Zmays Zm00001d017178
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_Zm00001d017178 [ Zm00001d017178] |
5 | 188138768 | 188141720 | 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_Zm00001d017178_T002 Zm00001d017178_T002 |
Low | Yes | 659 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.405 Folding energies... MFEI: -28.164 AMFE: -0.656 GC content %: 42.944 | |
| Zmays_Zm00001d017178_T003 Zm00001d017178_T003 |
Low | No | 1386 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.919 Folding energies... MFEI: -26.198 AMFE: -0.683 GC content %: 38.384 | |
| Zmays_Zm00001d017178_T005 Zm00001d017178_T005 |
Low | Yes | 697 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.488 Folding energies... MFEI: -32.697 AMFE: -0.712 GC content %: 45.911 | |
| Zmays_Zm00001d017178_T006 Zm00001d017178_T006 |
Low | Yes | 584 | [4] | Get ORF Coding potential... Type: noncoding Potential: -0.586 Folding energies... MFEI: -30.240 AMFE: -0.677 GC content %: 44.692 |
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_Zm00001d017178_T006 | Rfam | 14.6 | MIR408 | 1.7e-4 |
| Zmays_Zm00001d017178_T002 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d017178_T003 | RepBase (RepeatMasker) | 0000-00-00 | LTR/ERV1 | |
| Zmays_Zm00001d017178_T005 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d017178_T002 | Rfam | 14.6 | MIR408 | 1.9e-4 |
| Zmays_Zm00001d017178_T006 | RepBase (RepeatMasker) | 0000-00-00 | DNA/CMC-EnSpm | |
| Zmays_Zm00001d017178_T005 | Rfam | 14.6 | MIR408 | 2.1e-4 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
