Zmays Zm00001d053556
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_Zm00001d053556 [ Zm00001d053556] |
4 | 233911426 | 233914642 | v4 | Zea mays (Phytozome 13) | Coding? No |
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_Zm00001d053556_T001 Zm00001d053556_T001 |
Low | No | 2922 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.191 Folding energies... MFEI: -27.789 AMFE: -0.642 GC content %: 43.292 | |
| Zmays_Zm00001d053556_T002 Zm00001d053556_T002 |
High | No | 765 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -34.248 AMFE: -0.645 GC content %: 53.072 | |
| Zmays_Zm00001d053556_T003 Zm00001d053556_T003 |
Low | No | 740 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.105 Folding energies... MFEI: -35.865 AMFE: -0.672 GC content %: 53.378 | |
| Zmays_Zm00001d053556_T004 Zm00001d053556_T004 |
Low | No | 599 | [4] | Get ORF Coding potential... Type: noncoding Potential: -1.049 Folding energies... MFEI: -37.129 AMFE: -0.650 GC content %: 57.095 | |
| Zmays_Zm00001d053556_T005 Zm00001d053556_T005 |
Low | No | 673 | [5] | Get ORF Coding potential... Type: noncoding Potential: -1.081 Folding energies... MFEI: -36.627 AMFE: -0.664 GC content %: 55.126 |
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_Zm00001d053556_T003 | SwissProt | 2021-04-01 | Q6NNL9 | 5.96e-4 |
| Zmays_Zm00001d053556_T004 | SwissProt | 2021-04-01 | Q6NNL9 | 1.75e-5 |
| Zmays_Zm00001d053556_T005 | SwissProt | 2021-04-01 | Q6NNL9 | 2.64e-7 |
| Zmays_Zm00001d053556_T001 | RepBase (RepeatMasker) | 0000-00-00 | SINE/tRNA | |
| Zmays_Zm00001d053556_T001 | SwissProt | 2021-04-01 | Q6NNL9 | 9.03e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
