Zmays Zm00001d014327
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_Zm00001d014327 [ Zm00001d014327] |
5 | 41088658 | 41100169 | 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_Zm00001d014327_T006 Zm00001d014327_T006 |
Low | No | 860 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.788 Folding energies... MFEI: -29.814 AMFE: -0.677 GC content %: 44.070 | |
| Zmays_Zm00001d014327_T007 Zm00001d014327_T007 |
Low | No | 577 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.934 Folding energies... MFEI: -29.445 AMFE: -0.651 GC content %: 45.234 | |
| Zmays_Zm00001d014327_T008 Zm00001d014327_T008 |
Low | No | 4145 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.743 Folding energies... MFEI: -31.539 AMFE: -0.647 GC content %: 48.782 |
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_Zm00001d014327_T008 | SwissProt | 2021-04-01 | Q9LVA7 | 7.49e-7 |
| Zmays_Zm00001d014327_T008 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d014327_T006 | SwissProt | 2021-04-01 | Q9LVA7 | 4.46e-8 |
| Zmays_Zm00001d014327_T007 | SwissProt | 2021-04-01 | Q9LVA7 | 1.0e-3 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
