Spurpurea SapurV1A.0032s0500
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
|
|---|---|---|---|---|---|---|
| Spurpurea_SapurV1A.0032s0500 [ SapurV1A.0032s0500] |
chr11 | 3933778 | 3936265 | v1 | Salix purpurea (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
|
|---|---|---|---|---|---|---|
| Spurpurea_SapurV1A.0032s0500.3 SapurV1A.0032s0500.3 |
Low | No | 1217 | OG0014427 | Get ORF Coding potential... Type: noncoding Potential: -0.055 Folding energies... MFEI: -23.698 AMFE: -0.579 GC content %: 40.920 | |
| Spurpurea_SapurV1A.0032s0500.5 SapurV1A.0032s0500.5 |
Low | No | 685 | OG0014427 | Get ORF Coding potential... Type: noncoding Potential: -0.760 Folding energies... MFEI: -24.978 AMFE: -0.568 GC content %: 43.942 | |
| Spurpurea_SapurV1A.0032s0500.6 SapurV1A.0032s0500.6 |
Low | No | 761 | OG0014427 | Get ORF Coding potential... Type: noncoding Potential: -0.786 Folding energies... MFEI: -25.309 AMFE: -0.566 GC content %: 44.678 | |
| Spurpurea_SapurV1A.0032s0500.7 SapurV1A.0032s0500.7 |
Low | No | 897 | OG0014427 | Get ORF Coding potential... Type: noncoding Potential: -0.846 Folding energies... MFEI: -27.581 AMFE: -0.658 GC content %: 41.918 |
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 |
|---|---|---|---|---|
| Spurpurea_SapurV1A.0032s0500.3 | SwissProt | 2021-04-01 | Q93ZJ3 | 1.99e-12 |
| Spurpurea_SapurV1A.0032s0500.5 | SwissProt | 2021-04-01 | Q93ZJ3 | 1.58e-10 |
| Spurpurea_SapurV1A.0032s0500.6 | SwissProt | 2021-04-01 | Q93ZJ3 | 2.18e-10 |
| Spurpurea_SapurV1A.0032s0500.7 | SwissProt | 2021-04-01 | Q93ZJ3 | 3.36e-10 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
