Gene
Osativa LOC Os02g23823
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 | Source | Assembly | Species | Details
|
|---|---|---|---|---|---|---|---|
| Osativa_LOC_Os02g23823 LOC_Os02g23823 |
Chr2 | 13759211 | 13767271 | Phytozome | v7.0 | Oryza_sativa_Japonica_Group | 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 | Sequence | Details
|
|---|---|---|---|---|---|
| Osativa_LOC_Os02g23823.2 LOC_Os02g23823.2 PAC:24129150 |
Low | Yes | 698 | Get ORF Coding potential... Type: noncoding Potential: -0.979 Folding energies... MFEI: -33.223 AMFE: -0.748 GC content %: 44.413 | |
| Osativa_LOC_Os02g23823.3 LOC_Os02g23823.3 PAC:24129151 |
Low | No | 574 | Get ORF Coding potential... Type: noncoding Potential: -0.869 Folding energies... MFEI: -33.031 AMFE: -0.632 GC content %: 52.265 |
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 |
|---|---|---|---|---|
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812c | 3.0e-4 |
| Osativa_LOC_Os02g23823.2 | Rfam | 11.0 | MIR530 | 0.0081 |
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812b | 3.0e-4 |
| Osativa_LOC_Os02g23823.2 | RepBase (RepeatMasker) | 2014-01-31 | STOWAWAY44_OS | |
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812a | 3.0e-4 |
| Osativa_LOC_Os02g23823.3 | RepBase (RepeatMasker) | 2014-01-31 | DITTO3 | |
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812s | 1.0e-3 |
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812e | 3.0e-4 |
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812o-3p | 0.015 |
| Osativa_LOC_Os02g23823.2 | miRBase | 21.0 | osa-miR812d | 3.0e-4 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
