Zmays Zm00001d035560
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_Zm00001d035560 [ Zm00001d035560] |
6 | 33142628 | 33144237 | 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_Zm00001d035560_T004 Zm00001d035560_T004 |
Low | No | 703 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.509 Folding energies... MFEI: -36.629 AMFE: -0.623 GC content %: 58.748 | |
| Zmays_Zm00001d035560_T005 Zm00001d035560_T005 |
Low | No | 838 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.023 Folding energies... MFEI: -37.780 AMFE: -0.642 GC content %: 58.831 | |
| Zmays_Zm00001d035560_T009 Zm00001d035560_T009 |
Low | No | 737 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.109 Folding energies... MFEI: -34.505 AMFE: -0.619 GC content %: 55.767 | |
| Zmays_Zm00001d035560_T016 Zm00001d035560_T016 |
Low | No | 645 | [4] | Get ORF Coding potential... Type: noncoding Potential: -1.105 Folding energies... MFEI: -38.450 AMFE: -0.644 GC content %: 59.690 |
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_Zm00001d035560_T016 | SwissProt | 2021-04-01 | Q0JMY8 | 9.23e-5 |
| Zmays_Zm00001d035560_T004 | SwissProt | 2021-04-01 | A2WPN7 | 3.11e-11 |
| Zmays_Zm00001d035560_T005 | SwissProt | 2021-04-01 | A2WPN7 | 9.35e-17 |
| Zmays_Zm00001d035560_T009 | SwissProt | 2021-04-01 | P83304 | 1.37e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
