Zmays5 Zm00001eb139710
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
|
|---|---|---|---|---|---|---|
| Zmays5_Zm00001eb139710 Zm00001eb139710 |
3 | 145825022 | 145826307 | v5 | Zea mays (Ensembl Plants 51) | 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
|
|---|---|---|---|---|---|---|
| Zmays5_Zm00001eb139710_T001 Zm00001eb139710_T001 |
Low | No | 884 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.035 Folding energies... MFEI: -33.224 AMFE: -0.666 GC content %: 49.887 | |
| Zmays5_Zm00001eb139710_T002 Zm00001eb139710_T002 |
Low | No | 810 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.033 Folding energies... MFEI: -33.778 AMFE: -0.666 GC content %: 50.741 | |
| Zmays5_Zm00001eb139710_T004 Zm00001eb139710_T004 |
Low | No | 773 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.012 Folding energies... MFEI: -33.765 AMFE: -0.644 GC content %: 52.393 | |
| Zmays5_Zm00001eb139710_T005 Zm00001eb139710_T005 |
Low | No | 739 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.037 Folding energies... MFEI: -32.192 AMFE: -0.676 GC content %: 47.632 |
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 |
|---|---|---|---|---|
| Zmays5_Zm00001eb139710_T005 | SwissProt | 2021-04-01 | Q9SVM8 | 8.83e-15 |
| Zmays5_Zm00001eb139710_T001 | SwissProt | 2021-04-01 | Q9SVM8 | 1.49e-13 |
| Zmays5_Zm00001eb139710_T002 | SwissProt | 2021-04-01 | Q9SVM8 | 5.75e-14 |
| Zmays5_Zm00001eb139710_T004 | SwissProt | 2021-04-01 | Q9SVM8 | 4.8e-14 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
