.146 Folding energies... MFEI: -26.631 AMFE: -0.667 GC content %: 39.907 | |
| Zmays_Zm00001d027240_T016 Zm00001d027240_T016 |
Low | No | 3869 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.142 Folding energies... MFEI: -26.640 AMFE: -0.666 GC content %: 39.984 |
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_Zm00001d027240_T014 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d027240_T015 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d027240_T016 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d027240_T009 | SwissProt | 2021-04-01 | Q10M00 | 7.73e-11 |
| Zmays_Zm00001d027240_T013 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
