Zmays Zm00001d007655
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_Zm00001d007655 [ Zm00001d007655] |
2 | 237052725 | 237059681 | 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_Zm00001d007655_T003 Zm00001d007655_T003 |
Low | No | 5491 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.162 Folding energies... MFEI: -25.926 AMFE: -0.692 GC content %: 37.461 | |
| Zmays_Zm00001d007655_T004 Zm00001d007655_T004 |
Low | No | 2297 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.134 Folding energies... MFEI: -29.060 AMFE: -0.679 GC content %: 42.795 | |
| Zmays_Zm00001d007655_T006 Zm00001d007655_T006 |
Low | No | 4739 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.155 Folding energies... MFEI: -26.375 AMFE: -0.689 GC content %: 38.278 | |
| Zmays_Zm00001d007655_T007 Zm00001d007655_T007 |
Low | No | 3143 | [4] | Get ORF Coding potential... Type: noncoding Potential: -1.161 Folding energies... MFEI: -26.036 AMFE: -0.677 GC content %: 38.466 |
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_Zm00001d007655_T007 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger? | |
| Zmays_Zm00001d007655_T004 | SwissProt | 2021-04-01 | Q2M197 | 1.78e-4 |
| Zmays_Zm00001d007655_T006 | SwissProt | 2021-04-01 | Q7RZV2 | 4.96e-4 |
| Zmays_Zm00001d007655_T003 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger? | |
| Zmays_Zm00001d007655_T004 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger? | |
| Zmays_Zm00001d007655_T006 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger? | |
| Zmays_Zm00001d007655_T003 | SwissProt | 2021-04-01 | Q7RZV2 | 5.85e-4 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
