Zmays Zm00001d028375
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_Zm00001d028375 [ Zm00001d028375] |
1 | 32602769 | 32606650 | 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_Zm00001d028375_T003 Zm00001d028375_T003 |
Low | Yes | 2577 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.872 Folding energies... MFEI: -28.029 AMFE: -0.700 GC content %: 40.047 | |
| Zmays_Zm00001d028375_T004 Zm00001d028375_T004 |
Low | Yes | 3580 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.901 Folding energies... MFEI: -27.777 AMFE: -0.701 GC content %: 39.637 | |
| Zmays_Zm00001d028375_T005 Zm00001d028375_T005 |
Low | Yes | 3487 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.899 Folding energies... MFEI: -27.869 AMFE: -0.702 GC content %: 39.719 | |
| Zmays_Zm00001d028375_T006 Zm00001d028375_T006 |
Low | Yes | 3557 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.900 Folding energies... MFEI: -27.669 AMFE: -0.700 GC content %: 39.528 |
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_Zm00001d028375_T006 | Rfam | 14.6 | MIR2118 | 6.3e-5 |
| Zmays_Zm00001d028375_T003 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger | |
| Zmays_Zm00001d028375_T004 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger | |
| Zmays_Zm00001d028375_T003 | Rfam | 14.6 | MIR2118 | 4.5e-5 |
| Zmays_Zm00001d028375_T005 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger | |
| Zmays_Zm00001d028375_T004 | Rfam | 14.6 | MIR2118 | 6.3e-5 |
| Zmays_Zm00001d028375_T006 | RepBase (RepeatMasker) | 0000-00-00 | DNA/PIF-Harbinger | |
| Zmays_Zm00001d028375_T005 | Rfam | 14.6 | MIR2118 | 6.1e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
