Zmays Zm00001d027239
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_Zm00001d027239 [ Zm00001d027239] |
1 | 196942 | 199159 | 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_Zm00001d027239_T001 Zm00001d027239_T001 |
Low | No | 1930 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.201 Folding energies... MFEI: -29.420 AMFE: -0.642 GC content %: 45.803 | |
| Zmays_Zm00001d027239_T002 Zm00001d027239_T002 |
Low | No | 1936 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.201 Folding energies... MFEI: -27.944 AMFE: -0.631 GC content %: 44.267 | |
| Zmays_Zm00001d027239_T003 Zm00001d027239_T003 |
Low | No | 2178 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.061 Folding energies... MFEI: -29.913 AMFE: -0.631 GC content %: 47.383 | |
| Zmays_Zm00001d027239_T004 Zm00001d027239_T004 |
Low | No | 2069 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.984 Folding energies... MFEI: -29.140 AMFE: -0.622 GC content %: 46.834 |
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_Zm00001d027239_T001 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d027239_T002 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d027239_T003 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d027239_T004 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
