Zmays Zm00001d006453
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_Zm00001d006453 [ Zm00001d006453] |
2 | 208705755 | 208713297 | 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_Zm00001d006453_T002 Zm00001d006453_T002 |
Low | No | 915 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.048 Folding energies... MFEI: -37.672 AMFE: -0.672 GC content %: 56.066 | |
| Zmays_Zm00001d006453_T003 Zm00001d006453_T003 |
Low | No | 2166 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.983 Folding energies... MFEI: -30.499 AMFE: -0.672 GC content %: 45.383 | |
| Zmays_Zm00001d006453_T004 Zm00001d006453_T004 |
Low | No | 4140 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.949 Folding energies... MFEI: -28.568 AMFE: -0.633 GC content %: 45.145 | |
| Zmays_Zm00001d006453_T005 Zm00001d006453_T005 |
Low | No | 3665 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.211 Folding energies... MFEI: -27.405 AMFE: -0.679 GC content %: 40.355 |
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_Zm00001d006453_T003 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Copia | |
| Zmays_Zm00001d006453_T004 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d006453_T003 | SwissProt | 2021-04-01 | Q28CV2 | 4.71e-12 |
| Zmays_Zm00001d006453_T005 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d006453_T004 | SwissProt | 2021-04-01 | Q54PI4 | 3.75e-10 |
| Zmays_Zm00001d006453_T005 | SwissProt | 2021-04-01 | Q94CA0 | 2.75e-16 |
| Zmays_Zm00001d006453_T002 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Copia |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
