Zmays Zm00001d036530
From GreeNC
Gene information
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_Zm00001d036530 [ Zm00001d036530] |
6 | 91276762 | 91285762 | v4 | Zea mays (Phytozome 13) | Coding? Yes |
Transcript features
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_Zm00001d036530_T004 Zm00001d036530_T004 |
Low | No | 3090 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.284 Folding energies... MFEI: -32.845 AMFE: -0.648 GC content %: 50.680 | |
| Zmays_Zm00001d036530_T006 Zm00001d036530_T006 |
Low | No | 5651 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.240 Folding energies... MFEI: -29.501 AMFE: -0.641 GC content %: 46.010 | |
| Zmays_Zm00001d036530_T007 Zm00001d036530_T007 |
Low | No | 4973 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.165 Folding energies... MFEI: -30.350 AMFE: -0.634 GC content %: 47.838 | |
| Zmays_Zm00001d036530_T009 Zm00001d036530_T009 |
Low | No | 2224 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.218 Folding energies... MFEI: -31.407 AMFE: -0.642 GC content %: 48.921 | |
| Zmays_Zm00001d036530_T010 Zm00001d036530_T010 |
Low | No | 4052 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.186 Folding energies... MFEI: -30.629 AMFE: -0.616 GC content %: 49.729 | |
| Zmays_Zm00001d036530_T015 Zm00001d036530_T015 |
Low | No | 5323 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.235 Folding energies... MFEI: -30.148 AMFE: -0.641 GC content %: 47.022 | |
| Zmays_Zm00001d036530_T018 Zm00001d036530_T018 |
Low | No | 5105 | [7] | Get ORF Coding potential... Type: noncoding Potential: -0.154 Folding energies... MFEI: -30.184 AMFE: -0.641 GC content %: 47.071 | |
| Zmays_Zm00001d036530_T024 Zm00001d036530_T024 |
Low | No | 2276 | [8] | Get ORF Coding potential... Type: noncoding Potential: -0.206 Folding energies... MFEI: -31.481 AMFE: -0.647 GC content %: 48.638 | |
| Zmays_Zm00001d036530_T026 Zm00001d036530_T026 |
Low | No | 3993 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.167 Folding energies... MFEI: -30.568 AMFE: -0.647 GC content %: 47.283 | |
| Zmays_Zm00001d036530_T028 Zm00001d036530_T028 |
Low | No | 3729 | [10] | Get ORF Coding potential... Type: noncoding Potential: -0.132 Folding energies... MFEI: -30.700 AMFE: -0.639 GC content %: 48.056 | |
| Zmays_Zm00001d036530_T029 Zm00001d036530_T029 |
Low | No | 5769 | [11] | Get ORF Coding potential... Type: noncoding Potential: -0.241 Folding energies... MFEI: -29.511 AMFE: -0.649 GC content %: 45.484 | |
| Zmays_Zm00001d036530_T031 Zm00001d036530_T031 |
Low | No | 5224 | [12] | Get ORF Coding potential... Type: noncoding Potential: -0.132 Folding energies... MFEI: -30.195 AMFE: -0.644 GC content %: 46.861 | |
| Zmays_Zm00001d036530_T032 Zm00001d036530_T032 |
Low | No | 5828 | [13] | Get ORF Coding potential... Type: noncoding Potential: -0.242 Folding energies... MFEI: -29.518 AMFE: -0.648 GC content %: 45.522 | |
| Zmays_Zm00001d036530_T034 Zm00001d036530_T034 |
Low | No | 4937 | [14] | Get ORF Coding potential... Type: noncoding Potential: -0.228 Folding energies... MFEI: -30.480 AMFE: -0.650 GC content %: 46.871 | |
| Zmays_Zm00001d036530_T035 Zm00001d036530_T035 |
Low | No | 4625 | [15] | Get ORF Coding potential... Type: noncoding Potential: -0.221 Folding energies... MFEI: -29.909 AMFE: -0.646 GC content %: 46.314 | |
| Zmays_Zm00001d036530_T036 Zm00001d036530_T036 |
Low | No | 5120 | [16] | Get ORF Coding potential... Type: noncoding Potential: -0.230 Folding energies... MFEI: -29.248 AMFE: -0.650 GC content %: 45.000 | |
| Zmays_Zm00001d036530_T037 Zm00001d036530_T037 |
Low | No | 4796 | [17] | Get ORF Coding potential... Type: noncoding Potential: -0.225 Folding energies... MFEI: -30.006 AMFE: -0.656 GC content %: 45.746 | |
| Zmays_Zm00001d036530_T038 Zm00001d036530_T038 |
Low | No | 4419 | [18] | Get ORF Coding potential... Type: noncoding Potential: -0.177 Folding energies... MFEI: -29.670 AMFE: -0.657 GC content %: 45.169 | |
| Zmays_Zm00001d036530_T039 Zm00001d036530_T039 |
Low | No | 4657 | [19] | Get ORF Coding potential... Type: noncoding Potential: -0.223 Folding energies... MFEI: -27.874 AMFE: -0.658 GC content %: 42.345 | |
| Zmays_Zm00001d036530_T040 Zm00001d036530_T040 |
Low | No | 2879 | [20] | Get ORF Coding potential... Type: noncoding Potential: -0.076 Folding energies... MFEI: -29.319 AMFE: -0.631 GC content %: 46.474 | |
| Zmays_Zm00001d036530_T041 Zm00001d036530_T041 |
Low | No | 4486 | [21] | Get ORF Coding potential... Type: noncoding Potential: -0.219 Folding energies... MFEI: -27.889 AMFE: -0.661 GC content %: 42.176 | |
| Zmays_Zm00001d036530_T042 Zm00001d036530_T042 |
Low | No | 2793 | [22] | Get ORF Coding potential... Type: noncoding Potential: -0.194 Folding energies... MFEI: -26.831 AMFE: -0.665 GC content %: 40.351 |
Matches to external databases
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_Zm00001d036530_T009 | SwissProt | 2021-04-01 | Q9ZPX1 | 3.06e-25 |
| Zmays_Zm00001d036530_T040 | SwissProt | 2021-04-01 | Q9ZPX1 | 2.05e-26 |
| Zmays_Zm00001d036530_T037 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d036530_T035 | SwissProt | 2021-04-01 | Q9ZPX1 | 6.52e-25 |
| Zmays_Zm00001d036530_T031 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d036530_T028 | SwissProt | 2021-04-01 | Q9ZPX1 | 2.71e-26 |
| Zmays_Zm00001d036530_T015 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron | |
| Zmays_Zm00001d036530_T010 | SwissProt | 2021-04-01 | Q9ZPX1 | 2.97e-26 |
| Zmays_Zm00001d036530_T041 | SwissProt | 2021-04-01 | Q9ZPX1 | 6.31e-25 |
| Zmays_Zm00001d036530_T038 | RepBase (RepeatMasker) | 0000-00-00 | RC/Helitron |
... further results
Gene models
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
