Zmays Zm00001d046476
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_Zm00001d046476 [ Zm00001d046476] |
9 | 91656807 | 91661702 | 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_Zm00001d046476_T001 Zm00001d046476_T001 |
Low | No | 1399 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.242 Folding energies... MFEI: -27.984 AMFE: -0.639 GC content %: 43.817 | |
| Zmays_Zm00001d046476_T004 Zm00001d046476_T004 |
Low | No | 1058 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.000 Folding energies... MFEI: -28.894 AMFE: -0.590 GC content %: 48.960 | |
| Zmays_Zm00001d046476_T006 Zm00001d046476_T006 |
Low | No | 1091 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.003 Folding energies... MFEI: -29.148 AMFE: -0.599 GC content %: 48.671 | |
| Zmays_Zm00001d046476_T010 Zm00001d046476_T010 |
High | No | 1063 | [4] | Get ORF Coding potential... Type: noncoding Potential: -1.263 Folding energies... MFEI: -26.613 AMFE: -0.556 GC content %: 47.883 | |
| Zmays_Zm00001d046476_T013 Zm00001d046476_T013 |
Low | No | 1137 | [5] | Get ORF Coding potential... Type: noncoding Potential: -1.007 Folding energies... MFEI: -26.755 AMFE: -0.553 GC content %: 48.373 | |
| Zmays_Zm00001d046476_T014 Zm00001d046476_T014 |
High | No | 838 | [6] | Get ORF Coding potential... Type: noncoding Potential: -1.236 Folding energies... MFEI: -27.327 AMFE: -0.568 GC content %: 48.091 |
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_Zm00001d046476_T006 | SwissProt | 2021-04-01 | Q8RWC5 | 5.35e-5 |
| Zmays_Zm00001d046476_T013 | SwissProt | 2021-04-01 | Q8RWC5 | 5.78e-5 |
| Zmays_Zm00001d046476_T001 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d046476_T004 | SwissProt | 2021-04-01 | Q8RWC5 | 5.04e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
