Gene
Athaliana AT4G24415
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
|
|---|---|---|---|---|---|---|---|
| Athaliana_AT4G24415 AT4G24415 |
Chr4 | 12623536 | 12626432 | Phytozome | TAIR10 | Arabidopsis_thaliana | 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 | Sequence | Details
|
|---|---|---|---|---|---|
| Athaliana_AT4G24415.1 AT4G24415.1 |
Low | Yes | 1485 | Get ORF Coding potential... Type: noncoding Potential: -1.230 Folding energies... MFEI: -24.687 AMFE: -0.652 GC content %: 37.845 | |
| Athaliana_AT4G24415.2 AT4G24415.2 |
Low | Yes | 1440 | Get ORF Coding potential... Type: noncoding Potential: -1.226 Folding energies... MFEI: -25.840 AMFE: -0.662 GC content %: 39.027 | |
| Athaliana_AT4G24415.3 AT4G24415.3 |
High | No | 573 | Get ORF Coding potential... Type: noncoding Potential: -1.146 Folding energies... MFEI: -21.745 AMFE: -0.636 GC content %: 34.205 |
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 |
|---|---|---|---|---|
| Athaliana_AT4G24415.2 | NONCODE | 3 | NONATHT002956 | |
| Athaliana_AT4G24415.1 | Rfam | 11.0 | MIR824 | 4.5e-153 |
| Athaliana_AT4G24415.2 | Rfam | 11.0 | MIR824 | 4.3e-153 |
| Athaliana_AT4G24415.2 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-9_SB-I |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
