Zmays Zm00001d005858
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_Zm00001d005858 [ Zm00001d005858] |
2 | 190973608 | 190979528 | 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_Zm00001d005858_T002 Zm00001d005858_T002 |
Low | No | 5725 | [1] | Get ORF Coding potential... Type: noncoding Potential: -1.142 Folding energies... MFEI: -28.482 AMFE: -0.667 GC content %: 42.672 | |
| Zmays_Zm00001d005858_T003 Zm00001d005858_T003 |
Low | No | 605 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.971 Folding energies... MFEI: -33.355 AMFE: -0.664 GC content %: 50.248 | |
| Zmays_Zm00001d005858_T004 Zm00001d005858_T004 |
Low | No | 4238 | [3] | Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -29.658 AMFE: -0.661 GC content %: 44.856 | |
| Zmays_Zm00001d005858_T005 Zm00001d005858_T005 |
High | No | 668 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.853 Folding energies... MFEI: -30.479 AMFE: -0.642 GC content %: 47.455 |
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_Zm00001d005858_T004 | RepBase (RepeatMasker) | 0000-00-00 | LINE/Tad1 | |
| Zmays_Zm00001d005858_T003 | SwissProt | 2021-04-01 | Q54T60 | 5.52e-4 |
| Zmays_Zm00001d005858_T002 | RepBase (RepeatMasker) | 0000-00-00 | LINE/Tad1 | |
| Zmays_Zm00001d005858_T003 | RepBase (RepeatMasker) | 0000-00-00 | LINE/Tad1 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
