Zmays Zm00001d014261
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_Zm00001d014261 [ Zm00001d014261] |
5 | 38492577 | 38499065 | 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_Zm00001d014261_T001 Zm00001d014261_T001 |
Low | No | 1694 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.249 Folding energies... MFEI: -33.158 AMFE: -0.595 GC content %: 55.726 | |
| Zmays_Zm00001d014261_T002 Zm00001d014261_T002 |
Low | No | 2391 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.113 Folding energies... MFEI: -30.908 AMFE: -0.614 GC content %: 50.355 | |
| Zmays_Zm00001d014261_T006 Zm00001d014261_T006 |
Low | No | 3645 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.982 Folding energies... MFEI: -30.121 AMFE: -0.649 GC content %: 46.420 | |
| Zmays_Zm00001d014261_T008 Zm00001d014261_T008 |
Low | No | 4551 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.164 Folding energies... MFEI: -28.482 AMFE: -0.651 GC content %: 43.727 | |
| Zmays_Zm00001d014261_T009 Zm00001d014261_T009 |
Low | No | 2099 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.015 Folding energies... MFEI: -31.512 AMFE: -0.598 GC content %: 52.739 | |
| Zmays_Zm00001d014261_T010 Zm00001d014261_T010 |
Low | No | 2438 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.115 Folding energies... MFEI: -30.603 AMFE: -0.603 GC content %: 50.779 | |
| Zmays_Zm00001d014261_T012 Zm00001d014261_T012 |
Low | No | 3422 | [7] | Get ORF Coding potential... Type: noncoding Potential: -0.152 Folding energies... MFEI: -30.431 AMFE: -0.650 GC content %: 46.844 | |
| Zmays_Zm00001d014261_T013 Zm00001d014261_T013 |
Low | No | 4600 | [8] | Get ORF Coding potential... Type: noncoding Potential: -0.100 Folding energies... MFEI: -28.413 AMFE: -0.651 GC content %: 43.630 | |
| Zmays_Zm00001d014261_T015 Zm00001d014261_T015 |
Low | No | 2688 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.964 Folding energies... MFEI: -31.793 AMFE: -0.648 GC content %: 49.070 | |
| Zmays_Zm00001d014261_T016 Zm00001d014261_T016 |
Low | No | 3931 | [10] | Get ORF Coding potential... Type: noncoding Potential: -0.086 Folding energies... MFEI: -28.904 AMFE: -0.647 GC content %: 44.696 | |
| Zmays_Zm00001d014261_T018 Zm00001d014261_T018 |
Low | No | 2896 | [11] | Get ORF Coding potential... Type: noncoding Potential: -0.056 Folding energies... MFEI: -30.996 AMFE: -0.642 GC content %: 48.308 | |
| Zmays_Zm00001d014261_T020 Zm00001d014261_T020 |
Low | No | 3909 | [12] | Get ORF Coding potential... Type: noncoding Potential: -0.085 Folding energies... MFEI: -29.024 AMFE: -0.645 GC content %: 44.999 | |
| Zmays_Zm00001d014261_T023 Zm00001d014261_T023 |
Low | No | 2491 | [13] | Get ORF Coding potential... Type: noncoding Potential: -0.124 Folding energies... MFEI: -30.273 AMFE: -0.613 GC content %: 49.418 | |
| Zmays_Zm00001d014261_T024 Zm00001d014261_T024 |
Low | No | 3480 | [14] | Get ORF Coding potential... Type: noncoding Potential: -0.154 Folding energies... MFEI: -29.949 AMFE: -0.646 GC content %: 46.379 | |
| Zmays_Zm00001d014261_T026 Zm00001d014261_T026 |
Low | No | 3491 | [15] | Get ORF Coding potential... Type: noncoding Potential: -0.155 Folding energies... MFEI: -30.001 AMFE: -0.647 GC content %: 46.376 | |
| Zmays_Zm00001d014261_T029 Zm00001d014261_T029 |
Low | No | 4031 | [16] | Get ORF Coding potential... Type: noncoding Potential: -0.087 Folding energies... MFEI: -28.808 AMFE: -0.647 GC content %: 44.555 | |
| Zmays_Zm00001d014261_T031 Zm00001d014261_T031 |
Low | No | 4568 | [17] | Get ORF Coding potential... Type: noncoding Potential: 0.000 Folding energies... MFEI: -28.649 AMFE: -0.655 GC content %: 43.761 | |
| Zmays_Zm00001d014261_T032 Zm00001d014261_T032 |
Low | No | 3629 | [18] | Get ORF Coding potential... Type: noncoding Potential: -0.313 Folding energies... MFEI: -30.028 AMFE: -0.648 GC content %: 46.349 | |
| Zmays_Zm00001d014261_T033 Zm00001d014261_T033 |
Low | No | 3733 | [19] | Get ORF Coding potential... Type: noncoding Potential: -0.151 Folding energies... MFEI: -28.529 AMFE: -0.633 GC content %: 45.058 | |
| Zmays_Zm00001d014261_T034 Zm00001d014261_T034 |
Low | No | 4663 | [20] | Get ORF Coding potential... Type: noncoding Potential: -0.170 Folding energies... MFEI: -28.625 AMFE: -0.658 GC content %: 43.513 | |
| Zmays_Zm00001d014261_T035 Zm00001d014261_T035 |
Low | No | 3568 | [21] | Get ORF Coding potential... Type: noncoding Potential: -0.981 Folding energies... MFEI: -30.118 AMFE: -0.650 GC content %: 46.357 | |
| Zmays_Zm00001d014261_T036 Zm00001d014261_T036 |
Low | No | 4670 | [22] | Get ORF Coding potential... Type: noncoding Potential: -0.100 Folding energies... MFEI: -28.448 AMFE: -0.653 GC content %: 43.533 | |
| Zmays_Zm00001d014261_T037 Zm00001d014261_T037 |
Low | No | 4205 | [23] | Get ORF Coding potential... Type: noncoding Potential: -0.091 Folding energies... MFEI: -29.515 AMFE: -0.658 GC content %: 44.851 | |
| Zmays_Zm00001d014261_T038 Zm00001d014261_T038 |
Low | No | 4674 | [24] | Get ORF Coding potential... Type: noncoding Potential: -0.104 Folding energies... MFEI: -28.511 AMFE: -0.659 GC content %: 43.282 | |
| Zmays_Zm00001d014261_T042 Zm00001d014261_T042 |
Low | No | 2945 | [25] | Get ORF Coding potential... Type: noncoding Potential: -0.139 Folding energies... MFEI: -28.776 AMFE: -0.616 GC content %: 46.723 | |
| Zmays_Zm00001d014261_T043 Zm00001d014261_T043 |
Low | No | 3958 | [26] | Get ORF Coding potential... Type: noncoding Potential: -0.086 Folding energies... MFEI: -28.909 AMFE: -0.648 GC content %: 44.618 | |
| Zmays_Zm00001d014261_T044 Zm00001d014261_T044 |
Low | No | 1806 | [27] | Get ORF Coding potential... Type: noncoding Potential: -0.932 Folding energies... MFEI: -32.272 AMFE: -0.590 GC content %: 54.707 | |
| Zmays_Zm00001d014261_T046 Zm00001d014261_T046 |
Low | No | 3760 | [28] | Get ORF Coding potential... Type: noncoding Potential: -0.083 Folding energies... MFEI: -29.303 AMFE: -0.650 GC content %: 45.106 | |
| Zmays_Zm00001d014261_T048 Zm00001d014261_T048 |
Low | No | 3754 | [29] | Get ORF Coding potential... Type: noncoding Potential: -0.012 Folding energies... MFEI: -29.885 AMFE: -0.653 GC content %: 45.791 | |
| Zmays_Zm00001d014261_T050 Zm00001d014261_T050 |
Low | No | 3703 | [30] | Get ORF Coding potential... Type: noncoding Potential: -0.082 Folding energies... MFEI: -29.927 AMFE: -0.650 GC content %: 46.071 | |
| Zmays_Zm00001d014261_T051 Zm00001d014261_T051 |
Low | No | 1929 | [31] | Get ORF Coding potential... Type: noncoding Potential: -0.006 Folding energies... MFEI: -31.625 AMFE: -0.587 GC content %: 53.862 | |
| Zmays_Zm00001d014261_T052 Zm00001d014261_T052 |
Low | No | 2362 | [32] | Get ORF Coding potential... Type: noncoding Potential: -0.112 Folding energies... MFEI: -30.872 AMFE: -0.612 GC content %: 50.423 | |
| Zmays_Zm00001d014261_T057 Zm00001d014261_T057 |
Low | No | 3842 | [33] | Get ORF Coding potential... Type: noncoding Potential: -0.010 Folding energies... MFEI: -30.237 AMFE: -0.656 GC content %: 46.122 | |
| Zmays_Zm00001d014261_T060 Zm00001d014261_T060 |
Low | No | 4487 | [34] | Get ORF Coding potential... Type: noncoding Potential: -0.091 Folding energies... MFEI: -28.536 AMFE: -0.651 GC content %: 43.838 | |
| Zmays_Zm00001d014261_T061 Zm00001d014261_T061 |
Low | No | 4570 | [35] | Get ORF Coding potential... Type: noncoding Potential: -0.165 Folding energies... MFEI: -28.549 AMFE: -0.656 GC content %: 43.545 | |
| Zmays_Zm00001d014261_T062 Zm00001d014261_T062 |
Low | No | 1830 | [36] | Get ORF Coding potential... Type: noncoding Potential: 0.000 Folding energies... MFEI: -32.101 AMFE: -0.595 GC content %: 53.934 | |
| Zmays_Zm00001d014261_T063 Zm00001d014261_T063 |
Low | No | 3289 | [37] | Get ORF Coding potential... Type: noncoding Potential: -0.150 Folding energies... MFEI: -30.468 AMFE: -0.653 GC content %: 46.671 | |
| Zmays_Zm00001d014261_T064 Zm00001d014261_T064 |
Low | No | 2909 | [38] | Get ORF Coding potential... Type: noncoding Potential: -0.018 Folding energies... MFEI: -29.722 AMFE: -0.629 GC content %: 47.267 | |
| Zmays_Zm00001d014261_T068 Zm00001d014261_T068 |
Low | No | 2545 | [39] | Get ORF Coding potential... Type: noncoding Potential: -1.219 Folding energies... MFEI: -26.271 AMFE: -0.689 GC content %: 38.153 |
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_Zm00001d014261_T032 | SwissProt | 2021-04-01 | F4K1B4 | 7.02e-11 |
| Zmays_Zm00001d014261_T060 | SwissProt | 2021-04-01 | F4K1B4 | 3.33e-15 |
| Zmays_Zm00001d014261_T038 | RepBase (RepeatMasker) | 0000-00-00 | DNA/hAT-Tag1 | |
| Zmays_Zm00001d014261_T001 | SwissProt | 2021-04-01 | F4K1B4 | 5.75e-11 |
| Zmays_Zm00001d014261_T023 | SwissProt | 2021-04-01 | F4K1B4 | 1.52e-15 |
| Zmays_Zm00001d014261_T048 | SwissProt | 2021-04-01 | F4K1B4 | 1.02e-18 |
| Zmays_Zm00001d014261_T033 | RepBase (RepeatMasker) | 0000-00-00 | DNA/hAT-Tag1 | |
| Zmays_Zm00001d014261_T013 | SwissProt | 2021-04-01 | F4K1B4 | 3.94e-15 |
| Zmays_Zm00001d014261_T038 | SwissProt | 2021-04-01 | F4K1B4 | 3.7e-15 |
| Zmays_Zm00001d014261_T006 | RepBase (RepeatMasker) | 0000-00-00 | DNA/hAT-Tag1 |
... further results
Gene models
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
