Zmays Zm00001d036420
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_Zm00001d036420 [ Zm00001d036420] |
6 | 87683362 | 87688330 | 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_Zm00001d036420_T001 Zm00001d036420_T001 |
High | No | 4023 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.021 Folding energies... MFEI: -27.775 AMFE: -0.676 GC content %: 41.114 | |
| Zmays_Zm00001d036420_T002 Zm00001d036420_T002 |
Low | No | 4119 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.023 Folding energies... MFEI: -27.837 AMFE: -0.671 GC content %: 41.515 | |
| Zmays_Zm00001d036420_T003 Zm00001d036420_T003 |
Low | No | 3943 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.024 Folding energies... MFEI: -27.974 AMFE: -0.678 GC content %: 41.288 | |
| Zmays_Zm00001d036420_T005 Zm00001d036420_T005 |
Low | No | 2898 | [4] | Get ORF Coding potential... Type: noncoding Potential: -1.001 Folding energies... MFEI: -29.627 AMFE: -0.668 GC content %: 44.375 | |
| Zmays_Zm00001d036420_T006 Zm00001d036420_T006 |
Low | No | 2730 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.997 Folding energies... MFEI: -29.689 AMFE: -0.658 GC content %: 45.092 | |
| Zmays_Zm00001d036420_T007 Zm00001d036420_T007 |
High | No | 1439 | [6] | Get ORF Coding potential... Type: noncoding Potential: -1.113 Folding energies... MFEI: -25.010 AMFE: -0.680 GC content %: 36.762 | |
| Zmays_Zm00001d036420_T008 Zm00001d036420_T008 |
Low | No | 1821 | [7] | Get ORF Coding potential... Type: noncoding Potential: -0.960 Folding energies... MFEI: -25.299 AMFE: -0.648 GC content %: 39.044 | |
| Zmays_Zm00001d036420_T009 Zm00001d036420_T009 |
Low | No | 3058 | [8] | Get ORF Coding potential... Type: noncoding Potential: -1.005 Folding energies... MFEI: -29.424 AMFE: -0.676 GC content %: 43.558 | |
| Zmays_Zm00001d036420_T010 Zm00001d036420_T010 |
Low | No | 824 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.898 Folding energies... MFEI: -36.493 AMFE: -0.652 GC content %: 55.947 |
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_Zm00001d036420_T008 | SwissProt | 2021-04-01 | Q75IC7 | 5.61e-10 |
| Zmays_Zm00001d036420_T009 | SwissProt | 2021-04-01 | Q75IC7 | 1.41e-9 |
| Zmays_Zm00001d036420_T002 | SwissProt | 2021-04-01 | Q6IP65 | 4.71e-4 |
| Zmays_Zm00001d036420_T010 | SwissProt | 2021-04-01 | Q6IP65 | 6.78e-6 |
| Zmays_Zm00001d036420_T003 | SwissProt | 2021-04-01 | Q75IC7 | 1.57e-9 |
| Zmays_Zm00001d036420_T005 | SwissProt | 2021-04-01 | Q75IC7 | 1.32e-9 |
| Zmays_Zm00001d036420_T006 | SwissProt | 2021-04-01 | Q75IC7 | 1.22e-9 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
