Zmays Zm00001d021728
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_Zm00001d021728 [ Zm00001d021728] |
7 | 161522494 | 161527237 | 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_Zm00001d021728_T007 Zm00001d021728_T007 |
Low | No | 3032 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.004 Folding energies... MFEI: -30.660 AMFE: -0.642 GC content %: 47.757 | |
| Zmays_Zm00001d021728_T008 Zm00001d021728_T008 |
Low | No | 2106 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.096 Folding energies... MFEI: -31.975 AMFE: -0.611 GC content %: 52.374 | |
| Zmays_Zm00001d021728_T009 Zm00001d021728_T009 |
Low | No | 3445 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.255 Folding energies... MFEI: -30.644 AMFE: -0.654 GC content %: 46.880 | |
| Zmays_Zm00001d021728_T010 Zm00001d021728_T010 |
Low | No | 4161 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.269 Folding energies... MFEI: -28.995 AMFE: -0.651 GC content %: 44.509 | |
| Zmays_Zm00001d021728_T011 Zm00001d021728_T011 |
Low | No | 3730 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.042 Folding energies... MFEI: -29.933 AMFE: -0.652 GC content %: 45.925 | |
| Zmays_Zm00001d021728_T012 Zm00001d021728_T012 |
Low | No | 2692 | [6] | Get ORF Coding potential... Type: noncoding Potential: -1.008 Folding energies... MFEI: -31.857 AMFE: -0.648 GC content %: 49.183 | |
| Zmays_Zm00001d021728_T013 Zm00001d021728_T013 |
Low | No | 3964 | [7] | Get ORF Coding potential... Type: noncoding Potential: -0.266 Folding energies... MFEI: -28.996 AMFE: -0.648 GC content %: 44.753 | |
| Zmays_Zm00001d021728_T014 Zm00001d021728_T014 |
Low | No | 3532 | [8] | Get ORF Coding potential... Type: noncoding Potential: -0.129 Folding energies... MFEI: -30.413 AMFE: -0.647 GC content %: 46.971 | |
| Zmays_Zm00001d021728_T015 Zm00001d021728_T015 |
Low | No | 2900 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.132 Folding energies... MFEI: -31.214 AMFE: -0.647 GC content %: 48.276 | |
| Zmays_Zm00001d021728_T017 Zm00001d021728_T017 |
Low | No | 3942 | [10] | Get ORF Coding potential... Type: noncoding Potential: -0.266 Folding energies... MFEI: -29.264 AMFE: -0.650 GC content %: 45.003 | |
| Zmays_Zm00001d021728_T019 Zm00001d021728_T019 |
Low | No | 2514 | [11] | Get ORF Coding potential... Type: noncoding Potential: -0.218 Folding energies... MFEI: -30.628 AMFE: -0.619 GC content %: 49.483 | |
| Zmays_Zm00001d021728_T021 Zm00001d021728_T021 |
Low | No | 3503 | [12] | Get ORF Coding potential... Type: noncoding Potential: -0.257 Folding energies... MFEI: -30.240 AMFE: -0.651 GC content %: 46.446 | |
| Zmays_Zm00001d021728_T023 Zm00001d021728_T023 |
Low | No | 3515 | [13] | Get ORF Coding potential... Type: noncoding Potential: -0.257 Folding energies... MFEI: -30.242 AMFE: -0.651 GC content %: 46.458 | |
| Zmays_Zm00001d021728_T026 Zm00001d021728_T026 |
Low | No | 4064 | [14] | Get ORF Coding potential... Type: noncoding Potential: -0.268 Folding energies... MFEI: -28.974 AMFE: -0.649 GC content %: 44.636 | |
| Zmays_Zm00001d021728_T027 Zm00001d021728_T027 |
Low | No | 4190 | [15] | Get ORF Coding potential... Type: noncoding Potential: -0.270 Folding energies... MFEI: -28.800 AMFE: -0.649 GC content %: 44.368 | |
| Zmays_Zm00001d021728_T028 Zm00001d021728_T028 |
Low | No | 4164 | [16] | Get ORF Coding potential... Type: noncoding Potential: -0.259 Folding energies... MFEI: -28.910 AMFE: -0.650 GC content %: 44.476 | |
| Zmays_Zm00001d021728_T030 Zm00001d021728_T030 |
Low | No | 4138 | [17] | Get ORF Coding potential... Type: noncoding Potential: -0.269 Folding energies... MFEI: -28.891 AMFE: -0.649 GC content %: 44.514 | |
| Zmays_Zm00001d021728_T031 Zm00001d021728_T031 |
Low | No | 2977 | [18] | Get ORF Coding potential... Type: noncoding Potential: -0.236 Folding energies... MFEI: -28.878 AMFE: -0.618 GC content %: 46.758 | |
| Zmays_Zm00001d021728_T032 Zm00001d021728_T032 |
Low | No | 3994 | [19] | Get ORF Coding potential... Type: noncoding Potential: -0.266 Folding energies... MFEI: -29.051 AMFE: -0.650 GC content %: 44.692 | |
| Zmays_Zm00001d021728_T033 Zm00001d021728_T033 |
Low | No | 1809 | [20] | Get ORF Coding potential... Type: noncoding Potential: -0.967 Folding energies... MFEI: -32.814 AMFE: -0.601 GC content %: 54.561 | |
| Zmays_Zm00001d021728_T035 Zm00001d021728_T035 |
Low | No | 3794 | [21] | Get ORF Coding potential... Type: noncoding Potential: -0.263 Folding energies... MFEI: -29.428 AMFE: -0.650 GC content %: 45.256 | |
| Zmays_Zm00001d021728_T036 Zm00001d021728_T036 |
Low | No | 2377 | [22] | Get ORF Coding potential... Type: noncoding Potential: -0.211 Folding energies... MFEI: -31.325 AMFE: -0.623 GC content %: 50.273 | |
| Zmays_Zm00001d021728_T037 Zm00001d021728_T037 |
Low | No | 4021 | [23] | Get ORF Coding potential... Type: noncoding Potential: -0.109 Folding energies... MFEI: -29.224 AMFE: -0.646 GC content %: 45.213 | |
| Zmays_Zm00001d021728_T039 Zm00001d021728_T039 |
Low | No | 2410 | [24] | Get ORF Coding potential... Type: noncoding Potential: -0.212 Folding energies... MFEI: -30.946 AMFE: -0.615 GC content %: 50.290 | |
| Zmays_Zm00001d021728_T041 Zm00001d021728_T041 |
Low | No | 1910 | [25] | Get ORF Coding potential... Type: noncoding Potential: -0.073 Folding energies... MFEI: -32.387 AMFE: -0.605 GC content %: 53.508 | |
| Zmays_Zm00001d021728_T043 Zm00001d021728_T043 |
Low | No | 3181 | [26] | Get ORF Coding potential... Type: noncoding Potential: -0.122 Folding energies... MFEI: -30.346 AMFE: -0.644 GC content %: 47.124 | |
| Zmays_Zm00001d021728_T044 Zm00001d021728_T044 |
Low | No | 4002 | [27] | Get ORF Coding potential... Type: noncoding Potential: -0.255 Folding energies... MFEI: -28.296 AMFE: -0.639 GC content %: 44.278 | |
| Zmays_Zm00001d021728_T045 Zm00001d021728_T045 |
Low | No | 3138 | [28] | Get ORF Coding potential... Type: noncoding Potential: -0.065 Folding energies... MFEI: -30.328 AMFE: -0.641 GC content %: 47.291 | |
| Zmays_Zm00001d021728_T047 Zm00001d021728_T047 |
Low | No | 3125 | [29] | Get ORF Coding potential... Type: noncoding Potential: -1.007 Folding energies... MFEI: -30.381 AMFE: -0.643 GC content %: 47.264 | |
| Zmays_Zm00001d021728_T050 Zm00001d021728_T050 |
Low | No | 3305 | [30] | Get ORF Coding potential... Type: noncoding Potential: -0.063 Folding energies... MFEI: -30.714 AMFE: -0.645 GC content %: 47.625 | |
| Zmays_Zm00001d021728_T053 Zm00001d021728_T053 |
Low | No | 2449 | [31] | Get ORF Coding potential... Type: noncoding Potential: -0.001 Folding energies... MFEI: -32.703 AMFE: -0.636 GC content %: 51.409 | |
| Zmays_Zm00001d021728_T056 Zm00001d021728_T056 |
Low | No | 4122 | [32] | Get ORF Coding potential... Type: noncoding Potential: -0.269 Folding energies... MFEI: -28.819 AMFE: -0.649 GC content %: 44.396 | |
| Zmays_Zm00001d021728_T057 Zm00001d021728_T057 |
Low | No | 4001 | [33] | Get ORF Coding potential... Type: noncoding Potential: -0.271 Folding energies... MFEI: -29.028 AMFE: -0.648 GC content %: 44.764 | |
| Zmays_Zm00001d021728_T060 Zm00001d021728_T060 |
High | No | 3189 | [34] | Get ORF Coding potential... Type: noncoding Potential: -1.001 Folding energies... MFEI: -30.245 AMFE: -0.643 GC content %: 47.005 | |
| Zmays_Zm00001d021728_T061 Zm00001d021728_T061 |
Low | No | 4139 | [35] | Get ORF Coding potential... Type: noncoding Potential: -0.265 Folding energies... MFEI: -28.908 AMFE: -0.652 GC content %: 44.359 | |
| Zmays_Zm00001d021728_T062 Zm00001d021728_T062 |
Low | No | 1833 | [36] | Get ORF Coding potential... Type: noncoding Potential: -0.089 Folding energies... MFEI: -32.542 AMFE: -0.604 GC content %: 53.846 | |
| Zmays_Zm00001d021728_T063 Zm00001d021728_T063 |
Low | No | 3312 | [37] | Get ORF Coding potential... Type: noncoding Potential: -0.265 Folding energies... MFEI: -30.513 AMFE: -0.653 GC content %: 46.709 | |
| Zmays_Zm00001d021728_T064 Zm00001d021728_T064 |
Low | No | 2940 | [38] | Get ORF Coding potential... Type: noncoding Potential: -0.062 Folding energies... MFEI: -29.065 AMFE: -0.615 GC content %: 47.245 | |
| Zmays_Zm00001d021728_T065 Zm00001d021728_T065 |
Low | No | 3918 | [39] | Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -28.900 AMFE: -0.663 GC content %: 43.619 | |
| Zmays_Zm00001d021728_T066 Zm00001d021728_T066 |
Low | No | 3407 | [40] | Get ORF Coding potential... Type: noncoding Potential: -0.027 Folding energies... MFEI: -29.527 AMFE: -0.658 GC content %: 44.878 | |
| Zmays_Zm00001d021728_T068 Zm00001d021728_T068 |
Low | No | 782 | [41] | Get ORF Coding potential... Type: noncoding Potential: -1.073 Folding energies... MFEI: -28.900 AMFE: -0.623 GC content %: 46.419 | |
| Zmays_Zm00001d021728_T069 Zm00001d021728_T069 |
Low | No | 2952 | [42] | Get ORF Coding potential... Type: noncoding Potential: -1.194 Folding energies... MFEI: -27.791 AMFE: -0.674 GC content %: 41.260 |
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_Zm00001d021728_T021 | SwissProt | 2021-04-01 | F4K1B4 | 2.64e-13 |
| Zmays_Zm00001d021728_T045 | SwissProt | 2021-04-01 | F4K1B4 | 3.52e-18 |
| Zmays_Zm00001d021728_T011 | RepBase (RepeatMasker) | 0000-00-00 | DNA/TcMar-Tigger | |
| Zmays_Zm00001d021728_T039 | RepBase (RepeatMasker) | 0000-00-00 | DNA/TcMar-Tigger | |
| Zmays_Zm00001d021728_T069 | RepBase (RepeatMasker) | 0000-00-00 | DNA/TcMar-Tigger | |
| Zmays_Zm00001d021728_T013 | SwissProt | 2021-04-01 | F4K1B4 | 3.24e-13 |
| Zmays_Zm00001d021728_T037 | SwissProt | 2021-04-01 | Q6Z4P2 | 1.69e-17 |
| Zmays_Zm00001d021728_T066 | SwissProt | 2021-04-01 | F4K1B4 | 4.33e-21 |
| Zmays_Zm00001d021728_T031 | RepBase (RepeatMasker) | 0000-00-00 | DNA/TcMar-Tigger | |
| Zmays_Zm00001d021728_T008 | SwissProt | 2021-04-01 | F4K1B4 | 1.39e-17 |
... further results
Gene models
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
