Zmays Zm00001d019451
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_Zm00001d019451 [ Zm00001d019451] |
7 | 34375455 | 34379586 | 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_Zm00001d019451_T001 Zm00001d019451_T001 |
High | No | 1520 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.779 Folding energies... MFEI: -30.816 AMFE: -0.684 GC content %: 45.066 | |
| Zmays_Zm00001d019451_T002 Zm00001d019451_T002 |
Low | No | 2628 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.839 Folding energies... MFEI: -30.487 AMFE: -0.681 GC content %: 44.787 | |
| Zmays_Zm00001d019451_T004 Zm00001d019451_T004 |
High | No | 3087 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.793 Folding energies... MFEI: -30.010 AMFE: -0.660 GC content %: 45.449 | |
| Zmays_Zm00001d019451_T005 Zm00001d019451_T005 |
Low | No | 3659 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.806 Folding energies... MFEI: -28.959 AMFE: -0.668 GC content %: 43.373 | |
| Zmays_Zm00001d019451_T006 Zm00001d019451_T006 |
High | No | 1365 | [5] | Get ORF Coding potential... Type: noncoding Potential: -0.766 Folding energies... MFEI: -31.919 AMFE: -0.636 GC content %: 50.183 | |
| Zmays_Zm00001d019451_T007 Zm00001d019451_T007 |
High | No | 2177 | [6] | Get ORF Coding potential... Type: noncoding Potential: -0.821 Folding energies... MFEI: -31.594 AMFE: -0.659 GC content %: 47.910 | |
| Zmays_Zm00001d019451_T008 Zm00001d019451_T008 |
Low | No | 3604 | [7] | Get ORF Coding potential... Type: noncoding Potential: -1.166 Folding energies... MFEI: -29.123 AMFE: -0.673 GC content %: 43.257 | |
| Zmays_Zm00001d019451_T009 Zm00001d019451_T009 |
High | No | 2062 | [8] | Get ORF Coding potential... Type: noncoding Potential: -0.815 Folding energies... MFEI: -31.848 AMFE: -0.654 GC content %: 48.691 | |
| Zmays_Zm00001d019451_T010 Zm00001d019451_T010 |
Low | No | 2748 | [9] | Get ORF Coding potential... Type: noncoding Potential: -0.843 Folding energies... MFEI: -30.418 AMFE: -0.668 GC content %: 45.524 | |
| Zmays_Zm00001d019451_T011 Zm00001d019451_T011 |
Low | No | 2662 | [10] | Get ORF Coding potential... Type: noncoding Potential: -0.781 Folding energies... MFEI: -30.192 AMFE: -0.660 GC content %: 45.718 | |
| Zmays_Zm00001d019451_T012 Zm00001d019451_T012 |
Low | No | 2781 | [11] | Get ORF Coding potential... Type: noncoding Potential: -0.988 Folding energies... MFEI: -29.806 AMFE: -0.659 GC content %: 45.200 | |
| Zmays_Zm00001d019451_T013 Zm00001d019451_T013 |
High | No | 1975 | [12] | Get ORF Coding potential... Type: noncoding Potential: -0.752 Folding energies... MFEI: -31.580 AMFE: -0.644 GC content %: 49.013 | |
| Zmays_Zm00001d019451_T014 Zm00001d019451_T014 |
Low | No | 2762 | [13] | Get ORF Coding potential... Type: noncoding Potential: -0.987 Folding energies... MFEI: -29.613 AMFE: -0.655 GC content %: 45.185 | |
| Zmays_Zm00001d019451_T015 Zm00001d019451_T015 |
High | No | 1807 | [14] | Get ORF Coding potential... Type: noncoding Potential: -0.742 Folding energies... MFEI: -29.884 AMFE: -0.671 GC content %: 44.549 | |
| Zmays_Zm00001d019451_T016 Zm00001d019451_T016 |
High | No | 949 | [15] | Get ORF Coding potential... Type: noncoding Potential: -0.661 Folding energies... MFEI: -27.113 AMFE: -0.563 GC content %: 48.156 |
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_Zm00001d019451_T011 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d019451_T012 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d019451_T002 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d019451_T014 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d019451_T005 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d019451_T008 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d019451_T010 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
