Zmays Zm00001d025456
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_Zm00001d025456 [ Zm00001d025456] |
10 | 119082076 | 119083221 | v4 | Zea mays (Phytozome 13) | Coding? No |
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_Zm00001d025456_T001 Zm00001d025456_T001 |
Low | No | 612 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.400 Folding energies... MFEI: -22.042 AMFE: -0.630 GC content %: 34.967 | |
| Zmays_Zm00001d025456_T002 Zm00001d025456_T002 |
Low | No | 569 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -22.285 AMFE: -0.660 GC content %: 33.743 | |
| Zmays_Zm00001d025456_T003 Zm00001d025456_T003 |
Low | No | 456 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.976 Folding energies... MFEI: -22.127 AMFE: -0.635 GC content %: 34.868 |
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_Zm00001d025456_T001 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d025456_T002 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d025456_T003 | 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).
