Oglumipatula OGLUM09G03820
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
|
|---|---|---|---|---|---|---|
| Oglumipatula_OGLUM09G03820 [ OGLUM09G03820] |
9 | 5639399 | 5641660 | v1.5 | Oryza glumipatula (Ensembl Plants 51) | Coding? No |
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
|
|---|---|---|---|---|---|---|
| Oglumipatula_OGLUM09G03820.1 OGLUM09G03820.1 |
Low | No | 911 | OG0000651 | Get ORF Coding potential... Type: noncoding Potential: -0.739 Folding energies... MFEI: -34.918 AMFE: -0.626 GC content %: 55.763 | |
| Oglumipatula_OGLUM09G03820.2 OGLUM09G03820.2 |
Low | No | 1308 | OG0000651 | Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -32.194 AMFE: -0.636 GC content %: 50.612 | |
| Oglumipatula_OGLUM09G03820.3 OGLUM09G03820.3 |
High | No | 838 | OG0000651 | Get ORF Coding potential... Type: noncoding Potential: -0.846 Folding energies... MFEI: -35.107 AMFE: -0.617 GC content %: 56.921 | |
| Oglumipatula_OGLUM09G03820.4 OGLUM09G03820.4 |
Low | No | 1676 | OG0000651 | Get ORF Coding potential... Type: noncoding Potential: -1.067 Folding energies... MFEI: -30.823 AMFE: -0.651 GC content %: 47.315 |
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 |
|---|---|---|---|---|
| Oglumipatula_OGLUM09G03820.1 | RepBase (RepeatMasker) | 2014-01-31 | SINE | |
| Oglumipatula_OGLUM09G03820.2 | RepBase (RepeatMasker) | 2014-01-31 | SINE | |
| Oglumipatula_OGLUM09G03820.4 | RepBase (RepeatMasker) | 2014-01-31 | SINE |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
