Zmays Zm00001d011601
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_Zm00001d011601 [ Zm00001d011601] |
8 | 155555460 | 155561418 | v4 | Zea mays (Phytozome 13) | Coding? Yes |
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_Zm00001d011601_T003 Zm00001d011601_T003 |
Low | No | 3491 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.008 Folding energies... MFEI: -27.637 AMFE: -0.668 GC content %: 41.392 | |
| Zmays_Zm00001d011601_T004 Zm00001d011601_T004 |
Low | No | 4199 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.056 Folding energies... MFEI: -27.876 AMFE: -0.689 GC content %: 40.462 | |
| Zmays_Zm00001d011601_T010 Zm00001d011601_T010 |
Low | No | 1631 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.033 Folding energies... MFEI: -28.535 AMFE: -0.614 GC content %: 46.475 | |
| Zmays_Zm00001d011601_T014 Zm00001d011601_T014 |
Low | No | 4703 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.059 Folding energies... MFEI: -27.257 AMFE: -0.683 GC content %: 39.932 | |
| Zmays_Zm00001d011601_T021 Zm00001d011601_T021 |
Low | No | 3457 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.013 Folding energies... MFEI: -27.382 AMFE: -0.666 GC content %: 41.105 | |
| Zmays_Zm00001d011601_T032 Zm00001d011601_T032 |
Low | No | 3241 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.202 Folding energies... MFEI: -27.482 AMFE: -0.671 GC content %: 40.944 | |
| Zmays_Zm00001d011601_T036 Zm00001d011601_T036 |
Low | No | 3891 | [7] | Get ORF Coding potential... Type: noncoding Potential: -0.051 Folding energies... MFEI: -27.507 AMFE: -0.703 GC content %: 39.116 | |
| Zmays_Zm00001d011601_T048 Zm00001d011601_T048 |
Low | No | 4010 | [8] | Get ORF Coding potential... Type: noncoding Potential: -0.035 Folding energies... MFEI: -26.471 AMFE: -0.691 GC content %: 38.304 | |
| Zmays_Zm00001d011601_T049 Zm00001d011601_T049 |
Low | No | 4440 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.055 Folding energies... MFEI: -26.730 AMFE: -0.706 GC content %: 37.883 | |
| Zmays_Zm00001d011601_T052 Zm00001d011601_T052 |
Low | No | 3572 | [10] | Get ORF Coding potential... Type: noncoding Potential: -0.024 Folding energies... MFEI: -26.529 AMFE: -0.691 GC content %: 38.410 |
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_Zm00001d011601_T032 | SwissProt | 2021-04-01 | Q4VCM1 | 8.75e-42 |
| Zmays_Zm00001d011601_T003 | SwissProt | 2021-04-01 | Q4VCM1 | 5.93e-48 |
| Zmays_Zm00001d011601_T036 | SwissProt | 2021-04-01 | Q4VCM1 | 7.68e-19 |
| Zmays_Zm00001d011601_T004 | SwissProt | 2021-04-01 | Q4VCM1 | 1.02e-18 |
| Zmays_Zm00001d011601_T048 | SwissProt | 2021-04-01 | Q4VCM1 | 9.12e-48 |
| Zmays_Zm00001d011601_T010 | SwissProt | 2021-04-01 | Q4VCM1 | 5.57e-50 |
| Zmays_Zm00001d011601_T049 | SwissProt | 2021-04-01 | Q4VCM1 | 9.21e-19 |
| Zmays_Zm00001d011601_T014 | SwissProt | 2021-04-01 | Q4VCM1 | 1.19e-18 |
| Zmays_Zm00001d011601_T052 | SwissProt | 2021-04-01 | Q4VCM1 | 5.33e-42 |
| Zmays_Zm00001d011601_T021 | SwissProt | 2021-04-01 | Q4VCM1 | 5.8e-48 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
