Zmays Zm00001d004230
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_Zm00001d004230 [ Zm00001d004230] |
2 | 94054835 | 94067869 | 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_Zm00001d004230_T001 Zm00001d004230_T001 |
Low | No | 2191 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.377 Folding energies... MFEI: -27.141 AMFE: -0.693 GC content %: 39.160 | |
| Zmays_Zm00001d004230_T002 Zm00001d004230_T002 |
Low | No | 2178 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.377 Folding energies... MFEI: -27.319 AMFE: -0.681 GC content %: 40.129 | |
| Zmays_Zm00001d004230_T003 Zm00001d004230_T003 |
Low | No | 2175 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.549 Folding energies... MFEI: -28.155 AMFE: -0.690 GC content %: 40.782 | |
| Zmays_Zm00001d004230_T009 Zm00001d004230_T009 |
Low | No | 2476 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.389 Folding energies... MFEI: -28.977 AMFE: -0.674 GC content %: 43.013 | |
| Zmays_Zm00001d004230_T012 Zm00001d004230_T012 |
Low | No | 3621 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.417 Folding energies... MFEI: -31.689 AMFE: -0.666 GC content %: 47.556 | |
| Zmays_Zm00001d004230_T021 Zm00001d004230_T021 |
Low | No | 2184 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.377 Folding energies... MFEI: -27.595 AMFE: -0.690 GC content %: 40.018 |
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_Zm00001d004230_T001 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d004230_T002 | SwissProt | 2021-04-01 | Q9FW70 | 1.33e-9 |
| Zmays_Zm00001d004230_T002 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d004230_T003 | SwissProt | 2021-04-01 | Q39236 | 2.64e-5 |
| Zmays_Zm00001d004230_T009 | SwissProt | 2021-04-01 | Q9FW70 | 1.61e-9 |
| Zmays_Zm00001d004230_T012 | SwissProt | 2021-04-01 | Q9FW70 | 2.72e-9 |
| Zmays_Zm00001d004230_T021 | SwissProt | 2021-04-01 | Q9FW70 | 1.33e-9 |
| Zmays_Zm00001d004230_T001 | SwissProt | 2021-04-01 | Q9FW70 | 1.34e-9 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
