Zmays Zm00001d011075
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_Zm00001d011075 [ Zm00001d011075] |
8 | 138093685 | 138114618 | 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_Zm00001d011075_T002 Zm00001d011075_T002 |
Low | No | 4895 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.151 Folding energies... MFEI: -27.961 AMFE: -0.642 GC content %: 43.555 | |
| Zmays_Zm00001d011075_T003 Zm00001d011075_T003 |
Low | No | 4551 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.158 Folding energies... MFEI: -28.653 AMFE: -0.646 GC content %: 44.364 | |
| Zmays_Zm00001d011075_T005 Zm00001d011075_T005 |
Low | No | 4968 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.023 Folding energies... MFEI: -28.196 AMFE: -0.647 GC content %: 43.579 | |
| Zmays_Zm00001d011075_T007 Zm00001d011075_T007 |
Low | No | 4752 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.032 Folding energies... MFEI: -28.447 AMFE: -0.644 GC content %: 44.150 | |
| Zmays_Zm00001d011075_T023 Zm00001d011075_T023 |
Low | No | 4624 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.066 Folding energies... MFEI: -28.884 AMFE: -0.655 GC content %: 44.074 | |
| Zmays_Zm00001d011075_T024 Zm00001d011075_T024 |
Low | No | 2117 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.127 Folding energies... MFEI: -32.749 AMFE: -0.634 GC content %: 51.630 | |
| Zmays_Zm00001d011075_T026 Zm00001d011075_T026 |
Low | No | 2756 | [7] | Get ORF Coding potential... Type: noncoding Potential: -0.146 Folding energies... MFEI: -30.675 AMFE: -0.644 GC content %: 47.605 | |
| Zmays_Zm00001d011075_T031 Zm00001d011075_T031 |
Low | No | 7331 | [8] | Get ORF Coding potential... Type: noncoding Potential: -0.171 Folding energies... MFEI: -27.482 AMFE: -0.663 GC content %: 41.427 | |
| Zmays_Zm00001d011075_T033 Zm00001d011075_T033 |
Low | No | 4535 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.158 Folding energies... MFEI: -28.598 AMFE: -0.650 GC content %: 44.013 | |
| Zmays_Zm00001d011075_T039 Zm00001d011075_T039 |
Low | No | 4428 | [10] | Get ORF Coding potential... Type: noncoding Potential: -0.335 Folding energies... MFEI: -28.625 AMFE: -0.651 GC content %: 43.970 | |
| Zmays_Zm00001d011075_T040 Zm00001d011075_T040 |
Low | No | 3879 | [11] | Get ORF Coding potential... Type: noncoding Potential: -0.166 Folding energies... MFEI: -29.317 AMFE: -0.644 GC content %: 45.553 | |
| Zmays_Zm00001d011075_T043 Zm00001d011075_T043 |
Low | No | 6390 | [12] | Get ORF Coding potential... Type: noncoding Potential: -0.164 Folding energies... MFEI: -27.487 AMFE: -0.673 GC content %: 40.814 | |
| Zmays_Zm00001d011075_T044 Zm00001d011075_T044 |
Low | No | 3933 | [13] | Get ORF Coding potential... Type: noncoding Potential: -0.167 Folding energies... MFEI: -29.204 AMFE: -0.656 GC content %: 44.495 | |
| Zmays_Zm00001d011075_T045 Zm00001d011075_T045 |
Low | No | 4716 | [14] | Get ORF Coding potential... Type: noncoding Potential: -0.161 Folding energies... MFEI: -27.941 AMFE: -0.653 GC content %: 42.791 | |
| Zmays_Zm00001d011075_T046 Zm00001d011075_T046 |
Low | No | 5116 | [15] | Get ORF Coding potential... Type: noncoding Potential: -0.146 Folding energies... MFEI: -28.301 AMFE: -0.672 GC content %: 42.142 | |
| Zmays_Zm00001d011075_T047 Zm00001d011075_T047 |
Low | No | 4024 | [16] | Get ORF Coding potential... Type: noncoding Potential: -0.154 Folding energies... MFEI: -27.085 AMFE: -0.647 GC content %: 41.849 | |
| Zmays_Zm00001d011075_T051 Zm00001d011075_T051 |
Low | No | 3329 | [17] | Get ORF Coding potential... Type: noncoding Potential: -0.063 Folding energies... MFEI: -28.044 AMFE: -0.677 GC content %: 41.424 | |
| Zmays_Zm00001d011075_T052 Zm00001d011075_T052 |
Low | No | 3029 | [18] | Get ORF Coding potential... Type: noncoding Potential: -0.054 Folding energies... MFEI: -28.069 AMFE: -0.672 GC content %: 41.796 | |
| Zmays_Zm00001d011075_T056 Zm00001d011075_T056 |
Low | No | 3845 | [19] | Get ORF Coding potential... Type: noncoding Potential: -0.323 Folding energies... MFEI: -27.186 AMFE: -0.686 GC content %: 39.636 | |
| Zmays_Zm00001d011075_T057 Zm00001d011075_T057 |
Low | No | 3609 | [20] | Get ORF Coding potential... Type: noncoding Potential: -0.449 Folding energies... MFEI: -25.680 AMFE: -0.674 GC content %: 38.127 | |
| Zmays_Zm00001d011075_T070 Zm00001d011075_T070 |
Low | No | 4723 | [21] | Get ORF Coding potential... Type: noncoding Potential: -0.074 Folding energies... MFEI: -28.097 AMFE: -0.687 GC content %: 40.885 | |
| Zmays_Zm00001d011075_T074 Zm00001d011075_T074 |
Low | No | 4633 | [22] | Get ORF Coding potential... Type: noncoding Potential: -0.185 Folding energies... MFEI: -27.399 AMFE: -0.686 GC content %: 39.931 | |
| Zmays_Zm00001d011075_T075 Zm00001d011075_T075 |
Low | No | 4518 | [23] | Get ORF Coding potential... Type: noncoding Potential: -0.183 Folding energies... MFEI: -27.543 AMFE: -0.684 GC content %: 40.261 |
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_Zm00001d011075_T045 | SwissProt | 2021-04-01 | Q84L14 | 3.56e-18 |
| Zmays_Zm00001d011075_T074 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d011075_T033 | SwissProt | 2021-04-01 | Q84L14 | 3.41e-18 |
| Zmays_Zm00001d011075_T043 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 | |
| Zmays_Zm00001d011075_T007 | SwissProt | 2021-04-01 | Q84L14 | 3.59e-18 |
| Zmays_Zm00001d011075_T057 | SwissProt | 2021-04-01 | Q84L14 | 2.63e-18 |
| Zmays_Zm00001d011075_T046 | SwissProt | 2021-04-01 | Q84L14 | 3.9e-18 |
| Zmays_Zm00001d011075_T075 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d011075_T039 | SwissProt | 2021-04-01 | Q84L14 | 3.32e-18 |
| Zmays_Zm00001d011075_T046 | RepBase (RepeatMasker) | 0000-00-00 | LINE/L1 |
... further results
Gene models
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
