Zmays Zm00001d012794
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_Zm00001d012794 [ Zm00001d012794] |
5 | 32368 | 35621 | 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_Zm00001d012794_T006 Zm00001d012794_T006 |
Low | No | 2608 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.105 Folding energies... MFEI: -28.923 AMFE: -0.662 GC content %: 43.673 | |
| Zmays_Zm00001d012794_T007 Zm00001d012794_T007 |
Low | No | 2153 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.267 Folding energies... MFEI: -29.015 AMFE: -0.646 GC content %: 44.914 | |
| Zmays_Zm00001d012794_T008 Zm00001d012794_T008 |
Low | No | 902 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.907 Folding energies... MFEI: -29.501 AMFE: -0.628 GC content %: 47.007 | |
| Zmays_Zm00001d012794_T009 Zm00001d012794_T009 |
Low | No | 1434 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.169 Folding energies... MFEI: -27.845 AMFE: -0.632 GC content %: 44.073 | |
| Zmays_Zm00001d012794_T011 Zm00001d012794_T011 |
Low | No | 2304 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.373 Folding energies... MFEI: -28.659 AMFE: -0.650 GC content %: 44.097 | |
| Zmays_Zm00001d012794_T012 Zm00001d012794_T012 |
Low | No | 1537 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.223 Folding energies... MFEI: -28.426 AMFE: -0.642 GC content %: 44.307 | |
| Zmays_Zm00001d012794_T013 Zm00001d012794_T013 |
Low | No | 2256 | [7] | Get ORF Coding potential... Type: noncoding Potential: -1.086 Folding energies... MFEI: -28.488 AMFE: -0.647 GC content %: 44.016 |
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_Zm00001d012794_T007 | SwissProt | 2021-04-01 | Q3M3Q5 | 8.56e-11 |
| Zmays_Zm00001d012794_T013 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d012794_T006 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d012794_T008 | SwissProt | 2021-04-01 | B0JUK5 | 8.24e-4 |
| Zmays_Zm00001d012794_T007 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d012794_T009 | SwissProt | 2021-04-01 | Q3M3Q5 | 1.74e-9 |
| Zmays_Zm00001d012794_T009 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d012794_T011 | SwissProt | 2021-04-01 | B0JUK5 | 4.31e-12 |
| Zmays_Zm00001d012794_T011 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d012794_T012 | SwissProt | 2021-04-01 | Q3M3Q5 | 4.71e-11 |
... further results
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
